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Liang G, Lv XF, Huang W, Jin YJ, Roquid KA, Kawase H, Offermanns S. Loss of Smooth Muscle Tenascin-X Inhibits Vascular Remodeling Through Increased TGF-β Signaling. Arterioscler Thromb Vasc Biol 2024; 44:1748-1763. [PMID: 38934115 DOI: 10.1161/atvbaha.123.321067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Vascular smooth muscle cells (VSMCs) are highly plastic. Vessel injury induces a phenotypic transformation from differentiated to dedifferentiated VSMCs, which involves reduced expression of contractile proteins and increased production of extracellular matrix and inflammatory cytokines. This transition plays an important role in several cardiovascular diseases such as atherosclerosis, hypertension, and aortic aneurysm. TGF-β (transforming growth factor-β) is critical for VSMC differentiation and to counterbalance the effect of dedifferentiating factors. However, the mechanisms controlling TGF-β activity and VSMC phenotypic regulation under in vivo conditions are poorly understood. The extracellular matrix protein TN-X (tenascin-X) has recently been shown to bind TGF-β and to prevent it from activating its receptor. METHODS We studied the role of TN-X in VSMCs in various murine disease models using tamoxifen-inducible SMC-specific knockout and adeno-associated virus-mediated knockdown. RESULTS In hypertensive and high-fat diet-fed mice, after carotid artery ligation as well as in human aneurysmal aortae, expression of Tnxb, the gene encoding TN-X, was increased in VSMCs. Mice with smooth muscle cell-specific loss of TN-X (SMC-Tnxb-KO) showed increased TGF-β signaling in VSMCs, as well as upregulated expression of VSMC differentiation marker genes during vascular remodeling compared with controls. SMC-specific TN-X deficiency decreased neointima formation after carotid artery ligation and reduced vessel wall thickening during Ang II (angiotensin II)-induced hypertension. SMC-Tnxb-KO mice lacking ApoE showed reduced atherosclerosis and Ang II-induced aneurysm formation under high-fat diet. Adeno-associated virus-mediated SMC-specific expression of short hairpin RNA against Tnxb showed similar beneficial effects. Treatment with an anti-TGF-β antibody or additional SMC-specific loss of the TGF-β receptor reverted the effects of SMC-specific TN-X deficiency. CONCLUSIONS In summary, TN-X critically regulates VSMC plasticity during vascular injury by inhibiting TGF-β signaling. Our data indicate that inhibition of vascular smooth muscle TN-X may represent a strategy to prevent and treat pathological vascular remodeling.
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MESH Headings
- Animals
- Humans
- Male
- Mice
- Angiotensin II
- Aortic Aneurysm/metabolism
- Aortic Aneurysm/pathology
- Aortic Aneurysm/genetics
- Aortic Aneurysm/prevention & control
- Carotid Artery Injuries/pathology
- Carotid Artery Injuries/metabolism
- Carotid Artery Injuries/genetics
- Cells, Cultured
- Diet, High-Fat
- Disease Models, Animal
- Hypertension/metabolism
- Hypertension/pathology
- Hypertension/physiopathology
- Hypertension/genetics
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Knockout, ApoE
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Neointima
- Phenotype
- Signal Transduction
- Tenascin/metabolism
- Tenascin/genetics
- Tenascin/deficiency
- Transforming Growth Factor beta/metabolism
- Vascular Remodeling
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Affiliation(s)
- Guozheng Liang
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
| | - Xiao-Fei Lv
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
- Department of Pharmacology, Cardiac and Cerebral Vascular Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China (X.-F.L.)
| | - Wei Huang
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
| | - Young-June Jin
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
| | - Kenneth Anthony Roquid
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
| | - Haruya Kawase
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
| | - Stefan Offermanns
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (G.L., X.-F.L., W.H., Y.-J.J., K.A.R., H.K., S.O.)
- Center for Molecular Medicine, Goethe University Frankfurt, Germany (S.O.)
- Cardiopulmonary Institute, Bad Nauheim, Germany (S.O.)
- German Center for Cardiovascular Research, Bad Nauheim, Germany (S.O.)
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2
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Reichenbach P, Giordano Attianese GMP, Ouchen K, Cribioli E, Triboulet M, Ash S, Saillard M, Vuillefroy de Silly R, Coukos G, Irving M. A lentiviral vector for the production of T cells with an inducible transgene and a constitutively expressed tumour-targeting receptor. Nat Biomed Eng 2023; 7:1063-1080. [PMID: 37069267 PMCID: PMC10504085 DOI: 10.1038/s41551-023-01013-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/20/2023] [Indexed: 04/19/2023]
Abstract
Vectors that facilitate the engineering of T cells that can better harness endogenous immunity and overcome suppressive barriers in the tumour microenvironment would help improve the safety and efficacy of T-cell therapies for more patients. Here we report the design, production and applicability, in T-cell engineering, of a lentiviral vector leveraging an antisense configuration and comprising a promoter driving the constitutive expression of a tumour-directed receptor and a second promoter enabling the efficient activation-inducible expression of a genetic payload. The vector allows for the delivery of a variety of genes to human T cells, as we show for interleukin-2 and a microRNA-based short hairpin RNA for the knockdown of the gene coding for haematopoietic progenitor kinase 1, a negative regulator of T-cell-receptor signalling. We also show that a gene encoded under an activation-inducible promoter is specifically expressed by tumour-redirected T cells on encountering a target antigen in the tumour microenvironment. The single two-gene-encoding vector can be produced at high titres under an optimized protocol adaptable to good manufacturing practices.
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Affiliation(s)
- Patrick Reichenbach
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Greta Maria Paola Giordano Attianese
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Khaoula Ouchen
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Elisabetta Cribioli
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Melanie Triboulet
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Sarah Ash
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Margaux Saillard
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Romain Vuillefroy de Silly
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
| | - Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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3
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Qian H, Ma K, Feng J, Guo Z, Gong J, Chen H, Bai H, Qiu G. Transcriptome analysis of the post-larvae of giant freshwater prawn (Macrobrachium rosenbergii) after IAG gene knockdown with microRNA interference. Gen Comp Endocrinol 2022; 325:114054. [PMID: 35580689 DOI: 10.1016/j.ygcen.2022.114054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/04/2022]
Abstract
The insulin-like androgenic gland hormone gene (IAG) of crustaceans plays pivotal roles in the regulation of sex differentiation. MicroRNAs (miRNAs) are a class of short, non-coding RNAs that function as post-transcriptional gene regulators. However, little information about the regulatory relationship between miRNA and Macrobrachium rosenbergii IAG (MrIAG) were exposed. In this study, we used the 3' untranslated region (UTR) of MrIAG to predict potential target sites of miRNAs. The results showed that miR-184 has one target site in the 3'UTR of MrIAG. Dual-luciferase report assay in vitro confirmed that miR-184 can significantly down-regulate MrIAG expression. Besides, we constructed mutant plasmids of 3'UTR of MrIAG. The result displayed that after co-transfection of mutant plasmids and miR-184 agomir, the activity of luciferase was not affected compared to the control. These results indicated that miR-184 could directly regulate MrIAG. In addition, we found that overexpression of miR-184 in M. rosenbergii can lead to significant changes in the transcription level of genes. Compared with control group, we identified 1510 differentially expressed genes (DEGs) in the miR-184 injection group. Some DEGs were involved in sex differentiation, gonad development, growth and molting were found. qRT-PCR verification was performed on eight DEGs randomly, and the results showed that the expression level of sex-, growth-, and metabolism-related genes changed significantly after MrIAG gene knockdown. Collectively, findings from this study suggest that miR-184, by mediating IAG expression, may be involved in many physiological processes in M. rosenbergii. The current study lays a basic understanding for short-term silencing of MrIAG with miR-184, and facilitates miRNA function analysis in M. rosenbergii in future.
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Affiliation(s)
- Hongli Qian
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Keyi Ma
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China.
| | - Jianbin Feng
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Ziqi Guo
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Jinhua Gong
- Jiangsu Dinghe Aquatic Technology Development Co., Ltd., Taizhou 225300, PR China
| | - Huangen Chen
- Jiangsu Fishery Technology Extension Center, Nanjing 210036, PR China
| | - Haotian Bai
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China
| | - Gaofeng Qiu
- National Demonstration Center for Experimental Fisheries Science Education, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, PR China.
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4
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Duran AG, Schwestka M, Nazari-Shafti TZ, Neuber S, Stamm C, Gossen M. Limiting Transactivator Amounts Contribute to Transgene Mosaicism in Tet-On All-in-One Systems. ACS Synth Biol 2022; 11:2623-2635. [PMID: 35815862 DOI: 10.1021/acssynbio.2c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MicroRNAs play an essential role in cell homeostasis and have been proposed as therapeutic agents. One strategy to deliver microRNAs is to genetically engineer target cells to express microRNAs of interest. However, to control dosage and timing, as well as to limit potential side-effects, microRNAs' expression should ideally be under exogenous, inducible control. Conditional expression of miRNA-based short hairpin RNAs (shRNAmirs) via gene regulatory circuits such as the Tet-system is therefore a promising strategy to control shRNAmirs' expression in research and therapy. Single vector approaches like Tet-On all-in-one designs are more compatible with potential clinical applications by providing the Tet-On system components in a single round of genetic engineering. However, all-in-one systems often come at the expense of heterogeneous and unstable expression. In this study, we aimed to understand the causes that lead to such erratic transgene expression. By using a reporter cell, we found that the degree of heterogeneity mostly correlated with reverse tetracycline transactivator (rtTA) expression levels. Moreover, the targeted integration of a potent rtTA expression cassette into a genomic safe harbor locus functionally rescued previously silenced rtTA-responsive transcription units. Overall, our results suggest that ensuring homogenous and stable rtTA expression is essential for the robust and reliable performance of future Tet-On all-in-one designs.
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Affiliation(s)
- Ana G Duran
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Timo Z Nazari-Shafti
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Sebastian Neuber
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Christof Stamm
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
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5
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Abo-Al-Ela HG. RNA Interference in Aquaculture: A Small Tool for Big Potential. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4343-4355. [PMID: 33835783 DOI: 10.1021/acs.jafc.1c00268] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
For decades, the tight regulatory functions of DNA and RNA have been the focus of extensive research with the goal of harnessing RNA molecules (e.g., microRNA and small interfering RNA) to control gene expression and to study biological functions. RNA interference (RNAi) has shown evidence of mediating gene expression, has been utilized to study functional genomics, and recently has potential in therapeutic agents. RNAi is a natural mechanism and a well-studied tool that can be used to silence specific genes. This method is also used in aquaculture as a research tool and to enhance immune responses. RNAi methods do have their limitations (e.g., immune triggering); efficient and easy-to-use RNAi methods for large-scale applications need further development. Despite these limitations, RNAi methods have been successfully used in aquaculture, in particular shrimp. This review discusses the uses of RNAi in aquaculture, such as immune- and production-related issues and the possible limitations that may hinder the application of RNAi in the aquaculture industry. Our challenge is to develop a highly potent in vivo RNAi delivery platform that could complete the desired action with minimal side effects and which can be applied on a large-scale with relatively little expense in the aquaculture industry.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez 43518, Egypt
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6
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Fan J, Feng Y, Zhang R, Zhang W, Shu Y, Zeng Z, Huang S, Zhang L, Huang B, Wu D, Zhang B, Wang X, Lei Y, Ye Z, Zhao L, Cao D, Yang L, Chen X, Liu B, Wagstaff W, He F, Wu X, Zhang J, Moriatis Wolf J, Lee MJ, Haydon RC, Luu HH, Huang A, He TC, Yan S. A simplified system for the effective expression and delivery of functional mature microRNAs in mammalian cells. Cancer Gene Ther 2020; 27:424-437. [PMID: 31222181 PMCID: PMC6923634 DOI: 10.1038/s41417-019-0113-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/21/2019] [Accepted: 06/01/2019] [Indexed: 01/09/2023]
Abstract
MicroRNAs (miRNAs) are ~22 nucleotide noncoding RNAs that are involved in virtually all aspects of cellular process as their deregulations are associated with many pathological conditions. Mature miRNAs (mMIRs) are generated through a series of tightly-regulated nuclear and cytoplasmic processing events of the transcribed primary, precursor and mMIRs. Effective manipulations of miRNA expression enable us to gain insights into miRNA functions and to explore potential therapeutic applications. Currently, overexpression of miRNAs is achieved by using chemically-synthesized miRNA mimics, or shRNA-like stem-loop vectors to express primary or precursor miRNAs, which are limited by low transfection efficacy or rate-limiting miRNA processing. To overcome rate-limiting miRNA processing, we developed a novel strategy to express mMIRs which are driven by converging U6/H1 dual promoters. As a proof-of-concept study, we constructed mMIR expression vectors for hsa-miR-223 and hsa-Let-7a-1, and demonstrated that the expressed mMIRs effectively silenced target gene expression, specifically suppressed miRNA reporter activity, and significantly affected cell proliferation, similar to respective primary and precursor miRNAs. Furthermore, these mMIR expression vectors can be easily converted into retroviral and adenoviral vectors. Collectively, our simplified mMIR expression system should be a valuable tool to study miRNA functions and/or to deliver miRNA-based therapeutics.
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Affiliation(s)
- Jiaming Fan
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Yixiao Feng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Ruyi Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Guiyang College of Traditional Chinese Medicine, 550001, Guiyang, China
| | - Wenwen Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Yi Shu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Zongyue Zeng
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Shifeng Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Linghuan Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Bo Huang
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, 330006, Nanchang, China
| | - Di Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Bo Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Key Laboratory of Orthopaedic Surgery of Gansu Province, and the Departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, 730030, Lanzhou, China
| | - Xi Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Yan Lei
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Zhenyu Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, 215004, Suzhou, China
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Daigui Cao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
- Department of Orthopaedic Surgery, Chongqing General Hospital, 400021, Chongqing, China
| | - Lijuan Yang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Key Laboratory of Orthopaedic Surgery of Gansu Province, and the Departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, 730030, Lanzhou, China
| | - Xian Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Clinical Laboratory Medicine, The Affiliated Hospital of Qingdao University, 266061, Qingdao, China
| | - Bin Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- School of Life Sciences, Southwest University, 400715, Chongqing, China
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Xiaoxing Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Jing Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- The Affiliated Hospitals of Chongqing Medical University, 400016, Chongqing, China
| | - Jennifer Moriatis Wolf
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Michael J Lee
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Rex C Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Ailong Huang
- Ministry of Education Key Laboratory of Diagnostic Medicine, and the School of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA.
| | - Shujuan Yan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA.
- Department of Clinical Laboratory Medicine, Guizhou Provincial People's Hospital and Guizhou University, 550004, Guiyang, China.
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7
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Ramyasoma HPBKD, Dassanayake RS, Hapugoda M, Capurro ML, Silva Gunawardene YIN. Multiple dengue virus serotypes resistant transgenic Aedes aegypti fitness evaluated under laboratory conditions. RNA Biol 2020; 17:918-929. [PMID: 32138589 DOI: 10.1080/15476286.2020.1735210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dengue viruses (DENV) are the wildest transmitted arbovirus members of the family Flaviviridae, genus Flavivirus. Dengue viruses are composed of four serotypes, DENV1, 2, 3, and 4, and these viruses can cause dengue fever and dengue haemorrhagic fever or dengue shock syndrome, when infecting humans. RNA interference (RNAi) is a self-defence mechanism, which can be used to prevent invasions of RNA viruses to the host. Genetically engineering a host with an RNAi molecule that targets a single virus serotype may develop escape mutants, and can cause unusual dominance over other serotypes. Therefore, the simultaneous targeting of multiple serotypes is necessary to block DENV transmission. Here, we report the development of transgenic Aedes aegypti based on a bioinformatically designed multiple miRshRNA (microRNA-based shRNA) DNA sequence under the control of a blood-meal induced promoter, Carboxypeptidase A, to induce RNAi for DENV in Aedes aegypti, and demonstrate the expression of a synthetic multiple shRNA polycistronic cluster having RNA interference sequences to target DENV genomes. The transgenic mosquitoes have lower rates of infection, dissemination, and transmission for DENV2 and DENV4 compared to wild mosquitoes, with a significant reduction of dengue copy number and antigen levels in the midgut. These levels of DENV were low enough to make transgenic mosquitoes stop the DENV transmission from infected host to a susceptible host and refractory to DENV2 and DENV4 infection. Such multiple resistance in Ae. aegypti has not been documented previously. Laboratory fitness measurement of transgenic Ae. aegypti showed results comparable to other reported transgenic mosquitoes.
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Affiliation(s)
| | | | - Menaka Hapugoda
- Molecular Medicine Unit, Faculty of Medicine, University of Kelaniya , Kelaniya, Sri Lanka
| | - Margareth L Capurro
- Department of Parasitology (ICB), University of São Paulo , São Paulo, Brazil
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8
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John SP, Sun J, Carlson RJ, Cao B, Bradfield CJ, Song J, Smelkinson M, Fraser IDC. IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages. Cell Rep 2020; 25:95-106.e6. [PMID: 30282041 PMCID: PMC6492923 DOI: 10.1016/j.celrep.2018.09.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 07/06/2018] [Accepted: 08/30/2018] [Indexed: 12/15/2022] Open
Abstract
Activation of the TLR4 signaling pathway by lipopolysaccharide (LPS) leads to induction of both inflammatory and interferon-stimulated genes, but the mechanisms through which these coordinately activated transcriptional programs are balanced to promote an optimal innate immune response remain poorly understood. In a genome-wide small interfering RNA (siRNA) screen of the LPS-induced tumor necrosis factor α (TNF-α) response in macrophages, we identify the interferon-stimulated protein IFIT1 as a negative regulator of the inflammatory gene program. Transcriptional profiling further identifies a positive regulatory role for IFIT1 in type I interferon expression, implicating IFIT1 as a reciprocal modulator of LPS-induced gene classes. We demonstrate that these effects of IFIT1 are mediated through modulation of a Sin3A-HDAC2 transcriptional regulatory complex at LPS-induced gene loci. Beyond the well-studied role of cytosolic IFIT1 in restricting viral replication, our data demonstrate a function for nuclear IFIT1 in differential transcriptional regulation of separate branches of the LPS-induced gene program.
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Affiliation(s)
- Sinu P John
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Jing Sun
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Rebecca J Carlson
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Binh Cao
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Clinton J Bradfield
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jian Song
- Bioinformatics Group, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Margery Smelkinson
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Signaling Systems Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
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9
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Fujimoto Y, Kyogoku K, Takeda K, Ozaki K, Yamamoto S, Suyama H, Ono E. Antiviral effects against influenza A virus infection by a short hairpin RNA targeting the non-coding terminal region of the viral nucleoprotein gene. J Vet Med Sci 2019; 81:383-388. [PMID: 30674743 PMCID: PMC6451914 DOI: 10.1292/jvms.18-0436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RNA interference (RNAi) can inhibit Influenza A virus (IAV) infection in a gene-specific manner. In this study, we constructed a transgene expressing a short hairpin RNA
(shRNA) that targets the noncoding region of the IAV RNA gene encoding nucleoprotein (NP). To investigate the antiviral effects of the shRNA, we generated two transgenic mouse lines with
this transgene. Unfortunately, there was no apparent difference in IAV resistance between transgenic and non-transgenic littermates. To further investigate the antiviral effects of the
shRNA, we prepared mouse embryonic fibroblasts (MEFs) from transgenic and non-transgenic mice. In experimental infections using these MEFs, virus production of mouse-adapted IAV strain
A/Puerto Rico/8/1934 (PR8) in the transgenic MEFs was suppressed by means of the down-regulation of the viral RNA gene transcription in the early stages of infection in comparison with
non-transgenic MEFs. These results indicated that expression of the shRNA was able to confer antiviral properties against IAVs to MEFs, although the effects were limited. Our findings
suggest that the shRNA targeting the noncoding region of the viral RNA (vRNA) of NP might be a supporting tool in developing influenza-resistant poultry.
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Affiliation(s)
- Yoshikazu Fujimoto
- Department of Biomedicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan.,Joint Faculty of Veterinary Medicine, Transboundary Animal Diseases Research Center, Kagoshima University, 1-21-24 Kagoshima-shi, Kagoshima 890-0065, Japan
| | - Kenji Kyogoku
- Biotechnology Development Laboratories, Health Care Solutions Research Institute, Kaneka Corporation, 1-8 Takasago-shi, Hyogo 676-8688, Japan
| | - Keiko Takeda
- Department of Biomedicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
| | - Kinuyo Ozaki
- Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
| | - Sayo Yamamoto
- Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
| | - Haruka Suyama
- Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
| | - Etsuro Ono
- Department of Biomedicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan.,Center of Biomedical Research, Research Center for Human Disease Modeling, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka 812-8582, Japan
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10
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Du X, Cai Y, Xi W, Zhang R, Jia L, Yang A, Zhao J, Yan B. Multi‑target inhibition by four tandem shRNAs embedded in homo‑ or hetero‑miRNA backbones. Mol Med Rep 2017; 17:307-314. [PMID: 29115602 DOI: 10.3892/mmr.2017.7854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/02/2017] [Indexed: 11/06/2022] Open
Abstract
The functional influence of microRNA (miRNA)backbone selection remains unclear with respect to multiplexing miRNA‑based short hairpin RNAs (shRNAmiRs), due to a lack of comparative studies. To this end, a pair of shRNAmiR tetramers were designed in the present study that targeted four genes with a shared miR30a backbone (homo‑BB) or four miRNA backbones (hetero‑BB). A PBLT+ 293A cell line overexpressing four targets was established, which permitted simultaneous dissection of individual gene knockdown. Multi‑target inhibition was confirmed by a decrease in positive cell populations of the relative gene and mean fluorescence intensities, with almost comparable activities of homo‑ and hetero‑BB tetramers. Of note, this multi‑inhibition was sustained over a 1‑month period, with no notable difference, particularly in the late‑phased inhibitory effects between homo‑ and hetero‑BB tetra‑shRNA miRs. These preliminary data may indicate little influence of scaffold substitution in the functionalities of multiplexed shRNAmiRs and little recombination‑depleted risk of repetitively adopting the same miRNA backbone in this artificial in vitro system. More comparative studies are further required to explore extended repertoires of scaffold‑paralleled multi‑shRNAmiRs in more physiologically relevant models.
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Affiliation(s)
- Xiao Du
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yanhui Cai
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Wenjin Xi
- Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Angang Yang
- Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Jing Zhao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Bo Yan
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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11
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Wang T, Xie Y, Tan A, Li S, Xie Z. Construction and Characterization of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells. ACS Synth Biol 2016; 5:1193-1200. [PMID: 26639786 DOI: 10.1021/acssynbio.5b00180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
RNA interference (RNAi) technology is widely used in basic and translational research. By mimicking a natural primary microRNA (pri-miRNA) cluster, multiple engineered hairpins can be transcribed as a single transcript from the same Pol II promoter, enabling the formation of multiplex RNAi in mammalian cells. However, constructing a synthetic miRNA cluster is still time-consuming, and the processing and function of a miRNA cluster are incompletely understood. Here, we identified a miRNA precursor architecture that allows precise miRNA maturation. We established a hierarchical cloning method for the efficient construction of a synthetic miRNA cluster harboring up to 18 miRNA precursors. We demonstrated that the maturation and function of individual miRNA precursors were independent of their positions in the cluster. We then analyzed the integration efficiency of miRNA clusters having a varied number of miRNA precursors by using CRISPR/Cas9-mediated integration, a piggyBac transposon system, and a lentiviral system. This synthetic miRNA cluster system provides an important tool for multiplex RNAi in mammalian cells.
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Affiliation(s)
- Tingting Wang
- MOE Key Laboratory
of Bioinformatics
and Bioinformatics Division, Center for Synthetic and Systems Biology,
TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yue Xie
- MOE Key Laboratory
of Bioinformatics
and Bioinformatics Division, Center for Synthetic and Systems Biology,
TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Aidi Tan
- MOE Key Laboratory
of Bioinformatics
and Bioinformatics Division, Center for Synthetic and Systems Biology,
TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shao Li
- MOE Key Laboratory
of Bioinformatics
and Bioinformatics Division, Center for Synthetic and Systems Biology,
TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory
of Bioinformatics
and Bioinformatics Division, Center for Synthetic and Systems Biology,
TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
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12
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Seyhan AA. A multiplexed miRNA and transgene expression platform for simultaneous repression and expression of protein coding sequences. MOLECULAR BIOSYSTEMS 2016; 12:295-312. [PMID: 26617199 DOI: 10.1039/c5mb00506j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Knockdown of single or multiple gene targets by RNA interference (RNAi) is necessary to overcome escape mutants or isoform redundancy. It is also necessary to use multiple RNAi reagents to knockdown multiple targets. It is also desirable to express a transgene or positive regulatory elements and inhibit a target gene in a coordinated fashion. This study reports a flexible multiplexed RNAi and transgene platform using endogenous intronic primary microRNAs (pri-miRNAs) as a scaffold located in the green fluorescent protein (GFP) as a model for any functional transgene. The multiplexed intronic miRNA - GFP transgene platform was designed to co-express multiple small RNAs within the polycistronic cluster from a Pol II promoter at more moderate levels to reduce potential vector toxicity. The native intronic miRNAs are co-transcribed with a precursor GFP mRNA as a single transcript and presumably cleaved out of the precursor-(pre) mRNA by the RNA splicing machinery, spliceosome. The spliced intron with miRNA hairpins will be further processed into mature miRNAs or small interfering RNAs (siRNAs) capable of triggering RNAi effects, while the ligated exons become a mature messenger RNA for the translation of the functional GFP protein. Data show that this approach led to robust RNAi-mediated silencing of multiple Renilla Luciferase (R-Luc)-tagged target genes and coordinated expression of functional GFP from a single transcript in transiently transfected HeLa cells. The results demonstrated that this design facilitates the coordinated expression of all mature miRNAs either as individual miRNAs or as multiple miRNAs and the associated protein. The data suggest that, it is possible to simultaneously deliver multiple negative (miRNA or shRNA) and positive (transgene) regulatory elements. Because many cellular processes require simultaneous repression and activation of downstream pathways, this approach offers a platform technology to achieve that dual manipulation efficiently. In conclusion, the current platform technology offers a miRNA/shRNA scaffold for the expression of combinations of native or synthetic intronic miRNAs as singletons or polycistrons for combinatorial multiplexed RNAi silencing or RNA-based gene therapy applications.
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Affiliation(s)
- Attila A Seyhan
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton, St., Orlando, FL 32804, USA. and The Chemical Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
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13
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Czarnecki O, Bryan AC, Jawdy SS, Yang X, Cheng ZM, Chen JG, Tuskan GA. Simultaneous knockdown of six non-family genes using a single synthetic RNAi fragment in Arabidopsis thaliana. PLANT METHODS 2016; 12:16. [PMID: 26889205 PMCID: PMC4756541 DOI: 10.1186/s13007-016-0116-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/08/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Genetic engineering of plants that results in successful establishment of new biochemical or regulatory pathways requires stable introduction of one or more genes into the plant genome. It might also be necessary to down-regulate or turn off expression of endogenous genes in order to reduce activity of competing pathways. An established way to knockdown gene expression in plants is expressing a hairpin-RNAi construct, eventually leading to degradation of a specifically targeted mRNA. Knockdown of multiple genes that do not share homologous sequences is still challenging and involves either sophisticated cloning strategies to create vectors with different serial expression constructs or multiple transformation events that is often restricted by a lack of available transformation markers. RESULTS Synthetic RNAi fragments were assembled in yeast carrying homologous sequences to six or seven non-family genes and introduced into pAGRIKOLA. Transformation of Arabidopsis thaliana and subsequent expression analysis of targeted genes proved efficient knockdown of all target genes. CONCLUSIONS We present a simple and cost-effective method to create constructs to simultaneously knockdown multiple non-family genes or genes that do not share sequence homology. The presented method can be applied in plant and animal synthetic biology as well as traditional plant and animal genetic engineering.
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Affiliation(s)
- Olaf Czarnecki
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ; KWS SAAT SE, Grimsehlstraße 31, 37555 Einbeck, Germany
| | - Anthony C Bryan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Zong-Ming Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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14
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Epstein-Barr Virus (EBV) Tegument Protein BGLF2 Promotes EBV Reactivation through Activation of the p38 Mitogen-Activated Protein Kinase. J Virol 2015; 90:1129-38. [PMID: 26559845 DOI: 10.1128/jvi.01410-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/15/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus associated with both B cell and epithelial cell malignancies. EBV infection of B cells triggers activation of several signaling pathways that are critical for cell survival, virus latency, and growth transformation. To identify EBV proteins important for regulating cell signaling, we used a proteomic approach to screen viral proteins for AP-1 and NF-κB promoter activity in AP-1- and NF-κB-luciferase reporter assays. We found that EBV BGLF2 activated AP-1 but not NF-κB reporter activity. Expression of EBV BGLF2 in cells activated p38 and c-Jun N-terminal kinase (JNK), both of which are important for mitogen-activated protein kinase (MAPK) signaling. Deletion of the carboxyl-terminal 66 amino acids of BGLF2 reduced the ability of BGLF2 to activate JNK and p38. Expression of BGLF2 enhanced BZLF1 expression in latently EBV-infected lymphoblastoid cell lines, and knockdown of BGLF2 reduced EBV reactivation induced by IgG cross-linking. Expression of BGLF2 induced BZLF1 expression and virus production in EBV-infected gastric carcinoma cells. BGLF2 enhanced BZLF1 expression and EBV production by activating p38; chemical inhibition of p38 and MAPK/ERK kinases 1 and 2 (MEK1/2) reduced expression of BZLF1 and virus production induced by BGLF2. In summary, the EBV tegument protein BGLF2, which is delivered to the cell at the onset of virus infection, activates the AP-1 pathway and enhances EBV reactivation and virus production. IMPORTANCE Epstein-Barr virus (EBV) is associated with both B cell and epithelial cell malignancies, and the virus activates multiple signaling pathways important for its persistence in latently infected cells. We identified a viral tegument protein, BGLF2, which activates members of the mitogen-activated protein kinase signaling pathway. Expression of BGLF2 increased expression of EBV BZLF1, which activates a switch from latent to lytic virus infection, and increased production of EBV. Inhibition of BGFL2 expression or inhibition of p38/MAPK, which is activated by BGLF2, reduced virus reactivation from latency. These results indicate that a viral tegument protein which is delivered to cells upon infection activates signaling pathways to enhance virus production and facilitate virus reactivation from latency.
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15
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Calloni R, Bonatto D. Scaffolds for Artificial miRNA Expression in Animal Cells. Hum Gene Ther Methods 2015; 26:162-74. [PMID: 26406928 DOI: 10.1089/hgtb.2015.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Artificial miRNAs (amiRNAs) are molecules that have been developed to promote gene silencing in a similar manner to naturally occurring miRNAs. amiRNAs are generally constructed by replacing the mature miRNA sequence in the pre-miRNA stem-loop with a sequence targeting a gene of interest. These molecules offer an interesting alternative to silencing approaches that are based on shRNAs and siRNAs because they present the same efficiency as these options and are less cytotoxic. amiRNAs have mostly been applied to gene knockdown in plants; they have been examined to a lesser extent in animal cells. Therefore, this article reviews the amiRNAs that have been developed for animal cells and focuses on the miRNA scaffolds that can already be applied to construct the artificial counterparts, as well as on the different approaches that have been described to promote amiRNA expression and silencing efficiency. Furthermore, the availability of amiRNA libraries and other tools that can be used to design and construct these molecules is briefly discussed, along with an overview of the therapeutic applications for which amiRNAs have already been evaluated.
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Affiliation(s)
- Raquel Calloni
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, and Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Brazil
| | - Diego Bonatto
- Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, and Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul , Porto Alegre, Brazil
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16
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Hagen J, Scheerlinck JPY, Young ND, Gasser RB, Kalinna BH. Prospects for Vector-Based Gene Silencing to Explore Immunobiological Features of Schistosoma mansoni. ADVANCES IN PARASITOLOGY 2015; 88:85-122. [PMID: 25911366 DOI: 10.1016/bs.apar.2015.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Schistosomiasis is a prevalent, socioeconomically important disease of humans caused by parasites of the genus Schistosoma (schistosomes or blood flukes). Currently, more than 200 million people worldwide are infected with schistosomes. Despite major research efforts, there is only one drug routinely used for effective treatment, and no vaccine is available to combat schistosomiasis. The purpose of the present article is to (1) provide a background on the parasites and different forms of disease; (2) describe key immunomolecular aspects of disease induced in the host; and (3) critically appraise functional genomic methods employed to explore parasite biology, parasite-host interactions and disease at the molecular level. Importantly, the article also describes the features and advantages of lentiviral delivery of artificial microRNAs to silence genes. It also discusses the first successful application of such an approach in schistosomes, in order to explore the immunobiological role of selected target proteins known to be involved in egg-induced disease. The lentiviral transduction system provides exciting prospects for future, fundamental investigations of schistosomes, and is likely to have broad applicability to other eukaryotic pathogens and infectious diseases. The ability to achieve effective and stable gene perturbation in parasites has major biotechnological implications, and might facilitate the development of radically new methods for the treatment and control of parasitic diseases.
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Affiliation(s)
- Jana Hagen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jean-Pierre Y Scheerlinck
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Bernd H Kalinna
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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17
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Song HW, Bettegowda A, Oliver D, Yan W, Phan MH, de Rooij DG, Corbett MA, Wilkinson MF. shRNA off-target effects in vivo: impaired endogenous siRNA expression and spermatogenic defects. PLoS One 2015; 10:e0118549. [PMID: 25790000 PMCID: PMC4366048 DOI: 10.1371/journal.pone.0118549] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/20/2015] [Indexed: 12/23/2022] Open
Abstract
RNA interference (RNAi) is widely used to determine the function of genes. We chose this approach to assess the collective function of the highly related reproductive homeobox 3 (Rhox3) gene paralogs. Using a Rhox3 short hairpin (sh) RNA with 100% complementarity to all 8 Rhox3 paralogs, expressed from a CRE-regulated transgene, we successfully knocked down Rhox3 expression in male germ cells in vivo. These Rhox3-shRNA transgenic mice had dramatic defects in spermatogenesis, primarily in spermatocytes and round spermatids. To determine whether this phenotype was caused by reduced Rhox3 expression, we generated mice expressing the Rhox3-shRNA but lacking the intended target of the shRNA—Rhox3. These double-mutant mice had a phenotype indistinguishable from Rhox3-shRNA-expressing mice that was different from mice lacking the Rhox3 paralogs, indicating that the Rhox3 shRNA disrupts spermatogenesis independently of Rhox3. Rhox3-shRNA transgenic mice displayed few alterations in the expression of protein-coding genes, but instead exhibited reduced levels of all endogenous siRNAs we tested. This supported a model in which the Rhox3 shRNA causes spermatogenic defects by sequestering one or more components of the endogenous small RNA biogenesis machinery. Our study serves as a warning for those using shRNA approaches to investigate gene functions in vivo.
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Affiliation(s)
- Hye-Won Song
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Anilkumar Bettegowda
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Mimi H. Phan
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Dirk G. de Rooij
- Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Mark A. Corbett
- School of Pediatrics and Reproductive Health, The University of Adelaide, Adelaide, Australia
| | - Miles F. Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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18
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Fennell M, Xiang Q, Hwang A, Chen C, Huang CH, Chen CC, Pelossof R, Garippa RJ. Impact of RNA-guided technologies for target identification and deconvolution. JOURNAL OF BIOMOLECULAR SCREENING 2014; 19:1327-37. [PMID: 25163683 DOI: 10.1177/1087057114548414] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
For well over a decade, RNA interference (RNAi) has provided a powerful tool for investigators to query specific gene targets in an easily modulated loss-of-function setting, both in vitro and in vivo. Hundreds of publications have demonstrated the utility of RNAi in arrayed and pooled-based formats, in a wide variety of cell-based systems, including clonal, stem, transformed, and primary cells. Over the years, there have been significant improvements in the design of target-specific small-interfering RNA (siRNA) and short-hairpin RNA (shRNA), expression vectors, methods for mitigating off-target effects, and accurately interpreting screening results. Recent developments in RNAi technology include the Sensor assay, high-efficiency miR-E shRNAs, improved shRNA virus production with Pasha (DRGC8) knockdown, and assessment of RNAi off-target effects by using the C9-11 method. An exciting addition to the arsenal of RNA-mediated gene modulation is the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas) system for genomic editing, allowing for gene functional knockout rather than knockdown.
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Affiliation(s)
- Myles Fennell
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Qing Xiang
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Alexia Hwang
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Chong Chen
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Chun-Hao Huang
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Chi-Chao Chen
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Raphael Pelossof
- Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ralph J Garippa
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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19
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Geng J, Wei H, Sun R, Tian Z. Construction and application of a novel hepatocyte-directed vector to simultaneous knockdown and overexpression of multiple genes. Liver Int 2014; 34:e246-56. [PMID: 24125589 DOI: 10.1111/liv.12336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 09/15/2013] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Liver disease, such as malignancy and hepatitis, often correlates with several genetic disorders. We aimed to construct a hepatocyte-specific vector that could manipulate multiple genes simultaneously. METHODS We selected a highly efficient hepatocyte-specific α-foetoprotein (AFP) enhancer/albumin promoter (an RNA polymerase II promoter) to express our gene of interest and transcribe microRNA-based shRNAs (shRNAmir). Multiple shRNAmirs were assembled together in tandem to enhance the gene-silencing effect. By employing the AFP enhancer/albumin promoter and inserting an internal ribosome entry site (IRES), a hepatocyte-specific, multi-reporter vector that overexpressed both β-galactosidase (LacZ) and DsRed2 while simultaneously knocking down both EGFP and luciferase expression was successfully constructed and functionally tested in vitro. RESULTS The reporter genes in the multireporter vector were easily replaced by immune-related genes to construct the Multi-Vector, which overexpressed human interleukin 10 and silenced both CCL5 and CX3CL1 (FKN) simultaneously in vivo; visualization of DsRed2 coexpressed to monitor vector function in vivo confirmed that the Multi-Vector was successfully introduced into the host. Simultaneous manipulation of these multiple genes by the Multi-Vector synergistically inhibited acute liver injury induced by Poly I:C/D-GalN injection in mice. The multifunctional cassette was also packaged in and successfully delivered by an adenoviral vector. CONCLUSIONS We successfully engineered a vector that can simultaneously regulate multiple genes from a single multigene-containing vector in a hepatocyte-specific manner, suggesting the possibility that this method could be extensively and practically utilized in liver gene therapy.
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Affiliation(s)
- Jianlin Geng
- Department of Immunology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China; Hefei National Laboratory for Physical Sciences at Microscale, Hefei, Anhui, China
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20
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Tolani B, Gopalakrishnan R, Punj V, Matta H, Chaudhary PM. Targeting Myc in KSHV-associated primary effusion lymphoma with BET bromodomain inhibitors. Oncogene 2014; 33:2928-37. [PMID: 23792448 PMCID: PMC4892892 DOI: 10.1038/onc.2013.242] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 01/22/2023]
Abstract
Primary effusion lymphoma (PEL) is an aggressive form of non-Hodgkin's B-cell lymphoma associated with infection by Kaposi's sarcoma-associated herpes virus (KSHV). (+)-JQ1 and I-BET151 are two recently described novel small-molecule inhibitors of BET bromodomain chromatin-associated proteins that have shown impressive preclinical activity in cancers in which MYC is overexpressed at the transcriptional level due to chromosomal translocations that bring the MYC gene under the control of a super-enhancer. PEL cells, in contrast, lack structural alterations in the MYC gene, but have deregulated Myc protein due to the activity of KSHV-encoded latent proteins. We report that PEL cell lines are highly sensitive to bromodomain and extra-terminal (BET) bromodomain inhibitors-induced growth inhibition and undergo G0/G1 cell-cycle arrest, apoptosis and cellular senescence, but without the induction of lytic reactivation, upon treatment with these drugs. Treatment of PEL cell lines with BET inhibitors suppressed the expression of MYC and resulted in a genome-wide perturbation of MYC-dependent genes. Silencing of BRD4 and MYC expression blocked cell proliferation and cell-cycle progression, while ectopic expression of MYC from a retroviral promoter rescued cells from (+)-JQ1-induced growth arrest. In a xenograft model of PEL, (+)-JQ1 significantly reduced tumor growth and improved survival. Taken collectively, our results demonstrate that the utility of BET inhibitors may not be limited to cancers in which genomic alterations result in extremely high expression of MYC and they may have equal or perhaps greater activity against cancers in which the MYC genomic locus is structurally intact and c-Myc protein is deregulated at the post-translational level and is only modestly overexpressed.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Azepines/pharmacology
- Cell Cycle Checkpoints/drug effects
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cell Survival/genetics
- Cellular Senescence/drug effects
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Herpesvirus 8, Human
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Inhibitory Concentration 50
- Lymphoma, Primary Effusion/genetics
- Lymphoma, Primary Effusion/metabolism
- Lymphoma, Primary Effusion/pathology
- Lymphoma, Primary Effusion/virology
- Nuclear Proteins/antagonists & inhibitors
- Protein Binding/drug effects
- Protein Transport
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- Transcription Factors/antagonists & inhibitors
- Transcription, Genetic
- Triazoles/pharmacology
- Tumor Burden/drug effects
- Virus Replication/drug effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Bhairavi Tolani
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Ramakrishnan Gopalakrishnan
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Vasu Punj
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Hittu Matta
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Preet M. Chaudhary
- Jane Anne Nohl Division of Hematology and Center for the Study of Blood Diseases, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
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21
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Fellmann C, Hoffmann T, Sridhar V, Hopfgartner B, Muhar M, Roth M, Lai D, Barbosa I, Kwon J, Guan Y, Sinha N, Zuber J. An Optimized microRNA Backbone for Effective Single-Copy RNAi. Cell Rep 2013; 5:1704-13. [DOI: 10.1016/j.celrep.2013.11.020] [Citation(s) in RCA: 337] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/09/2013] [Accepted: 11/11/2013] [Indexed: 10/25/2022] Open
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22
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Osório L, Gijsbers R, Oliveras-Salvá M, Michiels A, Debyser Z, Van den Haute C, Baekelandt V. Viral vectors expressing a single microRNA-based short-hairpin RNA result in potent gene silencing in vitro and in vivo. J Biotechnol 2013; 169:71-81. [PMID: 24252659 DOI: 10.1016/j.jbiotec.2013.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 11/06/2013] [Accepted: 11/08/2013] [Indexed: 12/23/2022]
Abstract
The characterization of RNA interference and the accompanying microRNAs (miRs), together with the exogenous expression of artificial miR-like elements, has led to the development of strategies for specific and potent gene silencing. In turn, this allows manipulation of gene expression levels for target validation purposes in cell culture or for the generation of animal models. In this study we determined the optimal strategy to achieve the most potent knockdown using miR-based viral vectors. We studied polycistronic miRs in a viral vector context and evaluated knockdown potency of multiple-miRs targeting the same seed sequence in parallel with miRs targeting different seed sequences, both for a reporter and endogenous mRNA targets. We demonstrate that potent knockdown can be obtained in vitro and in vivo using viral vectors that encode a single miR-based short-hairpin RNA and report a generic and effective cloning platform for artificial miR30-based short-hairpin RNAs to generate potent knockdown viral vectors.
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Affiliation(s)
- Luísa Osório
- KU Leuven, Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven, Belgium
| | - Rik Gijsbers
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium; KU Leuven, Leuven Viral Vector Core, Leuven, Belgium
| | - Marusela Oliveras-Salvá
- KU Leuven, Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven, Belgium
| | - Annelies Michiels
- KU Leuven, Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven, Belgium; KU Leuven, Leuven Viral Vector Core, Leuven, Belgium
| | - Zeger Debyser
- KU Leuven, Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Leuven, Belgium
| | - Chris Van den Haute
- KU Leuven, Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven, Belgium
| | - Veerle Baekelandt
- KU Leuven, Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven, Belgium.
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23
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Inhibition of Bim enhances replication of varicella-zoster virus and delays plaque formation in virus-infected cells. J Virol 2013; 88:1381-8. [PMID: 24227856 DOI: 10.1128/jvi.01695-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Programmed cell death (apoptosis) is an important host defense mechanism against intracellular pathogens, such as viruses. Accordingly, viruses have evolved multiple mechanisms to modulate apoptosis to enhance replication. Varicella-zoster virus (VZV) induces apoptosis in human fibroblasts and melanoma cells. We found that VZV triggered the phosphorylation of the proapoptotic proteins Bim and BAD but had little or no effect on other Bcl-2 family members. Since phosphorylation of Bim and BAD reduces their proapoptotic activity, this may prevent or delay apoptosis in VZV-infected cells. Phosphorylation of Bim but not BAD in VZV-infected cells was dependent on activation of the MEK/extracellular signal-regulated kinase (ERK) pathway. Cells knocked down for Bim showed delayed VZV plaque formation, resulting in longer survival of VZV-infected cells and increased replication of virus, compared with wild-type cells infected with virus. Conversely, overexpression of Bim resulted in earlier plaque formation, smaller plaques, reduced virus replication, and increased caspase 3 activity. Inhibition of caspase activity in VZV-infected cells overexpressing Bim restored levels of virus production similar to those seen with virus-infected wild-type cells. Previously we showed that VZV ORF12 activates ERK and inhibits apoptosis in virus-infected cells. Here we found that VZV ORF12 contributes to Bim and BAD phosphorylation. In summary, VZV triggers Bim phosphorylation; reduction of Bim levels results in longer survival of VZV-infected cells and increased VZV replication.
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24
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Stoller ML, Chang HC, Fekete DM. Bicistronic gene transfer tools for delivery of miRNAs and protein coding sequences. Int J Mol Sci 2013; 14:18239-55. [PMID: 24013374 PMCID: PMC3794778 DOI: 10.3390/ijms140918239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a category of small RNAs that modulate levels of proteins via post-transcriptional inhibition. Currently, a standard strategy to overexpress miRNAs is as mature miRNA duplexes, although this method is cumbersome if multiple miRNAs need to be delivered. Many of these miRNAs are found within introns and processed through the RNA polymerase II pathway. We have designed a vector to exploit this naturally-occurring intronic pathway to deliver the three members of the sensory-specific miR-183 family from an artificial intron. In one version of the vector, the downstream exon encodes the reporter (GFP) while another version encodes a fusion protein created between the transcription factor Atoh1 and the hemaglutinin epitope, to distinguish it from endogenous Atoh1. In vitro analysis shows that the miRNAs contained within the artificial intron are processed and bind to their targets with specificity. The genes downstream are successfully translated into protein and identifiable through immunofluorescence. More importantly, Atoh1 is proven functional through in vitro assays. These results suggest that this cassette allows expression of miRNAs and proteins simultaneously, which provides the opportunity for joint delivery of specific translational repressors (miRNA) and possibly transcriptional activators (transcription factors). This ability is attractive for future gene therapy use.
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Affiliation(s)
- Michelle L. Stoller
- Department of Biological Sciences, Purdue University, 915 W State St, West Lafayette, IN 47907-1392, USA; E-Mails: (M.L.S.); (H.C.C.)
- Purdue University Center for Cancer Research, Purdue University, 201 S University Dr, West Lafayette, IN 47907-2064, USA
| | - Henry C. Chang
- Department of Biological Sciences, Purdue University, 915 W State St, West Lafayette, IN 47907-1392, USA; E-Mails: (M.L.S.); (H.C.C.)
- Purdue University Center for Cancer Research, Purdue University, 201 S University Dr, West Lafayette, IN 47907-2064, USA
| | - Donna M. Fekete
- Department of Biological Sciences, Purdue University, 915 W State St, West Lafayette, IN 47907-1392, USA; E-Mails: (M.L.S.); (H.C.C.)
- Purdue University Center for Cancer Research, Purdue University, 201 S University Dr, West Lafayette, IN 47907-2064, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-765-496-3058; Fax: +1-765-494-0876
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25
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Doxycycline-dependent inducible and reversible RNA interference mediated by a single lentivirus vector. Biosci Biotechnol Biochem 2013; 77:776-81. [PMID: 23563548 DOI: 10.1271/bbb.120917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA interference has been applied to the development of a method of silencing genes of interest. Short hairpin RNA (shRNA) expression vectors are useful in driving gene-silencing. Standard shRNA vectors produce a knockdown phenotype soon after transduction. An alternative strategy for conditional gene knockdown would be useful to investigate gene functions in a time-dependent manner. In this study, we developed an inducible gene knockdown system based on lentivirus-mediated gene transfer. A single lentivirus vector capable of inducible expression of a designed microRNA-based shRNA was generated using a tetracycline-dependent transactivation system. The lentiviral vector facilitated doxycycline-dependent inducible knockdown specific to the target gene. Withdrawal of doxycycline after transient treatment resulted in complete recovery of target gene expressions to normal levels. Thus the single lentiviral vector developed in this study should be a powerful tool for doxycycline-dependent inducible and reversible RNA interference in molecular genetic studies.
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26
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Abstract
Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNAs (shRNAs) for targeted gene silencing has become a benchmark technology. Using plasmid and viral vectoring systems, the transcription of shRNA precursors that are effectively processed by the RNAi pathway can lead to potent gene knockdown. The past decade has seen continual advancement and improvement to the various strategies that can be used for shRNA delivery, and the use of shRNAs for clinical applications is well underway. Driving these developments has been the many benefits afforded by shRNA technologies, including the stable integration of expression constructs for long-term expression, infection of difficult-to-target cell lines and tissues using viral vectors, and the temporal control of shRNA transcription by inducible promoters. The use of different effector molecule formats, promoters, and vector types, has meant that experiments can be tailored to target specific cell types and minimize cellular toxicities. Through the application of combinatorial RNAi (co-RNAi), multiple shRNA delivery strategies can improve gene knockdown, permit multiple transcripts to be targeted simultaneously, and curtail the emergence of viral escape mutants. This chapter reviews the history, cellular processing, and various applications of shRNAs in mammalian systems, including options for effector molecule design, vector and promoter types, and methods for multiple shRNA delivery.
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Affiliation(s)
- Luke S Lambeth
- Murdoch Childrens Research Institute, Royal Childrens Hospital, Melbourne, VIC, Australia.
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27
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Jun HJ, Acquaviva J, Chi D, Lessard J, Zhu H, Woolfenden S, Bronson RT, Pfannl R, White F, Housman DE, Iyer L, Whittaker CA, Boskovitz A, Raval A, Charest A. Acquired MET expression confers resistance to EGFR inhibition in a mouse model of glioblastoma multiforme. Oncogene 2012; 31:3039-50. [PMID: 22020333 PMCID: PMC3774279 DOI: 10.1038/onc.2011.474] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 08/25/2011] [Accepted: 09/08/2011] [Indexed: 12/16/2022]
Abstract
Glioblastoma multiforme (GBM) is an aggressive brain tumor for which there is no cure. Overexpression of wild-type epidermal growth factor receptor (EGFR) and loss of the tumor suppressor genes Ink4a/Arf and PTEN are salient features of this deadly cancer. Surprisingly, targeted inhibition of EGFR has been clinically disappointing, demonstrating an innate ability for GBM to develop resistance. Efforts at modeling GBM in mice using wild-type EGFR have proven unsuccessful to date, hampering endeavors at understanding molecular mechanisms of therapeutic resistance. Here, we describe a unique genetically engineered mouse model of EGFR-driven gliomagenesis that uses a somatic conditional overexpression and chronic activation of wild-type EGFR in cooperation with deletions in the Ink4a/Arf and PTEN genes in adult brains. Using this model, we establish that chronic activation of wild-type EGFR with a ligand is necessary for generating tumors with histopathological and molecular characteristics of GBMs. We show that these GBMs are resistant to EGFR kinase inhibition and we define this resistance molecularly. Inhibition of EGFR kinase activity using tyrosine kinase inhibitors in GBM tumor cells generates a cytostatic response characterized by a cell cycle arrest, which is accompanied by a substantial change in global gene expression levels. We demonstrate that an important component of this pattern is the transcriptional activation of the MET receptor tyrosine kinase and that pharmacological inhibition of MET overcomes the resistance to EGFR inhibition in these cells. These findings provide important new insights into mechanisms of resistance to EGFR inhibition and suggest that inhibition of multiple targets will be necessary to provide therapeutic benefit for GBM patients.
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Affiliation(s)
- Hyun Jung Jun
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Jaime Acquaviva
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Dorcas Chi
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Julie Lessard
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Haihao Zhu
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Steve Woolfenden
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | | | - Rolf Pfannl
- Department of Neurosurgery, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Forest White
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David E. Housman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Lakshmanan Iyer
- Tufts Center for Neuroscience Research, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Abraham Boskovitz
- Department of Neurosurgery, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Ami Raval
- Department of Neurosurgery, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Alain Charest
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
- Department of Neurosurgery, Tufts University School of Medicine, Boston, MA 02111, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
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Wu Z, Xue Y, Wang B, Du J, Jin Q. Broad-spectrum antiviral activity of RNA interference against four genotypes of Japanese encephalitis virus based on single microRNA polycistrons. PLoS One 2011; 6:e26304. [PMID: 22028851 PMCID: PMC3196537 DOI: 10.1371/journal.pone.0026304] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 09/23/2011] [Indexed: 11/30/2022] Open
Abstract
Japanese encephalitis virus (JEV), a neurotropic mosquito-borne flavivirus, causes acute viral encephalitis and neurologic disease with a high fatality rate in humans and a range of animals. Small interfering RNA (siRNA) is a powerful antiviral agent able to inhibit JEV replication. However, the high rate of genetic variability between JEV strains (of four confirmed genotypes, genotypes I, II, III and IV) hampers the broad-spectrum application of siRNAs, and mutations within the targeted sequences could facilitate JEV escape from RNA interference (RNAi)-mediated antiviral therapy. To improve the broad-spectrum application of siRNAs and prevent the generation of escape mutants, multiple siRNAs targeting conserved viral sequences need to be combined. In this study, using a siRNA expression vector based on the miR-155 backbone and promoted by RNA polymerase II, we initially identified nine siRNAs targeting highly conserved regions of seven JEV genes among strains of the four genotypes of JEV to effectively block the replication of the JEV vaccine strain SA14-14-2. Then, we constructed single microRNA-like polycistrons to simultaneously express these effective siRNAs under a single RNA polymerase II promoter. Finally, these single siRNAs or multiple siRNAs from the microRNA-like polycistrons showed effective anti-virus activity in genotype I and genotype III JEV wild type strains, which are the predominant genotypes of JEV in mainland China. The anti-JEV effect of these microRNA-like polycistrons was also predicted in other genotypes of JEV (genotypes II and IV), The inhibitory efficacy indicated that siRNAs×9 could theoretically inhibit the replication of JEV genotypes II and IV.
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Affiliation(s)
- Zhiqiang Wu
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Ying Xue
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Bei Wang
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jiang Du
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Qi Jin
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
- * E-mail:
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Chen B, Dores MR, Grimsey N, Canto I, Barker BL, Trejo J. Adaptor protein complex-2 (AP-2) and epsin-1 mediate protease-activated receptor-1 internalization via phosphorylation- and ubiquitination-dependent sorting signals. J Biol Chem 2011; 286:40760-70. [PMID: 21965661 DOI: 10.1074/jbc.m111.299776] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signaling by protease-activated receptor-1 (PAR1), a G protein-coupled receptor (GPCR) for thrombin, is regulated by desensitization and internalization. PAR1 desensitization is mediated by β-arrestins, like most classic GPCRs. In contrast, internalization of PAR1 occurs through a clathrin- and dynamin-dependent pathway independent of β-arrestins. PAR1 displays two modes of internalization. Constitutive internalization of unactivated PAR1 is mediated by the clathrin adaptor protein complex-2 (AP-2), where the μ2-adaptin subunit binds directly to a tyrosine-based motif localized within the receptor C-tail domain. However, AP-2 depletion only partially inhibits agonist-induced internalization of PAR1, suggesting a function for other clathrin adaptors in this process. Here, we now report that AP-2 and epsin-1 are both critical mediators of agonist-stimulated PAR1 internalization. We show that ubiquitination of PAR1 and the ubiquitin-interacting motifs of epsin-1 are required for epsin-1-dependent internalization of activated PAR1. In addition, activation of PAR1 promotes epsin-1 de-ubiquitination, which may increase its endocytic adaptor activity to facilitate receptor internalization. AP-2 also regulates activated PAR1 internalization via recognition of distal C-tail phosphorylation sites rather than the canonical tyrosine-based motif. Thus, AP-2 and epsin-1 are both required to promote efficient internalization of activated PAR1 and recognize discrete receptor sorting signals. This study defines a new pathway for internalization of mammalian GPCRs.
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Affiliation(s)
- Buxin Chen
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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Expression of multiple artificial microRNAs from a chicken miRNA126-based lentiviral vector. PLoS One 2011; 6:e22437. [PMID: 21789258 PMCID: PMC3138786 DOI: 10.1371/journal.pone.0022437] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 06/28/2011] [Indexed: 11/20/2022] Open
Abstract
Background The use of RNAi in both basic and translational research often requires expression of multiple siRNAs from the same vector. Methods/Principal Findings We have developed a novel chicken miR126-based artificial miRNA expression system that can express one, two or three miRNAs from a single cassette in a lentiviral vector. We show that each of the miRNAs expressed from the same lentiviral vector is capable of potent inhibition of reporter gene expression in transient transfection and stable integration assays in chicken fibroblast DF-1 cells. Transduction of Vero cells with lentivirus expressing two or three different anti-influenza miRNAs leads to inhibition of influenza virus production. In addition, the chicken miR126-based expression system effectively inhibits reporter gene expression in human, monkey, dog and mouse cells. These results demonstrate that the flanking regions of a single primary miRNA can support processing of three different stem-loops in a single vector. Conclusions/Significance This novel design expands the means to express multiple miRNAs from the same vector for potent and effective silencing of target genes and influenza virus.
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31
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Creating a flexible multiple microRNA expression vector by linking precursor microRNAs. Biochem Biophys Res Commun 2011; 411:276-80. [PMID: 21726537 DOI: 10.1016/j.bbrc.2011.06.123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 06/18/2011] [Indexed: 01/07/2023]
Abstract
MicroRNAs (miRNAs) are ∼22nt non-coding RNA molecules that usually function as endogenous repressors of target genes. Many biological processes depend on faithful miRNA expression and miRNA profiling has revealed dysregulation of many miRNAs in neurological, and cardiovascular diseases, and in cancer. Despite this finding, most studies have focused on the function of single miRNAs or miRNA clusters. To better address physiologically relevant collaborative miRNA interactions, we developed a simple and flexible platform which expresses several miRNAs that have different genomic locations from a single transcript using endogenous pre-miRNA sequences. As a proof of principle we cloned the miR-34 tumor suppressor family and showed that the miR-34a/34b/34c vector expresses each miRNA at similar levels to individual miRNA containing vectors. Moreover, the miR-34a/34b/34c vector suppressed cell growth more than the individual miRNA vectors. We expect that this platform will be invaluable as a tool to study the complex and synergistic interactions of aberrantly expressed miRNAs in human diseases and may have applications for use in gene therapy.
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Liu YP, Berkhout B. miRNA cassettes in viral vectors: problems and solutions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:732-45. [PMID: 21679781 DOI: 10.1016/j.bbagrm.2011.05.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/25/2011] [Accepted: 05/27/2011] [Indexed: 02/05/2023]
Abstract
The discovery of RNA interference (RNAi), an evolutionary conserved gene silencing mechanism that is triggered by double stranded RNA, has led to tremendous efforts to use this technology for basic research and new RNA therapeutics. RNAi can be induced via transfection of synthetic small interfering RNAs (siRNAs), which results in a transient knockdown of the targeted mRNA. For stable gene silencing, short hairpin RNA (shRNA) or microRNA (miRNA) constructs have been developed. In mammals and humans, the natural RNAi pathway is triggered via endogenously expressed miRNAs. The use of modified miRNA expression cassettes to elucidate fundamental biological questions or to develop therapeutic strategies has received much attention. Viral vectors are particularly useful for the delivery of miRNA genes to specific target cells. To date, many viral vectors have been developed, each with distinct characteristics that make one vector more suitable for a certain purpose than others. This review covers the recent progress in miRNA-based gene-silencing approaches that use viral vectors, with a focus on their unique properties, respective limitations and possible solutions. Furthermore, we discuss a related topic that involves the insertion of miRNA-target sequences in viral vector systems to restrict their cellular range of gene expression. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.
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Affiliation(s)
- Ying Poi Liu
- Department of Medical Microbiology, University of Amsterdam, Amsterdam, the Netherlands
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Li X, Liu S, Wang D, Chen H, Xia H. Adenoviral delivered eGFP-intron splicing system for multiple gene RNAi. Biotechnol Lett 2011; 33:1723-8. [PMID: 21544612 DOI: 10.1007/s10529-011-0633-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 04/19/2011] [Indexed: 01/19/2023]
Abstract
An eGFP-intron splicing system that allows for co-ordinated expression of up to four siRNAs from a single adenoviral vector has been developed. In this splicing structure the intron, embedded by a multiple miR30-based shRNAs, is located between two incomplete eGFP domains which require successful splicing for functionality. To prove the principle of the method, an adenoviral vector delivering four transcripts targeting survivin, XIAP, Hec1, and VEGF was developed which enabled the knockdown of target genes by 70, 70, 54 and 44%, respectively, in HeLa cells. This is the first report of multi-siRNA engineering technology in the context of adenoviral vector which would enable concomitant knockdown of tumor-related target genes. The results provide a strategy for gene function analysis and cancer gene therapy.
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Affiliation(s)
- Xing Li
- Laboratory of Gene Therapy, Department of Biochemistry, College of Life Sciences, Shaanxi Normal University, 199 South Chang'an Road, Xi'an 710062, People's Republic of China
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Mcintyre GJ, Arndt AJ, Gillespie KM, Mak WM, Fanning GC. A comparison of multiple shRNA expression methods for combinatorial RNAi. GENETIC VACCINES AND THERAPY 2011; 9:9. [PMID: 21496330 PMCID: PMC3098768 DOI: 10.1186/1479-0556-9-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 04/17/2011] [Indexed: 01/09/2023]
Abstract
RNAi gene therapies for HIV-1 will likely need to employ multiple shRNAs to counter resistant strains. We evaluated 3 shRNA co-expression methods to determine their suitability for present use; multiple expression vectors, multiple expression cassettes and single transcripts comprised of several dsRNA units (aka domains) with each being designed to a different target. Though the multiple vector strategy was effective with 2 shRNAs, the increasing number of vectors required is a major shortcoming. With single transcript configurations we only saw adequate activity from 1 of 10 variants tested, the variants being comprised of 2 - 3 different target domains. Whilst single transcript configurations have the most advantages on paper, these configurations can not yet be rapidly and reliably re-configured for new targets. However, our multiple cassette combinations of 2, 3 and 4 (29 bp) shRNAs were all successful, with suitable activity maintained in all positions and net activities comparable to that of the corresponding single shRNAs. We conclude that the multiple cassette strategy is the most suitably developed for present use as it is easy to design, assemble, is directly compatible with pre-existing shRNA and can be easily expanded.
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Affiliation(s)
- Glen J Mcintyre
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Allison J Arndt
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Kirsten M Gillespie
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Wendy M Mak
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Gregory C Fanning
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
- Tibotec BVBA, Gen De Wittelaan L 11 B3, 2800 Mechelen, Belgium
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Radulovich N, Leung L, Tsao MS. Modified gateway system for double shRNA expression and Cre/lox based gene expression. BMC Biotechnol 2011; 11:24. [PMID: 21418658 PMCID: PMC3070635 DOI: 10.1186/1472-6750-11-24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 03/22/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The growing need for functional studies of genes has set the stage for the development of versatile tools for genetic manipulations. RESULTS Aiming to provide tools for high throughput analysis of gene functions, we have developed a modified short hairpin RNA (shRNA) and gene expression system based on Gateway Technology. The system contains a series of entry and destination vectors that enables easy transfer of shRNA or cDNA into lentiviral expression systems with a variety of selection or marker genes (i.e. puromycin, hygromycin, green fluorescent protein-EGFP, yellow fluorescent protein-YFP and red fluorescent protein-dsRed2). Our shRNA entry vector pENTR.hU6.hH1 containing two tandem human shRNA expression promoters, H1 and U6, was capable of co-expressing two shRNA sequences simultaneously. The entry vector for gene overexpression, pENTR.CMV.ON was constructed to contain CMV promoter with a multiple cloning site flanked by loxP sites allowing for subsequent Cre/lox recombination. Both shRNA and cDNA expression vectors also contained attL sites necessary for recombination with attR sites in our destination expression vectors. As proof of principle we demonstrate the functionality and efficiency of this system by testing expression of several cDNA and shRNA sequences in a number of cell lines. CONCLUSION Our system is a valuable addition to already existing library of Gateway based vectors and can be an essential tool for many aspects of gene functional studies.
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Affiliation(s)
- Nikolina Radulovich
- University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Medical Sciences Buildings, 1 King's College Circle, Toronto, Ontario, M5 S 1A8, Canada
| | - Lisa Leung
- University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
- Department of Medical Biophysics, University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
| | - Ming-Sound Tsao
- University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Medical Sciences Buildings, 1 King's College Circle, Toronto, Ontario, M5 S 1A8, Canada
- Department of Medical Biophysics, University Health Network, Ontario Cancer Institute/Princess Margaret Hospital Site, 610 University Ave., Toronto, Ontario, M5G 2M9, Canada
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Mcintyre GJ, Groneman JL, Yu YH, Tran A, Applegate TL. Multiple shRNA combinations for near-complete coverage of all HIV-1 strains. AIDS Res Ther 2011; 8:1. [PMID: 21226969 PMCID: PMC3033792 DOI: 10.1186/1742-6405-8-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 01/13/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Combinatorial RNA interference (co-RNAi) approaches are needed to account for viral variability in treating HIV-1 with RNAi, as single short hairpin RNAs (shRNA) are rapidly rendered ineffective by resistant strains. Current work suggests that 4 simultaneously expressed shRNAs may prevent the emergence of resistant strains. RESULTS In this study we assembled combinations of highly-conserved shRNAs to target as many HIV-1 strains as possible. We analyzed intersecting conservations of 10 shRNAs to find combinations with 4+ matching the maximum number of strains using 1220+ HIV-1 sequences from the Los Alamos National Laboratory (LANL). We built 26 combinations of 2 to 7 shRNAs with up to 87% coverage for all known strains and 100% coverage of clade B subtypes, and characterized their intrinsic suppressive activities in transient expression assays. We found that all combinations had high combined suppressive activities, though there were also large changes in the individual activities of the component shRNAs in our multiple expression cassette configurations. CONCLUSION By considering the intersecting conservations of shRNA combinations we have shown that it is possible to assemble combinations of 6 and 7 highly active, highly conserved shRNAs such that there is always at least 4 shRNAs within each combination covering all currently known variants of entire HIV-1 subtypes. By extension, it may be possible to combine several combinations for complete global coverage of HIV-1 variants.
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Affiliation(s)
- Glen J Mcintyre
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Jennifer L Groneman
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Yi-Hsin Yu
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Anna Tran
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Tanya L Applegate
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
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Abstract
For effective RNA interference (RNAi)-based therapies against viral infection, particularly highly mutational viruses like HCV and HIV, combinational strategies that target multiple regions within a viral genome are required to prevent resistance. The use of lentiviral vectors for combinatorial RNAi (coRNAi) offers possibilities to deliver multiple short hairpin RNA (shRNA) sequences simultaneously to individual cells while maintaining high expression levels required to suppress viral replication. By applying coRNAi, one can impart either a protective strategy, i.e., treatment prior to infection, or a long-term treatment postinfection without the eventuality of mutational outgrowth due to incomplete selection pressure. In this chapter, we provide a detailed description of the methods available to create coRNAi vectors and discuss some of the current problems and technical limitations.
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Lambeth LS, Van Hateren NJ, Wilson SA, Nair V. A direct comparison of strategies for combinatorial RNA interference. BMC Mol Biol 2010; 11:77. [PMID: 20937117 PMCID: PMC2958852 DOI: 10.1186/1471-2199-11-77] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 10/11/2010] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Combinatorial RNA interference (co-RNAi) is a valuable tool for highly effective gene suppression of single and multiple-genes targets, and can be used to prevent the escape of mutation-prone transcripts. There are currently three main approaches used to achieve co-RNAi in animal cells; multiple promoter/shRNA cassettes, long hairpin RNAs (lhRNA) and miRNA-embedded shRNAs, however, the relative effectiveness of each is not known. The current study directly compares the ability of each co-RNAi method to deliver pre-validated siRNA molecules to the same gene targets. RESULTS Double-shRNA expression vectors were generated for each co-RNAi platform and their ability to suppress both single and double-gene reporter targets were compared. The most reliable and effective gene silencing was achieved from the multiple promoter/shRNA approach, as this method induced additive suppression of single-gene targets and equally effective knockdown of double-gene targets. Although both lhRNA and microRNA-embedded strategies provided efficient gene knockdown, suppression levels were inconsistent and activity varied greatly for different siRNAs tested. Furthermore, it appeared that not only the position of siRNAs within these multi-shRNA constructs impacted upon silencing activity, but also local properties of each individual molecule. In addition, it was also found that the insertion of up to five promoter/shRNA cassettes into a single construct did not negatively affect the efficacy of each individual shRNA. CONCLUSIONS By directly comparing the ability of shRNAs delivered from different co-RNA platforms to initiate knockdown of the same gene targets, we found that multiple U6/shRNA cassettes offered the most reliable and predictable suppression of both single and multiple-gene targets. These results highlight some important strengths and pitfalls of the currently used methods for multiple shRNA delivery, and provide valuable insights for the design and application of reliable co-RNAi.
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Affiliation(s)
- Luke S Lambeth
- Institute for Animal Health, Compton, Berkshire, UK
- Tumour Suppression Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Australia
| | - Nick J Van Hateren
- Department of Molecular Biology & Biotechnology, University of Sheffield, Western Bank, Sheffield, UK
| | - Stuart A Wilson
- Department of Molecular Biology & Biotechnology, University of Sheffield, Western Bank, Sheffield, UK
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Zhang Y, Tang W, Jones MC, Xu W, Halene S, Wu D. Different roles of G protein subunits beta1 and beta2 in neutrophil function revealed by gene expression silencing in primary mouse neutrophils. J Biol Chem 2010; 285:24805-14. [PMID: 20525682 PMCID: PMC2915716 DOI: 10.1074/jbc.m110.142885] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 06/03/2010] [Indexed: 11/06/2022] Open
Abstract
Neutrophils play important roles in host innate immunity and various inflammation-related diseases. In addition, neutrophils represent an excellent system for studying directional cell migration. However, neutrophils are terminally differentiated cells that are short lived and refractory to transfection; thus, they are not amenable for existing gene silencing techniques. Here we describe the development of a method to silence gene expression efficiently in primary mouse neutrophils. A mouse stem cell virus-based retroviral vector was modified to express short hairpin RNAs and fluorescent marker protein at high levels in hematopoietic cells and used to infect mouse bone marrow cells prior to reconstitution of the hematopoietic system in lethally irradiated mice. This method was used successfully to silence the expression of Gbeta(1) and/or Gbeta(2) in mouse neutrophils. Knockdown of Gbeta(2) appeared to affect primarily the directionality of neutrophil chemotaxis rather than motility, whereas knockdown of Gbeta(1) had no significant effect. However, knockdown of both Gbeta(1) and Gbeta(2) led to significant reduction in motility and responsiveness. In addition, knockdown of Gbeta(1) but not Gbeta(2) inhibited the ability of neutrophils to kill ingested bacteria, and only double knockdown resulted in significant reduction in bacterial phagocytosis. Therefore, we have developed a short hairpin RNA-based method to effectively silence gene expression in mouse neutrophils for the first time, which allowed us to uncover divergent roles of Gbeta(1) and Gbeta(2) in the regulation of neutrophil functions.
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Affiliation(s)
- Yong Zhang
- From the Program in Vascular Biology and Therapeutics and Department of Pharmacology and
| | - Wenwen Tang
- From the Program in Vascular Biology and Therapeutics and Department of Pharmacology and
| | - Matthew C. Jones
- From the Program in Vascular Biology and Therapeutics and Department of Pharmacology and
| | - Wenwen Xu
- From the Program in Vascular Biology and Therapeutics and Department of Pharmacology and
| | - Stephanie Halene
- Section of Hematology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut 06520
| | - Dianqing Wu
- From the Program in Vascular Biology and Therapeutics and Department of Pharmacology and
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Leong IUS, Skinner JR, Shelling AN, Love DR. Zebrafish as a model for long QT syndrome: the evidence and the means of manipulating zebrafish gene expression. Acta Physiol (Oxf) 2010; 199:257-76. [PMID: 20331541 DOI: 10.1111/j.1748-1716.2010.02111.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Congenital long QT syndrome (LQT) is a group of cardiac disorders associated with the dysfunction of cardiac ion channels. It is characterized by prolongation of the QT-interval, episodes of syncope and even sudden death. Individuals may remain asymptomatic for most of their lives while others present with severe symptoms. This heterogeneity in phenotype makes diagnosis difficult with a greater emphasis on more targeted therapy. As a means of understanding the molecular mechanisms underlying LQT syndrome, evaluating the effect of modifier genes on disease severity as well as to test new therapies, the development of model systems remains an important research tool. Mice have predominantly been the animal model of choice for cardiac arrhythmia research, but there have been varying degrees of success in recapitulating the human symptoms; the mouse cardiac action potential (AP) and surface electrocardiograms exhibit major differences from those of the human heart. Against this background, the zebrafish is an emerging vertebrate disease modelling species that offers advantages in analysing LQT syndrome, not least because its cardiac AP much more closely resembles that of the human. This article highlights the use and potential of this species in LQT syndrome modelling, and as a platform for the in vivo assessment of putative disease-causing mutations in LQT genes, and of therapeutic interventions.
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Hu T, Chen P, Fu Q, Liu Y, Ishaq M, Li J, Ma L, Guo D. Comparative Studies of Various Artificial microRNA Expression Vectors for RNAi in Mammalian Cells. Mol Biotechnol 2010; 46:34-40. [DOI: 10.1007/s12033-010-9264-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Li F, Mahato RI. Bipartite vectors for co-expression of a growth factor cDNA and short hairpin RNA against an apoptotic gene. J Gene Med 2009; 11:764-71. [PMID: 19554613 DOI: 10.1002/jgm.1357] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Although human islet transplantation is a promising approach for treating type I diabetes, its success is limited as a result of the poor survival rate of transplanted islets. Expression of a growth factor gene to promote revascularization and silencing of pro-apoptotic genes before transplantation may improve the outcome of islet transplantation. METHODS In the present study, we constructed bipartite plasmid vectors to co-express a vascular endothelial growth factor (VEGF) cDNA and short hairpin (sh)RNA targeting inducible NO synthase (iNOS) gene. First, we screened shRNA sequences against human iNOS by transfecting plasmids encoding shRNA targeting different start sites of human iNOS. Then, the effect of different promoters [such as H1, U6 and cytomegalovirus (CMV)] and micro RNA backbones on gene silencing was determined. RESULTS No statistical difference in iNOS gene silencing was observed for the shRNA with H1, U6 and CMV promoters. In addition, a conventional shRNA showed better silencing of the iNOS gene compared to shRNA containing mir375 and mir30 backbones. A bipartite plasmid was also constructed with mir30-shRNA and a VEGF cDNA controlled by a single CMV promoter. This plasmid showed a better silencing effect compared to plasmid without VEGF cDNA. CONCLUSIONS In the present study, we have successfully constructed bipartite vectors co-expressing a VEGF cDNA and a shRNA against the iNOS gene. These vectors could be attractive candidates for improving the survival of transplanted islets.
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Affiliation(s)
- Feng Li
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38103-3308, USA
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Mcintyre GJ, Yu YH, Tran A, Jaramillo AB, Arndt AJ, Millington ML, Boyd MP, Elliott FA, Shen SW, Murray JM, Applegate TL. Cassette deletion in multiple shRNA lentiviral vectors for HIV-1 and its impact on treatment success. Virol J 2009; 6:184. [PMID: 19878571 PMCID: PMC2775741 DOI: 10.1186/1743-422x-6-184] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 10/30/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple short hairpin RNA (shRNA) gene therapy strategies are currently being investigated for treating viral diseases such as HIV-1. It is important to use several different shRNAs to prevent the emergence of treatment-resistant strains. However, there is evidence that repeated expression cassettes delivered via lentiviral vectors may be subject to recombination-mediated repeat deletion of 1 or more cassettes. RESULTS The aim of this study was to determine the frequency of deletion for 2 to 6 repeated shRNA cassettes and mathematically model the outcomes of different frequencies of deletion in gene therapy scenarios. We created 500+ clonal cell lines and found deletion frequencies ranging from 2 to 36% for most combinations. While the central positions were the most frequently deleted, there was no obvious correlation between the frequency or extent of deletion and the number of cassettes per combination. We modeled the progression of infection using combinations of 6 shRNAs with varying degrees of deletion. Our in silico modeling indicated that if at least half of the transduced cells retained 4 or more shRNAs, the percentage of cells harboring multiple-shRNA resistant viral strains could be suppressed to < 0.1% after 13 years. This scenario afforded a similar protection to all transduced cells containing the full complement of 6 shRNAs. CONCLUSION Deletion of repeated expression cassettes within lentiviral vectors of up to 6 shRNAs can be significant. However, our modeling showed that the deletion frequencies observed here for 6x shRNA combinations was low enough that the in vivo suppression of replication and escape mutants will likely still be effective.
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Affiliation(s)
- Glen J Mcintyre
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Yi-Hsin Yu
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Anna Tran
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Angel B Jaramillo
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Allison J Arndt
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Michelle L Millington
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Maureen P Boyd
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Fiona A Elliott
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Sylvie W Shen
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - John M Murray
- School of Mathematics and Statistics, The University of New South Wales, Sydney, NSW, 2052, Australia
- The National Center in HIV Epidemiology and Clinical Research, The University of New South Wales, 376 Victoria St. Darlinghurst, NSW, 2010, Australia
| | - Tanya L Applegate
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
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A versatile viral system for expression and depletion of proteins in mammalian cells. PLoS One 2009; 4:e6529. [PMID: 19657394 PMCID: PMC2717805 DOI: 10.1371/journal.pone.0006529] [Citation(s) in RCA: 696] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Accepted: 07/08/2009] [Indexed: 12/12/2022] Open
Abstract
The ability to express or deplete proteins in living cells is crucial for the study of biological processes. Viral vectors are often useful to deliver DNA constructs to cells that are difficult to transfect by other methods. Lentiviruses have the additional advantage of being able to integrate into the genomes of non-dividing mammalian cells. However, existing viral expression systems generally require different vector backbones for expression of cDNA, small hairpin RNA (shRNA) or microRNA (miRNA) and provide limited drug selection markers. Furthermore, viral backbones are often recombinogenic in bacteria, complicating the generation and maintenance of desired clones. Here, we describe a collection of 59 vectors that comprise an integrated system for constitutive or inducible expression of cDNAs, shRNAs or miRNAs, and use a wide variety of drug selection markers. These vectors are based on the Gateway technology (Invitrogen) whereby the cDNA, shRNA or miRNA of interest is cloned into an Entry vector and then recombined into a Destination vector that carries the chosen viral backbone and drug selection marker. This recombination reaction generates the desired product with >95% efficiency and greatly reduces the frequency of unwanted recombination in bacteria. We generated Destination vectors for the production of both retroviruses and lentiviruses. Further, we characterized each vector for its viral titer production as well as its efficiency in expressing or depleting proteins of interest. We also generated multiple types of vectors for the production of fusion proteins and confirmed expression of each. We demonstrated the utility of these vectors in a variety of functional studies. First, we show that the FKBP12 Destabilization Domain system can be used to either express or deplete the protein of interest in mitotically-arrested cells. Also, we generate primary fibroblasts that can be induced to senesce in the presence or absence of DNA damage. Finally, we determined that both isoforms of the AT-Rich Interacting Domain 4B (ARID4B) protein could induce G1 arrest when overexpressed. As new technologies emerge, the vectors in this collection can be easily modified and adapted without the need for extensive recloning.
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Nonviral vector-mediated RNA interference: its gene silencing characteristics and important factors to achieve RNAi-based gene therapy. Adv Drug Deliv Rev 2009; 61:760-6. [PMID: 19386274 DOI: 10.1016/j.addr.2009.04.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/05/2009] [Indexed: 01/03/2023]
Abstract
RNA interference (RNAi) is a potent and specific gene silencing event in which small interfering RNA (siRNA) degrades target mRNA. Therefore, RNAi is of potential use as a therapeutic approach for the treatment of a variety of diseases in which aberrant expression of mRNA causes a problem. RNAi can be achieved by delivering siRNA or vectors that transcribe siRNA or short-hairpin RNA (shRNA). The aim of this review is to examine the potential of nonviral vector-mediated RNAi technology in treating diseases. The characteristics of plasmid DNA expressing shRNA were compared with those of siRNA, focusing on the duration of gene silencing, delivery to target cells and target specificity. Recent progresses in prolonging the RNAi effect, improving the delivery to target cells and increasing the specificity of RNAi in vivo are also reviewed.
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Wall EA, Zavzavadjian JR, Chang MS, Randhawa B, Zhu X, Hsueh RC, Liu J, Driver A, Bao XR, Sternweis PC, Simon MI, Fraser IDC. Suppression of LPS-induced TNF-alpha production in macrophages by cAMP is mediated by PKA-AKAP95-p105. Sci Signal 2009; 2:ra28. [PMID: 19531803 DOI: 10.1126/scisignal.2000202] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The activation of macrophages through Toll-like receptor (TLR) pathways leads to the production of a broad array of cytokines and mediators that coordinate the immune response. The inflammatory potential of this response can be reduced by compounds, such as prostaglandin E(2), that induce the production of cyclic adenosine monophosphate (cAMP). Through experiments with cAMP analogs and multigene RNA interference (RNAi), we showed that key anti-inflammatory effects of cAMP were mediated specifically by cAMP-dependent protein kinase (PKA). Selective inhibitors of PKA anchoring, time-lapse microscopy, and RNAi screening suggested that differential mechanisms of PKA action existed. We showed a specific role for A kinase-anchoring protein 95 in suppressing the expression of the gene encoding tumor necrosis factor-alpha, which involved phosphorylation of p105 (also known as Nfkb1) by PKA at a site adjacent to the region targeted by inhibitor of nuclear factor kappaB kinases. These data suggest that crosstalk between the TLR4 and cAMP pathways in macrophages can be coordinated through PKA-dependent scaffolds that localize specific pools of the kinase to distinct substrates.
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Affiliation(s)
- Estelle A Wall
- Alliance for Cellular Signaling, Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Amendola M, Passerini L, Pucci F, Gentner B, Bacchetta R, Naldini L. Regulated and multiple miRNA and siRNA delivery into primary cells by a lentiviral platform. Mol Ther 2009; 17:1039-52. [PMID: 19293777 PMCID: PMC2835189 DOI: 10.1038/mt.2009.48] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 02/18/2009] [Indexed: 01/21/2023] Open
Abstract
RNA interference (RNAi) has tremendous potential for investigating gene function and developing new therapies. However, the design and validation of proficient vehicles for stable and safe microRNA (miR) and small interfering RNA (siRNA) delivery into relevant target cells remains an active area of investigation. Here, we developed a lentiviral platform to efficiently coexpress one or more natural/artificial miR together with a gene of interest from constitutive or regulated polymerase-II (Pol-II) promoters. By swapping the stem-loop (sl) sequence of a selected primary transcript (pri-miR) with that of other miR or replacing the stem with an siRNA of choice, we consistently obtained robust expression of the chimeric/artificial miR in several cell types. We validated our platform transducing a panel of engineered cells stably expressing sensitive reporters for miR activity and on a natural target. This approach allowed us to quantitatively assess at steady state the target suppression activity and expression level of each delivered miR and to compare it to those of endogenous miR. Exogenous/artificial miR reached the concentration and activity typical of highly expressed natural miR without perturbing endogenous miR maturation or regulation. Finally, we demonstrate the robust performance of the platform reversing the anergic/suppressive phenotype of human primary regulatory T cells (Treg) by knocking-down their master gene Forkhead Transcription Factor P3 (FOXP3).
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Affiliation(s)
- Mario Amendola
- San Raffaele Telethon Institute for Gene Therapy, Milan, Italy
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Hu T, Fu Q, Chen P, Ma L, Sin O, Guo D. Construction of an artificial MicroRNA expression vector for simultaneous inhibition of multiple genes in mammalian cells. Int J Mol Sci 2009; 10:2158-2168. [PMID: 19564946 PMCID: PMC2695274 DOI: 10.3390/ijms10052158] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 04/16/2009] [Accepted: 05/14/2009] [Indexed: 12/20/2022] Open
Abstract
Recently, artificial microRNA (amiRNA) has become a promising RNA interference (RNAi) technology. Here, we describe a flexible and reliable method for constructing both single- and multi-amiRNA expression vectors. Two universal primers, together with two specific primers carrying the encoding sequence of amiRNA were designed and utilized to synthesize the functional amiRNA cassette through a one-step PCR. With appropriate restriction sites, the synthesized amiRNA cassettes can be cloned into any site of different destination vectors. Using the method, we constructed both single- and multi-amiRNA expression vectors to target three reporter genes, which code firefly luciferase (Fluc), enhanced green fluorescent protein (EGFP) and β-galactosidase (LacZ), respectively. The expressions of three genes were all specifically inhibited by either the corresponding single- or the multi-amiRNA expression vector in 293T cells. And the RNAi efficiency of each amiRNA produced by both single- and multi-amiRNA expression vectors was comparable.
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Affiliation(s)
- Tao Hu
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Qiong Fu
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Ping Chen
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China; E-Mail:
(P.C.)
| | - Li Ma
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Onsam Sin
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Deyin Guo
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +86-27-6875-2506; Fax: +86-27-6875-2897
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A quick and efficient approach for gene silencing by using triple putative microRNA-based short hairpin RNAs. Mol Cell Biochem 2008; 323:81-9. [DOI: 10.1007/s11010-008-9966-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 11/13/2008] [Indexed: 12/27/2022]
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McIntyre GJ, Groneman JL, Tran A, Applegate TL. An infinitely expandable cloning strategy plus repeat-proof PCR for working with multiple shRNA. PLoS One 2008; 3:e3827. [PMID: 19043584 PMCID: PMC2584233 DOI: 10.1371/journal.pone.0003827] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 11/06/2008] [Indexed: 11/19/2022] Open
Abstract
Vector construction with restriction enzymes (REs) typically involves the ligation of a digested donor fragment (insert) to a reciprocally digested recipient fragment (vector backbone). Creating a suitable cloning plan becomes increasingly difficult for complex strategies requiring repeated insertions such as constructing multiple short hairpin RNA (shRNA) expression vectors for RNA interference (RNAi) studies. The problem lies in the reduced availability of suitable RE recognition sites with an increasing number of cloning events and or vector size. This report details a technically simple, directional cloning solution using REs with compatible cohesive ends that are repeatedly destroyed and simultaneously re-introduced with each round of cloning. Donor fragments can be made by PCR or sub-cloned from pre-existing vectors and inserted ad infinitum in any combination. The design incorporates several cloning cores in order to be compatible with as many donor sequences as possible. We show that joining sub-combinations made in parallel is more time-efficient than sequential construction (of one cassette at a time) for any combination of 4 or more insertions. Screening for the successful construction of combinations using Taq polymerase based PCR became increasingly difficult with increasing number of repeated sequence elements. A Pfu polymerase based PCR was developed and successfully used to amplify combinations of up to eleven consecutive hairpin expression cassettes. The identified PCR conditions can be beneficial to others working with multiple shRNA or other repeated sequences, and the infinitely expandable cloning strategy serves as a general solution applicable to many cloning scenarios.
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Affiliation(s)
- Glen John McIntyre
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia.
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