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Senís E, Mockenhaupt S, Rupp D, Bauer T, Paramasivam N, Knapp B, Gronych J, Grosse S, Windisch MP, Schmidt F, Theis FJ, Eils R, Lichter P, Schlesner M, Bartenschlager R, Grimm D. TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus. Nucleic Acids Res 2016; 45:e3. [PMID: 27614072 PMCID: PMC5224498 DOI: 10.1093/nar/gkw805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/12/2022] Open
Abstract
Successful RNAi applications depend on strategies allowing robust and persistent expression of minimal gene silencing triggers without perturbing endogenous gene expression. Here, we propose a novel avenue which is integration of a promoterless shmiRNA, i.e. a shRNA embedded in a micro-RNA (miRNA) scaffold, into an engineered genomic miRNA locus. For proof-of-concept, we used TALE or CRISPR/Cas9 nucleases to site-specifically integrate an anti-hepatitis C virus (HCV) shmiRNA into the liver-specific miR-122/hcr locus in hepatoma cells, with the aim to obtain cellular clones that are genetically protected against HCV infection. Using reporter assays, Northern blotting and qRT-PCR, we confirmed anti-HCV shmiRNA expression as well as miR-122 integrity and functionality in selected cellular progeny. Moreover, we employed a comprehensive battery of PCR, cDNA/miRNA profiling and whole genome sequencing analyses to validate targeted integration of a single shmiRNA molecule at the expected position, and to rule out deleterious effects on the genomes or transcriptomes of the engineered cells. Importantly, a subgenomic HCV replicon and a full-length reporter virus, but not a Dengue virus control, were significantly impaired in the modified cells. Our original combination of DNA engineering and RNAi expression technologies benefits numerous applications, from miRNA, genome and transgenesis research, to human gene therapy.
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Affiliation(s)
- Elena Senís
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, 69120, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, 69120, Germany
| | - Stefan Mockenhaupt
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, 69120, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, 69120, Germany
| | - Daniel Rupp
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, 69120, Germany.,Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Tobias Bauer
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.,Medical Faculty Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Bettina Knapp
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Jan Gronych
- Division of Molecular Genetics (B060), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
| | - Stefanie Grosse
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, 69120, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, 69120, Germany
| | - Marc P Windisch
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Florian Schmidt
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, 69120, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, 69120, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Department of Mathematics, Technische Universität München, Garching, 85748, Germany
| | - Roland Eils
- BioQuant Center, University of Heidelberg, Heidelberg, 69120, Germany.,Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, 69120, Germany
| | - Peter Lichter
- Division of Molecular Genetics (B060), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, 69120, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, 69120, Germany.,Division of Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, 69120, Germany .,BioQuant Center, University of Heidelberg, Heidelberg, 69120, Germany
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Dai Z, Wu R, Zhao YC, Wang KK, Huang YY, Yang X, Xie ZC, Tu CC, Ouyang HS, Wang TD, Pang DX. Early lethality of shRNA-transgenic pigs due to saturation of microRNA pathways. J Zhejiang Univ Sci B 2015; 15:466-73. [PMID: 24793764 DOI: 10.1631/jzus.b1400001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RNA interference (RNAi) is considered as a potential modality for clinical treatment and anti-virus animal breeding. Here, we investigate the feasibility of inhibiting classical swine fever virus (CSFV) replication by short hairpin RNA (shRNA) in vitro and in vivo. We generate four different shRNA-positive clonal cells and two types of shRNA-transgenic pigs. CSFV could be effectively inhibited in shRNA-positive clonal cells and tail tip fibroblasts of shRNA-transgenic pigs. Unexpectedly, an early lethality due to shRNA is observed in these shRNA-transgenic pigs. With further research on shRNA-positive clonal cells and transgenic pigs, we report a great induction of interferon (IFN)-responsive genes in shRNA-positive clonal cells, altered levels of endogenous microRNAs (miRNA), and their processing enzymes in shRNA-positive cells. What is more, abnormal expressions of miRNAs and their processing enzymes are also observed in the livers of shRNA-transgenic pigs, indicating saturation of miRNA/shRNA pathways induced by shRNA. In addition, we investigate the effects of shRNAs on the development of somatic cell nuclear transfer (SCNT) embryos. These results show that shRNA causes adverse effects in vitro and in vivo and shRNA-induced disruption of the endogenous miRNA pathway may lead to the early lethality of shRNA-transgenic pigs. We firstly report abnormalities of the miRNA pathway in shRNA-transgenic animals, which may explain the early lethality of shRNA-transgenic pigs and has important implications for shRNA-transgenic animal preparation.
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Affiliation(s)
- Zhen Dai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun 130062, China; Department of Life Sciences, Northeast Forestry University, Harbin 150040, China; Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun 130062, China
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Sun CP, Wu TH, Chen CC, Wu PY, Shih YM, Tsuneyama K, Tao MH. Studies of efficacy and liver toxicity related to adeno-associated virus-mediated RNA interference. Hum Gene Ther 2014; 24:739-50. [PMID: 23829557 DOI: 10.1089/hum.2012.239] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Adeno-associated virus (AAV)-mediated RNA interference shows promise as a therapy for chronic hepatitis B virus (HBV) infection, but its low efficacy and hepatotoxicity pose major challenges. We have generated AAV vectors containing different promoters and a panel of HBV-specific short hairpin RNAs (shRNAs) to investigate factors that contribute to the efficacy and pathogenesis of AAV-mediated RNA interference. HBV transgenic mice injected with high doses of AAV vectors containing the U6 promoter produced abundant shRNAs, transiently inhibited HBV, but induced severe hepatotoxicity. Sustained HBV suppression without liver toxicity can be achieved by lowering the dose of AAV-U6 vectors. AAVs containing the weaker H1 promoter did not cause liver injury, but their therapeutic efficacy was highly dependent on the sequence of the shRNA. Mice treated with the toxic U6-promoter-driven shRNA showed little change in hepatic microRNA levels, but a dramatic increase in hepatic leukocytes and inflammatory cytokines and chemokines. Hepatotoxicity was completely absent in immunodeficient mice and significantly alleviated in wild-type mice depleted of macrophages and granulocytes, suggesting that host inflammatory responses are the major cause of liver injury induced by the overexpressed shRNAs from AAV-U6 vectors. Our results demonstrate that selection of a highly potent shRNA and control its expression level is critical to achieve sustained HBV suppression without inducing inflammatory side effects.
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Affiliation(s)
- Cheng-Pu Sun
- Molecular Medicine Program, Taiwan International Graduate Program, Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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Hou KK, Pan H, Ratner L, Schlesinger PH, Wickline SA. Mechanisms of nanoparticle-mediated siRNA transfection by melittin-derived peptides. ACS NANO 2013; 7:8605-15. [PMID: 24053333 PMCID: PMC4013830 DOI: 10.1021/nn403311c] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Traditional peptide-mediated siRNA transfection via peptide transduction domains exhibits limited cytoplasmic delivery of siRNA due to endosomal entrapment. This work overcomes these limitations with the use of membrane-destabilizing peptides derived from melittin for the knockdown of NFkB signaling in a model of adult T-cell leukemia/lymphoma. While the mechanism of siRNA delivery into the cytoplasmic compartment by peptide transduction domains has not been well studied, our analysis of melittin derivatives indicates that concurrent nanocomplex disassembly and peptide-mediated endosomolysis are crucial to siRNA transfection. Importantly, in the case of the most active derivative, p5RHH, this process is initiated by acidic pH, indicating that endosomal acidification after macropinocytosis can trigger siRNA release into the cytoplasm. These data provide general principles regarding nanocomplex response to endocytosis, which may guide the development of peptide/siRNA nanocomplex-based transfection.
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Affiliation(s)
- Kirk K. Hou
- Computational and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO. 63108, USA
| | - Hua Pan
- Department of Medicine, Washington University School of Medicine, St Louis, MO. 63108, USA
| | - Lee Ratner
- Department of Medicine, Washington University School of Medicine, St Louis, MO. 63108, USA
| | - Paul H. Schlesinger
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO. 63108, USA
| | - Samuel A. Wickline
- Department of Medicine, Washington University School of Medicine, St Louis, MO. 63108, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO. 63108, USA
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO. 63108, USA
- CORRESPONDING AUTHOR: Washington University in St. Louis School of Medicine, Campus Box 8215, 660 S. Euclid Ave., St. Louis, MO 63110. Fax: 1 314 454 5265.
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Wooddell CI, Rozema DB, Hossbach M, John M, Hamilton HL, Chu Q, Hegge JO, Klein JJ, Wakefield DH, Oropeza CE, Deckert J, Roehl I, Jahn-Hofmann K, Hadwiger P, Vornlocher HP, McLachlan A, Lewis DL. Hepatocyte-targeted RNAi therapeutics for the treatment of chronic hepatitis B virus infection. Mol Ther 2013; 21:973-85. [PMID: 23439496 PMCID: PMC3666629 DOI: 10.1038/mt.2013.31] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA interference (RNAi)-based therapeutics have the potential to treat chronic hepatitis B virus (HBV) infection in a fundamentally different manner than current therapies. Using RNAi, it is possible to knock down expression of viral RNAs including the pregenomic RNA from which the replicative intermediates are derived, thus reducing viral load, and the viral proteins that result in disease and impact the immune system's ability to eliminate the virus. We previously described the use of polymer-based Dynamic PolyConjugate (DPC) for the targeted delivery of siRNAs to hepatocytes. Here, we first show in proof-of-concept studies that simple coinjection of a hepatocyte-targeted, N-acetylgalactosamine-conjugated melittin-like peptide (NAG-MLP) with a liver-tropic cholesterol-conjugated siRNA (chol-siRNA) targeting coagulation factor VII (F7) results in efficient F7 knockdown in mice and nonhuman primates without changes in clinical chemistry or induction of cytokines. Using transient and transgenic mouse models of HBV infection, we show that a single coinjection of NAG-MLP with potent chol-siRNAs targeting conserved HBV sequences resulted in multilog repression of viral RNA, proteins, and viral DNA with long duration of effect. These results suggest that coinjection of NAG-MLP and chol-siHBVs holds great promise as a new therapeutic for patients chronically infected with HBV.
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Affiliation(s)
- Christine I Wooddell
- Arrowhead Research Corporation, Arrowhead Madison, Madison, Wisconsin 53711, USA.
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