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Wong B, Birtch R, Rezaei R, Jamieson T, Crupi MJF, Diallo JS, Ilkow CS. Optimal delivery of RNA interference by viral vectors for cancer therapy. Mol Ther 2023; 31:3127-3145. [PMID: 37735876 PMCID: PMC10638062 DOI: 10.1016/j.ymthe.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
In recent years, there has been a surge in the innovative modification and application of the viral vector-based gene therapy field. Significant and consistent improvements in the engineering, delivery, and safety of viral vectors have set the stage for their application as RNA interference (RNAi) delivery tools. Viral vector-based delivery of RNAi has made remarkable breakthroughs in the treatment of several debilitating diseases and disorders (e.g., neurological diseases); however, their novelty has yet to be fully applied and utilized for the treatment of cancer. This review highlights the most promising and emerging viral vector delivery tools for RNAi therapeutics while discussing the variables limiting their success and suitability for cancer therapy. Specifically, we outline different integrating and non-integrating viral platforms used for gene delivery, currently employed RNAi targets for anti-cancer effect, and various strategies used to optimize the safety and efficacy of these RNAi therapeutics. Most importantly, we provide great insight into what challenges exist in their application as cancer therapeutics and how these challenges can be effectively navigated to advance the field.
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Affiliation(s)
- Boaz Wong
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Rayanna Birtch
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Reza Rezaei
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Taylor Jamieson
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu J F Crupi
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jean-Simon Diallo
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Carolina S Ilkow
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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Nakamura M, Fujiwara K, Doi N. Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide. J Nanobiotechnology 2022; 20:458. [PMID: 36303212 DOI: 10.1186/s12951-022-01667-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although protein-based methods using cell-penetrating peptides such as TAT have been expected to provide an alternative approach to siRNA delivery, the low efficiency of endosomal escape of siRNA/protein complexes taken up into cells by endocytosis remains a problem. Here, to overcome this problem, we adopted the membrane penetration-enhancing peptide S19 from human syncytin 1 previously identified in our laboratory. RESULTS We prepared fusion proteins in which the S19 and TAT peptides were fused to the viral RNA-binding domains (RBDs) as carrier proteins, added the RBD-S19-TAT/siRNA complex to human cultured cells, and investigated the cytoplasmic delivery of the complex and the knockdown efficiency of target genes. We found that the intracellular uptake of the RBD-S19-TAT/siRNA complex was increased compared to that of the RBD-TAT/siRNA complex, and the expression level of the target mRNA was decreased. Because siRNA must dissociate from RBD and bind to Argonaute 2 (Ago2) to form the RNA-induced silencing complex (RISC) after the protein/siRNA complex is delivered into the cytoplasm, a dilemma arises: stronger binding between RBD and siRNA increases intracellular uptake but makes RISC formation more difficult. Thus, we next prepared fusion proteins in which the S19 and TAT peptides were fused with Ago2 instead of RBD and found that the efficiencies of siRNA delivery and knockdown obtained using TAT-S19-Ago2 were higher than those using TAT-Ago2. In addition, we found that the smallest RISC delivery induced faster knockdown than traditional siRNA lipofection, probably due to the decreased time required for RISC formation in the cytoplasm. CONCLUSION These results indicated that S19 and TAT-fused siRNA-binding proteins, especially Ago2, should be useful for the rapid and efficient delivery of siRNA without the addition of any endosome-disrupting agent.
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Affiliation(s)
- Momoko Nakamura
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
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3
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El Andari J, Renaud-Gabardos E, Tulalamba W, Weinmann J, Mangin L, Pham QH, Hille S, Bennett A, Attebi E, Bourges E, Leborgne C, Guerchet N, Fakhiri J, Krämer C, Wiedtke E, McKenna R, Guianvarc’h L, Toueille M, Ronzitti G, Hebben M, Mingozzi F, VandenDriessche T, Agbandje-McKenna M, Müller OJ, Chuah MK, Buj-Bello A, Grimm D. Semirational bioengineering of AAV vectors with increased potency and specificity for systemic gene therapy of muscle disorders. SCIENCE ADVANCES 2022; 8:eabn4704. [PMID: 36129972 PMCID: PMC9491714 DOI: 10.1126/sciadv.abn4704] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/03/2022] [Indexed: 05/31/2023]
Abstract
Bioengineering of viral vectors for therapeutic gene delivery is a pivotal strategy to reduce doses, facilitate manufacturing, and improve efficacy and patient safety. Here, we engineered myotropic adeno-associated viral (AAV) vectors via a semirational, combinatorial approach that merges AAV capsid and peptide library screens. We first identified shuffled AAVs with increased specificity in the murine skeletal muscle, diaphragm, and heart, concurrent with liver detargeting. Next, we boosted muscle specificity by displaying a myotropic peptide on the capsid surface. In a mouse model of X-linked myotubular myopathy, the best vectors-AAVMYO2 and AAVMYO3-prolonged survival, corrected growth, restored strength, and ameliorated muscle fiber size and centronucleation. In a mouse model of Duchenne muscular dystrophy, our lead capsid induced robust microdystrophin expression and improved muscle function. Our pipeline is compatible with complementary AAV genome bioengineering strategies, as demonstrated here with two promoters, and could benefit many clinical applications beyond muscle gene therapy.
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Affiliation(s)
- Jihad El Andari
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Edith Renaud-Gabardos
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Warut Tulalamba
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
| | - Jonas Weinmann
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Louise Mangin
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Quang Hong Pham
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
| | - Susanne Hille
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105 Kiel, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | - Christian Leborgne
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | | | - Julia Fakhiri
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Chiara Krämer
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ellen Wiedtke
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | - Giuseppe Ronzitti
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | | | - Federico Mingozzi
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Oliver J. Müller
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105 Kiel, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Marinee K. Chuah
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Ana Buj-Bello
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Dirk Grimm
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Heidelberg, Heidelberg, Germany
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4
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Bauer A, Puglisi M, Nagl D, Schick JA, Werner T, Klingl A, El Andari J, Hornung V, Kessler H, Götz M, Grimm D, Brack‐Werner R. Molecular Signature of Astrocytes for Gene Delivery by the Synthetic Adeno-Associated Viral Vector rAAV9P1. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104979. [PMID: 35398994 PMCID: PMC9165502 DOI: 10.1002/advs.202104979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/24/2022] [Indexed: 06/01/2023]
Abstract
Astrocytes have crucial functions in the central nervous system (CNS) and are major players in many CNS diseases. Research on astrocyte-centered diseases requires efficient and well-characterized gene transfer vectors. Vectors derived from the Adeno-associated virus serotype 9 (AAV9) target astrocytes in the brains of rodents and nonhuman primates. A recombinant (r) synthetic peptide-displaying AAV9 variant, rAAV9P1, that efficiently and selectively transduces cultured human astrocytes, has been described previously. Here, it is shown that rAAV9P1 retains astrocyte-targeting properties upon intravenous injection in mice. Detailed analysis of putative receptors on human astrocytes shows that rAAV9P1 utilizes integrin subunits αv, β8, and either β3 or β5 as well as the AAV receptor AAVR. This receptor pattern is distinct from that of vectors derived from wildtype AAV2 or AAV9. Furthermore, a CRISPR/Cas9 genome-wide knockout screening revealed the involvement of several astrocyte-associated intracellular signaling pathways in the transduction of human astrocytes by rAAV9P1. This study delineates the unique receptor and intracellular pathway signatures utilized by rAAV9P1 for targeting human astrocytes. These results enhance the understanding of the transduction biology of synthetic rAAV vectors for astrocytes and can promote the development of advanced astrocyte-selective gene delivery vehicles for research and clinical applications.
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Affiliation(s)
- Amelie Bauer
- Institute of VirologyHelmholtz Center MunichNeuherberg85764Germany
| | - Matteo Puglisi
- Physiological GenomicsBiomedical Center (BMC)Ludwig‐Maximilians‐Universität (LMU)Planegg‐Martinsried82152Germany
- Institute for Stem Cell ResearchHelmholtz Center MunichBiomedical Center (BMC)Ludwig‐Maximilians‐Universität (LMU)Planegg‐Martinsried82152Germany
| | - Dennis Nagl
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐UniversitätMunich81377Germany
| | - Joel A Schick
- Institute of Molecular Toxicology and PharmacologyGenetics and Cellular Engineering GroupHelmholtz Center MunichNeuherberg85764Germany
| | - Thomas Werner
- Department of Computational Medicine and Bioinformatics & Department of Internal MedicineUniversity of MichiganAnn ArborMI48109USA
| | - Andreas Klingl
- Plant Development and Electron MicroscopyDepartment Biology IBiocenterLudwig‐Maximilians‐Universität (LMU)Planegg‐Martinsried82152Germany
| | - Jihad El Andari
- BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg UniversityHeidelberg69120Germany
- Department of Infectious DiseasesVirologyMedical FacultyHeidelberg UniversityHeidelberg69120Germany
| | - Veit Hornung
- Gene Center and Department of BiochemistryLudwig‐Maximilians‐UniversitätMunich81377Germany
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM)Department ChemieTechnische Universität MünchenGarching85748Germany
| | - Magdalena Götz
- Physiological GenomicsBiomedical Center (BMC)Ludwig‐Maximilians‐Universität (LMU)Planegg‐Martinsried82152Germany
- Institute for Stem Cell ResearchHelmholtz Center MunichBiomedical Center (BMC)Ludwig‐Maximilians‐Universität (LMU)Planegg‐Martinsried82152Germany
- Excellence Cluster of Systems Neurology (SYNERGY)Munich81377Germany
| | - Dirk Grimm
- BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg UniversityHeidelberg69120Germany
- Department of Infectious DiseasesVirologyMedical FacultyHeidelberg UniversityHeidelberg69120Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK)Partner site HeidelbergHeidelberg69120Germany
| | - Ruth Brack‐Werner
- Institute of VirologyHelmholtz Center MunichNeuherberg85764Germany
- Department of Biology IILudwig‐Maximilians‐Universität (LMU)Planegg‐Martinsried82152Germany
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5
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Van de Vyver T, De Smedt SC, Raemdonck K. Modulating intracellular pathways to improve non-viral delivery of RNA therapeutics. Adv Drug Deliv Rev 2022; 181:114041. [PMID: 34763002 DOI: 10.1016/j.addr.2021.114041] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022]
Abstract
RNA therapeutics (e.g. siRNA, oligonucleotides, mRNA, etc.) show great potential for the treatment of a myriad of diseases. However, to reach their site of action in the cytosol or nucleus of target cells, multiple intra- and extracellular barriers have to be surmounted. Several non-viral delivery systems, such as nanoparticles and conjugates, have been successfully developed to meet this requirement. Unfortunately, despite these clear advances, state-of-the-art delivery agents still suffer from relatively low intracellular delivery efficiencies. Notably, our current understanding of the intracellular delivery process is largely oversimplified. Gaining mechanistic insight into how RNA formulations are processed by cells will fuel rational design of the next generation of delivery carriers. In addition, identifying which intracellular pathways contribute to productive RNA delivery could provide opportunities to boost the delivery performance of existing nanoformulations. In this review, we discuss both established as well as emerging techniques that can be used to assess the impact of different intracellular barriers on RNA transfection performance. Next, we highlight how several modulators, including small molecules but also genetic perturbation technologies, can boost RNA delivery by intervening at differing stages of the intracellular delivery process, such as cellular uptake, intracellular trafficking, endosomal escape, autophagy and exocytosis.
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Affiliation(s)
- Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
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6
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Kremer LP, Cerrizuela S, Dehler S, Stiehl T, Weinmann J, Abendroth H, Kleber S, Laure A, El Andari J, Anders S, Marciniak-Czochra A, Grimm D, Martin-Villalba A. High throughput screening of novel AAV capsids identifies variants for transduction of adult NSCs within the subventricular zone. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:33-50. [PMID: 34553001 PMCID: PMC8427210 DOI: 10.1016/j.omtm.2021.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022]
Abstract
The adult mammalian brain entails a reservoir of neural stem cells (NSCs) generating glial cells and neurons. However, NSCs become increasingly quiescent with age, which hampers their regenerative capacity. New means are therefore required to genetically modify adult NSCs for re-enabling endogenous brain repair. Recombinant adeno-associated viruses (AAVs) are ideal gene-therapy vectors due to an excellent safety profile and high transduction efficiency. We thus conducted a high-throughput screening of 177 intraventricularly injected barcoded AAV variants profiled by RNA sequencing. Quantification of barcoded AAV mRNAs identified two synthetic capsids, peptide-modified derivative of wild-type AAV9 (AAV9_A2) and peptide-modified derivative of wild-type AAV1 (AAV1_P5), both of which transduce active and quiescent NSCs. Further optimization of AAV1_P5 by judicious selection of the promoter and dose of injected viral genomes enabled labeling of 30%–60% of the NSC compartment, which was validated by fluorescence-activated cell sorting (FACS) analyses and single-cell RNA sequencing. Importantly, transduced NSCs readily produced neurons. The present study identifies AAV variants with a high regional tropism toward the ventricular-subventricular zone (v-SVZ) with high efficiency in targeting adult NSCs, thereby paving the way for preclinical testing of regenerative gene therapy.
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Affiliation(s)
- Lukas P.M. Kremer
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Santiago Cerrizuela
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sascha Dehler
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Stiehl
- Institute of Applied Mathematics, Interdisciplinary Center for Scientific Computing and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Jonas Weinmann
- Virus-Host Interaction Group, Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence Cell Networks, BioQuant, 69120 Heidelberg, Germany
| | - Heike Abendroth
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Susanne Kleber
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alexander Laure
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jihad El Andari
- Virus-Host Interaction Group, Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence Cell Networks, BioQuant, 69120 Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Anna Marciniak-Czochra
- Institute of Applied Mathematics, Interdisciplinary Center for Scientific Computing and BioQuant, Heidelberg University, 69120 Heidelberg, Germany
| | - Dirk Grimm
- Virus-Host Interaction Group, Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence Cell Networks, BioQuant, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Heidelberg, 69120 Heidelberg, Germany
| | - Ana Martin-Villalba
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Corresponding author: Ana Martin-Villalba, Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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7
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Zhang C, Freistaedter A, Schmelas C, Gunkel M, Dao Thi VL, Grimm D. An RNA Interference/Adeno-Associated Virus Vector-Based Combinatorial Gene Therapy Approach Against Hepatitis E Virus. Hepatol Commun 2021; 6:878-888. [PMID: 34719133 PMCID: PMC8948557 DOI: 10.1002/hep4.1842] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/10/2021] [Accepted: 10/10/2021] [Indexed: 12/22/2022] Open
Abstract
Hepatitis E virus (HEV) is a major public health problem with limited therapeutic options. Here, we engineered adeno-associated viral vectors of serotype 6 (AAV6) to express short hairpin RNAs (shRNAs) against HEV transcripts with the prospect of down-regulating HEV replication in vivo. We designed 20 different shRNAs, targeting the genome of the HEV genotype 3 (GT3) Kernow-C1 p6 strain, for delivery upon AAV6 transduction. Using an original selectable HEV GT3 reporter replicon, we identified three shRNAs that efficiently down-regulated HEV replication. We further confirmed their inhibitory potency with full-length HEV infection. Seventy-two hours following transduction, HEV replication in both systems decreased by up to 95%. The three most potent inhibitory shRNAs identified were directed against the methyltransferase domain, the junction region between the open reading frames (ORFs), and the 3´ end of ORF2. Targeting all three regions by multiplexing the shRNAs further enhanced their inhibitory potency over a prolonged period of up to 21 days following transduction. Conclusion: Combining RNA interference and AAV vector-based gene therapy has great potential for suppressing HEV replication. Our strategy to target the viral RNA with multiplexed shRNAs should help to counteract viral escape through mutations. Considering the widely documented safety of AAV vector-based gene therapies, our approach is, in principle, amenable to clinical translation.
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Affiliation(s)
- Cindy Zhang
- Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Cluster of Excellence CellNetworks, BioQuant, Center for Integrative Infectious Diseases Research, Heidelberg, Germany.,Schaller Research group at Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Center for Integrative Infectious Diseases Research, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - Andrew Freistaedter
- Schaller Research group at Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Carolin Schmelas
- Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Cluster of Excellence CellNetworks, BioQuant, Center for Integrative Infectious Diseases Research, Heidelberg, Germany
| | - Manuel Gunkel
- High-Content Analysis of the Cell and Advanced Biological Screening Facility, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Viet Loan Dao Thi
- Schaller Research group at Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Center for Integrative Infectious Diseases Research, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Medical Faculty, Heidelberg University, Cluster of Excellence CellNetworks, BioQuant, Center for Integrative Infectious Diseases Research, Heidelberg, Germany.,German Center for Infection Research, Heidelberg, Germany.,German Center for Cardiovascular Research, Heidelberg, Germany
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8
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Carullo G, Mazzotta S, Koch A, Hartmann KM, Friedrich O, Gilbert DF, Vega-Holm M, Schneider-Stock R, Aiello F. New Oleoyl Hybrids of Natural Antioxidants: Synthesis and In Vitro Evaluation as Inducers of Apoptosis in Colorectal Cancer Cells. Antioxidants (Basel) 2020; 9:antiox9111077. [PMID: 33153029 PMCID: PMC7692320 DOI: 10.3390/antiox9111077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Nowadays, the beneficial role of a healthy lifestyle, particularly emphasizing the quality of foods and cancer management, is accepted worldwide. Polyphenols and oleic acid play a key role in this context, but are still scarcely used as anti-cancer agents due to their bio-accessibility limits. Therefore, we aimed to synthesize a set of new oleoyl-hybrids of quercetin, morin, pinocembrin, and catechin to overcome the low bioavailability of polyphenols, throughout a bio-catalytic approach using pancreatic porcine lipase as a catalyst. The in vitro assays, using a wide panel of human cancer cell lines showed, mainly for two novel regioisomer oleoyl-hybrids of quercetin, a remarkable increase in apoptotic cell populations. We suggested that the DNA damage shown as ɣH2AX signals might be the major cause of apoptotic cell death. Finally, we demonstrated convincing data about two novel polyphenol-based hybrids displaying a highly selective anti-cancer cytotoxicity and being superior compared to their reference/parental compounds.
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Affiliation(s)
- Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Edificio Polifunzionale, 87036 Rende (CS), Italy
| | - Sarah Mazzotta
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Edificio Polifunzionale, 87036 Rende (CS), Italy
- Department of Pharmaceutical Sciences, University of Milan Via Luigi Mangiagalli 25, 20133 Milano, Italy;
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, 41071 Seville, Spain;
| | - Adrian Koch
- Institiute of Pathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany;
- Experimental Tumorpathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany
| | - Kristin M. Hartmann
- Institute of Medical Biotechnology Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany; (K.M.H.); (O.F.); (D.F.G.)
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052 Erlangen, Germany
| | - Oliver Friedrich
- Institute of Medical Biotechnology Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany; (K.M.H.); (O.F.); (D.F.G.)
| | - Daniel F. Gilbert
- Institute of Medical Biotechnology Friedrich-Alexander-University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany; (K.M.H.); (O.F.); (D.F.G.)
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, Profesor García González 2, 41071 Seville, Spain;
| | - Regine Schneider-Stock
- Institiute of Pathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany;
- Experimental Tumorpathology, University Hospital, Friedrich-Alexander University Erlangen-Nürnberg Universitätsstr. 22, 91054 Erlangen, Germany
- Correspondence: (R.S.-S.); (F.A.)
| | - Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences, Department of Excellence 2018-2022, University of Calabria, Edificio Polifunzionale, 87036 Rende (CS), Italy
- Correspondence: (R.S.-S.); (F.A.)
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9
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Weinmann J, Weis S, Sippel J, Tulalamba W, Remes A, El Andari J, Herrmann AK, Pham QH, Borowski C, Hille S, Schönberger T, Frey N, Lenter M, VandenDriessche T, Müller OJ, Chuah MK, Lamla T, Grimm D. Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants. Nat Commun 2020; 11:5432. [PMID: 33116134 PMCID: PMC7595228 DOI: 10.1038/s41467-020-19230-w] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
Adeno-associated virus (AAV) forms the basis for several commercial gene therapy products and for countless gene transfer vectors derived from natural or synthetic viral isolates that are under intense preclinical evaluation. Here, we report a versatile pipeline that enables the direct side-by-side comparison of pre-selected AAV capsids in high-throughput and in the same animal, by combining DNA/RNA barcoding with multiplexed next-generation sequencing. For validation, we create three independent libraries comprising 183 different AAV variants including widely used benchmarks and screened them in all major tissues in adult mice. Thereby, we discover a peptide-displaying AAV9 mutant called AAVMYO that exhibits superior efficiency and specificity in the musculature including skeletal muscle, heart and diaphragm following peripheral delivery, and that holds great potential for muscle gene therapy. Our comprehensive methodology is compatible with any capsids, targets and species, and will thus facilitate and accelerate the stratification of optimal AAV vectors for human gene therapy. Adeno-associated virus is the basis of many gene therapies and gene transfer vectors. Here the authors report a pipeline to enable side-by-side comparison of pre-selected capsids in a high throughput manner.
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Affiliation(s)
- Jonas Weinmann
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, 69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Sabrina Weis
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, 69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Josefine Sippel
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, 69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Warut Tulalamba
- Vrije Universiteit Brussel, Department of Gene Therapy & Regenerative Medicine, 1090, Brussels, Belgium
| | - Anca Remes
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105, Kiel, Germany.,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, 24105, Kiel, Germany
| | - Jihad El Andari
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, 69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Anne-Kathrin Herrmann
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, 69120, Heidelberg, Germany.,BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Quang H Pham
- Vrije Universiteit Brussel, Department of Gene Therapy & Regenerative Medicine, 1090, Brussels, Belgium
| | - Christopher Borowski
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105, Kiel, Germany.,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, 24105, Kiel, Germany
| | - Susanne Hille
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105, Kiel, Germany.,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, 24105, Kiel, Germany
| | - Tanja Schönberger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400, Biberach an der Riß, Germany
| | - Norbert Frey
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105, Kiel, Germany.,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, 24105, Kiel, Germany
| | - Martin Lenter
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400, Biberach an der Riß, Germany
| | - Thierry VandenDriessche
- Vrije Universiteit Brussel, Department of Gene Therapy & Regenerative Medicine, 1090, Brussels, Belgium.,University of Leuven, Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, Leuven, 3000, Belgium
| | - Oliver J Müller
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105, Kiel, Germany.,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, 24105, Kiel, Germany
| | - Marinee K Chuah
- Vrije Universiteit Brussel, Department of Gene Therapy & Regenerative Medicine, 1090, Brussels, Belgium.,University of Leuven, Center for Molecular & Vascular Biology, Department of Cardiovascular Sciences, Leuven, 3000, Belgium
| | - Thorsten Lamla
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, 88400, Biberach an der Riß, Germany
| | - Dirk Grimm
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, 69120, Heidelberg, Germany. .,BioQuant, University of Heidelberg, 69120, Heidelberg, Germany. .,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Heidelberg, 69120, Heidelberg, Germany.
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10
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Abstract
Short regulatory RNA molecules underpin gene expression and govern cellular state and physiology. To establish an alternative layer of control over these processes, we generated chimeric regulatory RNAs that interact reversibly and light-dependently with the light-oxygen-voltage photoreceptor PAL. By harnessing this interaction, the function of micro RNAs (miRs) and short hairpin (sh) RNAs in mammalian cells can be regulated in a spatiotemporally precise manner. The underlying strategy is generic and can be adapted to near-arbitrary target sequences. Owing to full genetic encodability, it establishes optoribogenetic control of cell state and physiology. The method stands to facilitate the non-invasive, reversible and spatiotemporally resolved study of regulatory RNAs and protein function in cellular and organismal environments. Short hairpin RNAs can be used to modulate and regulate gene expression. Here the authors generate chimeric RNAs that interact with the photoreceptor PAL, allowing for optoribogenetic control of cell physiology.
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11
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Angeles AK, Heckmann D, Flosdorf N, Duensing S, Sültmann H. The ERG-Regulated LINC00920 Promotes Prostate Cancer Cell Survival via the 14-3-3ε-FOXO Pathway. Mol Cancer Res 2020; 18:1545-1559. [PMID: 32646965 DOI: 10.1158/1541-7786.mcr-20-0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/04/2020] [Accepted: 06/29/2020] [Indexed: 11/16/2022]
Abstract
Numerous noncoding transcripts have been reported to correlate with cancer development and progression. Nevertheless, there remains a paucity of long noncoding RNAs (lncRNA) with well-elucidated functional roles. Here, we leverage the International Cancer Genome Consortium-Early Onset Prostate Cancer transcriptome and identify the previously uncharacterized lncRNA LINC00920 to be upregulated in prostate tumors. Phenotypic characterization of LINC00920 revealed its positive impact on cellular proliferation, colony formation, and migration. We demonstrate that LINC00920 transcription is directly activated by ERG, an oncogenic transcription factor overexpressed in 50% of prostate cancers. Chromatin isolation by RNA purification-mass spectrometry revealed the interaction of LINC00920 with the 14-3-3ε protein, leading to enhanced sequestration of tumor suppressive FOXO1. Altogether, our results provide a rationale on how ERG overexpression, partly by driving LINC00920 transcription, could confer survival advantage to prostate cancer cells and potentially prime PTEN-intact prostate cells for cellular transformation through FOXO inactivation. IMPLICATIONS: The study describes a novel lncRNA-mediated mechanism of regulating the FOXO signaling pathway and provides additional insight into the role of ERG in prostate cancer cells.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Doreen Heckmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Niclas Flosdorf
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, Section of Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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12
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Mathony J, Harteveld Z, Schmelas C, Upmeier Zu Belzen J, Aschenbrenner S, Sun W, Hoffmann MD, Stengl C, Scheck A, Georgeon S, Rosset S, Wang Y, Grimm D, Eils R, Correia BE, Niopek D. Computational design of anti-CRISPR proteins with improved inhibition potency. Nat Chem Biol 2020; 16:725-730. [PMID: 32284602 DOI: 10.1038/s41589-020-0518-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 02/12/2020] [Accepted: 03/12/2020] [Indexed: 11/09/2022]
Abstract
Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, to improve its efficacy on different targets. We first show that inserting exogenous protein domains into a selected AcrIIC1 surface site dramatically enhances inhibition of Neisseria meningitidis (Nme)Cas9. Then, applying structure-guided design to the Cas9-binding surface, we converted AcrIIC1 into AcrIIC1X, a potent inhibitor of the Staphylococcus aureus (Sau)Cas9, an orthologue widely applied for in vivo genome editing. Finally, to demonstrate the utility of AcrIIC1X for genome engineering applications, we implemented a hepatocyte-specific SauCas9 ON-switch by placing AcrIIC1X expression under regulation of microRNA-122. Our work introduces designer Acrs as important biotechnological tools and provides an innovative strategy to safeguard CRISPR technologies.
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Affiliation(s)
- Jan Mathony
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
| | - Zander Harteveld
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Carolin Schmelas
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, Germany
| | - Julius Upmeier Zu Belzen
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany
| | - Sabine Aschenbrenner
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mareike D Hoffmann
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Stengl
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sandrine Georgeon
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| | - Roland Eils
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Dominik Niopek
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany.
- Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany.
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13
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Hentzschel F, Mitesser V, Fraschka SAK, Krzikalla D, Carrillo EH, Berkhout B, Bártfai R, Mueller AK, Grimm D. Gene knockdown in malaria parasites via non-canonical RNAi. Nucleic Acids Res 2020; 48:e2. [PMID: 31680162 PMCID: PMC7145648 DOI: 10.1093/nar/gkz927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The lack of endogenous RNAi machinery in the malaria parasite Plasmodium hampers gene annotation and hence antimalarial drug and vaccine development. Here, we engineered rodent Plasmodium berghei to express a minimal, non-canonical RNAi machinery that solely requires Argonaute 2 (Ago2) and a modified short hairpin RNA, so-called AgoshRNA. Using this strategy, we achieved robust and specific gene knockdown throughout the entire parasite life cycle. We also successfully silenced the endogenous gene perforin-like protein 2, phenocopying a full gene knockout. Transcriptionally restricting Ago2 expression to the liver stage further enabled us to perform a stage-specific gene knockout. The RNAi-competent Plasmodium lines reported here will be a valuable resource for loss-of-function phenotyping of the many uncharacterized genes of Plasmodium in low or high throughput, without the need to engineer the target gene locus. Thereby, our new strategy and transgenic Plasmodium lines will ultimately benefit the discovery of urgently needed antimalarial drug and vaccine candidates. Generally, the ability to render RNAi-negative organisms RNAi-competent by mere introduction of two components, Ago2 and AgoshRNA, is a unique paradigm that should find broad applicability in other species.
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Affiliation(s)
- Franziska Hentzschel
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Vera Mitesser
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | | | - Daria Krzikalla
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Elena Herrera Carrillo
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Meibergdreef 15, K3-110, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Meibergdreef 15, K3-110, 1105 AZ Amsterdam, The Netherlands
| | - Richárd Bártfai
- Radboud University, Dept. of Molecular Biology, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Ann-Kristin Mueller
- Heidelberg University Hospital, Center for Infectious Diseases / Parasitology, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg
| | - Dirk Grimm
- Heidelberg University Hospital, Center for Infectious Diseases / Virology, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,BioQuant Center, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg.,German Center for Cardiovascular Research (DZHK), partner site Heidelberg
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14
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Course MM, Gudsnuk K, Desai N, Chamberlain JR, Valdmanis PN. Endogenous MicroRNA Competition as a Mechanism of shRNA-Induced Cardiotoxicity. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:572-580. [PMID: 31927330 PMCID: PMC6957822 DOI: 10.1016/j.omtn.2019.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/12/2019] [Accepted: 12/12/2019] [Indexed: 11/29/2022]
Abstract
Gene knockdown using short hairpin RNAs (shRNAs) is a promising strategy for targeting dominant mutations; however, delivering too much shRNA can disrupt the processing of endogenous microRNAs (miRNAs) and lead to toxicity. Here, we sought to understand the effect that excessive shRNAs have on muscle miRNAs by treating mice with recombinant adeno-associated viral vectors (rAAVs) that produce shRNAs with 19-nt or 21-nt stem sequences. Small RNA sequencing of their muscle and liver tissues revealed that shRNA expression was highest in the heart, where mice experienced substantial cardiomyopathy when shRNAs accumulated to 51.2% ± 13.7% of total small RNAs. With the same treatment, shRNAs in other muscle tissues reached only 12.1% ± 5.0% of total small RNAs. Regardless of treatment, the predominant heart miRNAs remained relatively stable across samples. Instead, the lower-expressed miR-451, one of the few miRNAs processed independently of Dicer, changed in relation to shRNA level and toxicity. Our data suggest that a protective mechanism exists in cardiac tissue for maintaining the levels of most miRNAs in response to shRNA delivery, in contrast with what has been shown in the liver. Quantifying miRNA profiles after excessive shRNA delivery illuminates the host response to rAAV-shRNA, allowing for safer and more robust therapeutic gene knockdown.
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Affiliation(s)
- Meredith M Course
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Kathryn Gudsnuk
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Nitin Desai
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Joel R Chamberlain
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Paul N Valdmanis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA.
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15
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Hoffmann MD, Aschenbrenner S, Grosse S, Rapti K, Domenger C, Fakhiri J, Mastel M, Börner K, Eils R, Grimm D, Niopek D. Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. Nucleic Acids Res 2020; 47:e75. [PMID: 30982889 PMCID: PMC6648350 DOI: 10.1093/nar/gkz271] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/16/2022] Open
Abstract
The rapid development of CRISPR–Cas technologies brought a personalized and targeted treatment of genetic disorders into closer reach. To render CRISPR-based therapies precise and safe, strategies to confine the activity of Cas(9) to selected cells and tissues are highly desired. Here, we developed a cell type-specific Cas-ON switch based on miRNA-regulated expression of anti-CRISPR (Acr) proteins. We inserted target sites for miR-122 or miR-1, which are abundant specifically in liver and cardiac muscle cells, respectively, into the 3′UTR of Acr transgenes. Co-expressing these with Cas9 and sgRNAs resulted in Acr knockdown and released Cas9 activity solely in hepatocytes or cardiomyocytes, while Cas9 was efficiently inhibited in off-target cells. We demonstrate control of genome editing and gene activation using a miR-dependent AcrIIA4 in combination with different Streptococcus pyogenes (Spy)Cas9 variants (full-length Cas9, split-Cas9, dCas9-VP64). Finally, to showcase its modularity, we adapted our Cas-ON system to the smaller and more target-specific Neisseria meningitidis (Nme)Cas9 orthologue and its cognate inhibitors AcrIIC1 and AcrIIC3. Our Cas-ON switch should facilitate cell-specific activity of any CRISPR–Cas orthologue, for which a potent anti-CRISPR protein is known.
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Affiliation(s)
- Mareike D Hoffmann
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany.,Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Sabine Aschenbrenner
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany.,Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Stefanie Grosse
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
| | - Kleopatra Rapti
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg 69120, Germany
| | - Claire Domenger
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg 69120, Germany
| | - Julia Fakhiri
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg 69120, Germany
| | - Manuel Mastel
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg 69120, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg 69120, Germany
| | - Roland Eils
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany.,Health Data Science Unit, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg 69120, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg, Heidelberg 69120, Germany
| | - Dominik Niopek
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg 69120, Germany
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16
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A simplified system for the effective expression and delivery of functional mature microRNAs in mammalian cells. Cancer Gene Ther 2019; 27:424-437. [PMID: 31222181 PMCID: PMC6923634 DOI: 10.1038/s41417-019-0113-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [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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17
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van den Berg FT, Makoah NA, Ali SA, Scott TA, Mapengo RE, Mutsvunguma LZ, Mkhize NN, Lambson BE, Kgagudi PD, Crowther C, Abdool Karim SS, Balazs AB, Weinberg MS, Ely A, Arbuthnot PB, Morris L. AAV-Mediated Expression of Broadly Neutralizing and Vaccine-like Antibodies Targeting the HIV-1 Envelope V2 Region. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 14:100-112. [PMID: 31334303 PMCID: PMC6616373 DOI: 10.1016/j.omtm.2019.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
Abstract
HIV-1 infection continues to be a global health challenge and a vaccine is urgently needed. Broadly neutralizing antibodies (bNAbs) are considered essential as they inhibit multiple HIV-1 strains, but they are difficult to elicit by conventional immunization. In contrast, non-neutralizing antibodies that correlated with reduced risk of infection in the RV144 HIV vaccine trial are relatively easy to induce, but responses are not durable. To overcome these obstacles, adeno-associated virus (AAV) vectors were used to provide long-term expression of antibodies targeting the V2 region of the HIV-1 envelope protein, including the potent CAP256-VRC26.25 bNAb, as well as non-neutralizing CAP228 antibodies that resemble those elicited by vaccination. AAVs mediated effective antibody expression in cell culture and immunocompetent mice. Mean concentrations of human immunoglobulin G (IgG) in mouse sera increased rapidly following a single AAV injection, reaching 8–60 μg/mL for CAP256 antibodies and 44–220 μg/mL for CAP228 antibodies over 24 weeks, but antibody concentrations varied for individual mice. Secreted antibodies collected from serum retained the expected binding and neutralizing activity. The vectors generated here are, therefore, suitable for the delivery of V2-targeting HIV antibodies, and they could be used in a vectored immunoprophylaxis (VIP) approach to sustain the level of antibody expression required to prevent HIV infection.
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Affiliation(s)
- Fiona T van den Berg
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel A Makoah
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stuart A Ali
- HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tristan A Scott
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Rutendo E Mapengo
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Lorraine Z Mutsvunguma
- HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonhlanhla N Mkhize
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Bronwen E Lambson
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Prudence D Kgagudi
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Carol Crowther
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,Department of Epidemiology, Columbia University, New York, NY, USA
| | | | - Marc S Weinberg
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,HIV Pathogenesis Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Abdullah Ely
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick B Arbuthnot
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine & Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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18
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Phua YL, Chen KH, Hemker SL, Marrone AK, Bodnar AJ, Liu X, Clugston A, Kostka D, Butterworth MB, Ho J. Loss of miR-17~92 results in dysregulation of Cftr in nephron progenitors. Am J Physiol Renal Physiol 2019; 316:F993-F1005. [PMID: 30838872 DOI: 10.1152/ajprenal.00450.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have previously demonstrated that loss of miR-17~92 in nephron progenitors in a mouse model results in renal hypodysplasia and chronic kidney disease. Clinically, decreased congenital nephron endowment because of renal hypodysplasia is associated with an increased risk of hypertension and chronic kidney disease, and this is at least partly dependent on the self-renewal of nephron progenitors. Here, we present evidence for a novel molecular mechanism regulating the self-renewal of nephron progenitors and congenital nephron endowment by the highly conserved miR-17~92 cluster. Whole transcriptome sequencing revealed that nephron progenitors lacking this cluster demonstrated increased Cftr expression. We showed that one member of the cluster, miR-19b, is sufficient to repress Cftr expression in vitro and that perturbation of Cftr activity in nephron progenitors results in impaired proliferation. Together, these data suggest that miR-19b regulates Cftr expression in nephron progenitors, with this interaction playing a role in appropriate nephron progenitor self-renewal during kidney development to generate normal nephron endowment.
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Affiliation(s)
- Yu Leng Phua
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Kevin Hong Chen
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania
| | - Shelby L Hemker
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - April K Marrone
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Andrew J Bodnar
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Xiaoning Liu
- Department of Cell Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Andrew Clugston
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania.,Department of Developmental Biology and Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Dennis Kostka
- Department of Developmental Biology and Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Michael B Butterworth
- Department of Cell Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Jacqueline Ho
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
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19
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Herrmann AK, Bender C, Kienle E, Grosse S, El Andari J, Botta J, Schürmann N, Wiedtke E, Niopek D, Grimm D. A Robust and All-Inclusive Pipeline for Shuffling of Adeno-Associated Viruses. ACS Synth Biol 2019; 8:194-206. [PMID: 30513195 DOI: 10.1021/acssynbio.8b00373] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adeno-associated viruses (AAV) are attractive templates for engineering of synthetic gene delivery vectors. A particularly powerful technology for breeding of novel vectors with improved properties is DNA family shuffling, i.e., generation of chimeric capsids by homology-driven DNA recombination. Here, to make AAV DNA shuffling available to a wider community, we present a robust experimental and bioinformatical pipeline comprising: (i) standardized and partially codon-optimized plasmids carrying 12 different AAV capsid genes; (ii) a scalable protocol including troubleshooting guide for viral library production; and (iii) the freely available software SALANTO for comprehensive analysis of chimeric AAV DNA and protein sequences. Moreover, we describe a set of 12 premade and ready-to-use AAV libraries. Finally, we demonstrate the usefulness of DNA barcoding technology to trace AAV capsid libraries within a complex mixture. Our protocols and resources facilitate the implementation and tailoring of AAV evolution technology in any laboratory interested in customized viral gene transfer.
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Affiliation(s)
- Anne-Kathrin Herrmann
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Christian Bender
- Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, 55131, Germany
| | - Eike Kienle
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Stefanie Grosse
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Jihad El Andari
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Julia Botta
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg, 69120, Germany
| | - Nina Schürmann
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Ellen Wiedtke
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Dominik Niopek
- Synthetic Biology Group, Institute for Pharmacy and Biotechnology (IPMB) and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg, 69120, Germany
| | - Dirk Grimm
- Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology and Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University Hospital, Heidelberg, 69120, Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), Heidelberg, 69120, Germany
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20
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Herrmann AK, Große S, Börner K, Krämer C, Wiedtke E, Gunkel M, Grimm D. Impact of the Assembly-Activating Protein on Molecular Evolution of Synthetic Adeno-Associated Virus Capsids. Hum Gene Ther 2018; 30:21-35. [PMID: 29978729 DOI: 10.1089/hum.2018.085] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Over the last decade, the role of the assembly-activating protein (AAP) has begun to be dissected for the formation of adeno-associated virus (AAV) capsids based on different viral serotypes. Recently, the authors' group has specifically studied AAP's relevance during production of AAV gene therapy vectors in mammalian or insect cells, and AAP was found to be essential for capsid protein stabilization and generation of functional vector particles. Here, the lingering question is additionally addressed of whether molecular AAV evolution via DNA family shuffling of viral capsid genes would perturb AAP functionality due to concurrent and inadvertent recombination of the AAP open reading frame. To this end, a battery of complementary experiments was conducted in which: (1) the ability of chimeric AAP from AAVDJ, a hybrid of serotypes 2, 8, and 9, was tested to rescue AAP knockouts in the three parental serotypes; (2) the functionality of 60 chimeric AAPs extracted from five shuffled, unselected capsid libraries was measured; (3) whether production of different shuffled libraries, 10 wild-type serotypes or 25 individual chimeric capsids, can be enhanced by overexpression of AAP cocktails was assessed; and (4) the activity of 12 chimeric AAPs isolated from a shuffled library that was iteratively selected in vivo in mouse livers was studied. Collectively, the data demonstrate a remarkable tolerance of AAP for recombination via DNA family shuffling, evidenced by the findings that (1) all chimeric AAPs studied here retained at least partial activity, even in cases where the cognate hybrid capsid may be non-functional, and that (2) ectopic AAP overexpression did not enhance production of shuffled AAV chimeras or libraries, implying that the inherently encoded hybrid AAP variants are sufficiently active. Together, this work provides compelling evidence that AAP is not rate limiting during AAV capsid shuffling and thereby relieves a major concern in the field of AAV vector evolution.
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Affiliation(s)
- Anne-Kathrin Herrmann
- 1 Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany.,2 BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Stefanie Große
- 1 Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany.,2 BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Kathleen Börner
- 1 Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany.,2 BioQuant Center, University of Heidelberg, Heidelberg, Germany.,3 German Center for Infection Research (DZIF), partner site Heidelberg, Germany
| | - Chiara Krämer
- 1 Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany.,2 BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Ellen Wiedtke
- 1 Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany.,2 BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Manuel Gunkel
- 2 BioQuant Center, University of Heidelberg, Heidelberg, Germany.,4 CellNetworks Advanced Biological Screening Facility, University of Heidelberg, Heidelberg, Germany
| | - Dirk Grimm
- 1 Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany.,2 BioQuant Center, University of Heidelberg, Heidelberg, Germany.,3 German Center for Infection Research (DZIF), partner site Heidelberg, Germany
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21
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Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. Nat Methods 2018; 15:924-927. [PMID: 30377362 DOI: 10.1038/s41592-018-0178-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 12/20/2022]
Abstract
Anti-CRISPR proteins are powerful tools for CRISPR-Cas9 regulation; the ability to precisely modulate their activity could facilitate spatiotemporally confined genome perturbations and uncover fundamental aspects of CRISPR biology. We engineered optogenetic anti-CRISPR variants comprising hybrids of AcrIIA4, a potent Streptococcus pyogenes Cas9 inhibitor, and the LOV2 photosensor from Avena sativa. Coexpression of these proteins with CRISPR-Cas9 effectors enabled light-mediated genome and epigenome editing, and revealed rapid Cas9 genome targeting in human cells.
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22
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Wolff G, Taranko AE, Meln I, Weinmann J, Sijmonsma T, Lerch S, Heide D, Billeter AT, Tews D, Krunic D, Fischer-Posovszky P, Müller-Stich BP, Herzig S, Grimm D, Heikenwälder M, Kao WW, Vegiopoulos A. Diet-dependent function of the extracellular matrix proteoglycan Lumican in obesity and glucose homeostasis. Mol Metab 2018; 19:97-106. [PMID: 30409703 PMCID: PMC6323191 DOI: 10.1016/j.molmet.2018.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 02/06/2023] Open
Abstract
Objective Extracellular matrix remodeling is required for adipose expansion under increased caloric intake. In turn, inhibited expandability due to aberrant collagen deposition promotes insulin resistance and progression towards the metabolic syndrome. An emerging role for the small leucine-rich proteoglycan Lumican in metabolically driven nonalcoholic fatty liver disease sparks an interest in further understanding its role in diet-induced obesity and metabolic complications. Methods Whole body ablation of Lumican (Lum−/−) gene and adeno-associated virus-mediated over-expression were used in combination with control or high fat diet to assess energy balance, glucose homeostasis as well as adipose tissue health and remodeling. Results Lumican was found to be particularly enriched in the stromal cells isolated from murine gonadal white adipose tissue. Likewise murine and human visceral fat showed a robust increase in Lumican as compared to fat from the subcutaneous depot. Lumican null female mice exhibited moderately increased fat mass, decreased insulin sensitivity and increased liver triglycerides in a diet-dependent manner. These changes coincided with inflammation in adipose tissue and no overt effects in adipose expandability, i.e. adipocyte formation and hypertrophy. Lumican over-expression in visceral fat and liver resulted in improved insulin sensitivity and glucose clearance. Conclusions These data indicate that Lumican may represent a functional link between the extracellular matrix, glucose homeostasis, and features of the metabolic syndrome. The extracellular matrix proteoglycan Lumican (Lum) is particularly enriched in stromal cells within white adipose tissue. Visceral fat from obese patients displays increased levels of Lum compared to subcutaneous fat. Lum-Ko female mice exhibit decreased insulin sensitivity and increased triglycerides upon high-fat diet (HFD) feeding. Lum-Ko female mice on HFD have increased inflammation in white fat in the absence of overt effects on adipocyte formation. · Lum over-expression in visceral fat and liver resulted in improved insulin sensitivity and glucose clearance.
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Affiliation(s)
- G Wolff
- DKFZ Junior Group Metabolism and Stem Cell Plasticity, German Cancer Research Center, Heidelberg, Germany.
| | - A E Taranko
- DKFZ Junior Group Metabolism and Stem Cell Plasticity, German Cancer Research Center, Heidelberg, Germany
| | - I Meln
- DKFZ Junior Group Metabolism and Stem Cell Plasticity, German Cancer Research Center, Heidelberg, Germany
| | - J Weinmann
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, BioQuant Center, Heidelberg, Germany
| | - T Sijmonsma
- Division Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - S Lerch
- DKFZ Junior Group Metabolism and Stem Cell Plasticity, German Cancer Research Center, Heidelberg, Germany
| | - D Heide
- Division Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A T Billeter
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - D Tews
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - D Krunic
- Light Microscopy Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Fischer-Posovszky
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - B P Müller-Stich
- Department of General, Visceral, and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - S Herzig
- Helmholtz Center Munich, Institute for Diabetes and Cancer IDC, Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, Heidelberg, Germany
| | - D Grimm
- Heidelberg University Hospital, Dept. of Infectious Diseases/Virology, BioQuant Center, Heidelberg, Germany; German Center for Infection Research, Partner Site Heidelberg, Germany
| | - M Heikenwälder
- Division Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - W W Kao
- Department of Ophthalmology, University of Cincinnati, Cincinnati, OH, USA
| | - A Vegiopoulos
- DKFZ Junior Group Metabolism and Stem Cell Plasticity, German Cancer Research Center, Heidelberg, Germany.
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23
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Hüser L, Sachindra S, Granados K, Federico A, Larribère L, Novak D, Umansky V, Altevogt P, Utikal J. SOX2-mediated upregulation of CD24 promotes adaptive resistance toward targeted therapy in melanoma. Int J Cancer 2018; 143:3131-3142. [PMID: 29905375 DOI: 10.1002/ijc.31609] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/06/2018] [Accepted: 05/03/2018] [Indexed: 12/19/2022]
Abstract
Melanoma is often characterized by a constitutively active RAS-RAF-MEK-ERK pathway. For targeted therapy, BRAF inhibitors are available that are powerful in the beginning but resistance occurs rather fast. A better understanding of the mechanisms of resistance is urgently needed to increase the success of the treatment. Here, we observed that SOX2 and CD24 are upregulated upon BRAF inhibitor treatment. A similar upregulation was seen in targeted therapy-resistant, melanoma-derived induced pluripotent cancer cells (iPCCs). SOX2 and CD24 are known to promote an undifferentiated and cancer stem cell-like phenotype associated with resistance. We, therefore, elucidated the role of SOX2 and CD24 in targeted therapy resistance in more detail. We found that the upregulation of SOX2 and CD24 required activation of STAT3 and that SOX2 induced the expression of CD24 by binding to its promoter. We find that the overexpression of SOX2 or CD24 significantly increases the resistance toward BRAF inhibitors, while SOX2 knock-down rendered cells more sensitivity toward treatment. The overexpression of CD24 or SOX2 induced Src and STAT3 activity. Importantly, by either CD24 knock-down or Src/STAT3 inhibition in resistant SOX2-overexpressing cells, the sensitivity toward BRAF inhibitors was re-established. Hence, we suggest a novel mechanism of adaptive resistance whereby BRAF inhibition is circumvented via the activation of STAT3, SOX2 and CD24. Thus, to prevent adaptive resistance, it might be beneficial to combine Src/STAT3 inhibitors together with MAPK pathway inhibitors.
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Affiliation(s)
- Laura Hüser
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Sachindra Sachindra
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Karol Granados
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Aniello Federico
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Lionel Larribère
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Daniel Novak
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Viktor Umansky
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, D-68135, Germany
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24
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Li X, Guo X, Cheng Y, Zhao X, Fang Z, Luo Y, Xia S, Feng Y, Chen J, Yuan WE. pH-Responsive Cross-Linked Low Molecular Weight Polyethylenimine as an Efficient Gene Vector for Delivery of Plasmid DNA Encoding Anti-VEGF-shRNA for Tumor Treatment. Front Oncol 2018; 8:354. [PMID: 30319959 PMCID: PMC6167493 DOI: 10.3389/fonc.2018.00354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/10/2018] [Indexed: 01/23/2023] Open
Abstract
RNA interference (RNAi) is a biological process through which gene expression can be inhibited by RNA molecules with high selectivity and specificity, providing a promising tool for tumor treatment. Two types of molecules are often applied to inactivate target gene expression: synthetic double stranded small interfering RNA (siRNA) and plasmid DNA encoding short hairpin RNA (shRNA). Vectors with high transfection efficiency and low toxicity are essential for the delivery of siRNA and shRNA. In this study, TDAPEI, the synthetic derivative of low-molecular-weight polyethylenimine (PEI), was cross-linked with imine bonds by the conjugation of branched PEI (1.8 kDa) and 2,5-thiophenedicarboxaldehyde (TDA). This biodegradable cationic polymer was utilized as the vector for the delivery of plasmid DNA expressing anti-VEGF-shRNA. Compared to PEI (25 kDa), TDAPEI had a better performance since experimental results suggest its higher transfection efficiency as well as lower toxicity both in cell and animal studies. TDAPEI did not stimulate innate immune response, which is a significant factor that should be considered in vector design for gene delivery. All the results suggested that TDAPEI delivering anti-VEGF-shRNA may provide a promising method for tumor treatment.
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Affiliation(s)
- Xiaoming Li
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoshuang Guo
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Cheng
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaotian Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Fang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Yanli Luo
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shujun Xia
- Department of Ultrasound, Rui Jin Hospital Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Feng
- Department of Respiration, Institute of Respiratory Diseases, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Wei-En Yuan
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
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25
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AAVvector-mediated in vivo reprogramming into pluripotency. Nat Commun 2018; 9:2651. [PMID: 29985406 PMCID: PMC6037684 DOI: 10.1038/s41467-018-05059-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
In vivo reprogramming of somatic cells into induced pluripotent stem cells (iPSC) holds vast potential for basic research and regenerative medicine. However, it remains hampered by a need for vectors to express reprogramming factors (Oct-3/4, Klf4, Sox2, c-Myc; OKSM) in selected organs. Here, we report OKSM delivery vectors based on pseudotyped Adeno-associated virus (AAV). Using the AAV-DJ capsid, we could robustly reprogram mouse embryonic fibroblasts with low vector doses. Swapping to AAV8 permitted to efficiently reprogram somatic cells in adult mice by intravenous vector delivery, evidenced by hepatic or extra-hepatic teratomas and iPSC in the blood. Notably, we accomplished full in vivo reprogramming without c-Myc. Most iPSC generated in vitro or in vivo showed transcriptionally silent, intronic or intergenic vector integration, likely reflecting the increased host genome accessibility during reprogramming. Our approach crucially advances in vivo reprogramming technology, and concurrently facilitates investigations into the mechanisms and consequences of AAV persistence. In vivo reprogramming of somatic cells is hampered by the need for vectors to express the OKSM factors in selected organs. Here the authors report new AAV-based vectors capable of in vivo reprogramming at low doses.
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26
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Cordas Dos Santos DM, Eilers J, Sosa Vizcaino A, Orlova E, Zimmermann M, Stanulla M, Schrappe M, Börner K, Grimm D, Muckenthaler MU, Kulozik AE, Kunz JB. MAP3K7 is recurrently deleted in pediatric T-lymphoblastic leukemia and affects cell proliferation independently of NF-κB. BMC Cancer 2018; 18:663. [PMID: 29914415 PMCID: PMC6006985 DOI: 10.1186/s12885-018-4525-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/18/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Deletions of 6q15-16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has a crucial role in innate immune signaling and was observed to be functionally and prognostically relevant in different cancer entities. Therefore, we correlated the presence of MAP3K7 deletions with clinical parameters in a cohort of 327 pediatric T-ALL patients and investigated the function of MAP3K7 in the T-ALL cell lines CCRF-CEM, Jurkat and MOLT-4. METHODS MAP3K7 deletions were detected by multiplex ligation-dependent probe amplification (MLPA). T-ALL cell lines were transduced with adeno-associated virus (AAV) vectors expressing anti-MAP3K7 shRNA or a non-silencing shRNA together with a GFP reporter. Transduction efficiency was measured by flow cytometry and depletion efficiency by RT-PCR and Western blots. Induction of apoptosis was measured by flow cytometry after staining with PE-conjugated Annexin V. In order to assess the contribution of NF-κB signaling to the effects of MAP3K7 depletion, cells were treated with TNF-α and cell lysates analyzed for components of the NF-κB pathway by Western blotting and for expression of the NF-κB target genes BCL2, CMYC, FAS, PTEN and TNF-α by RT-PCR. RESULTS MAP3K7 is deleted in approximately 10% and point-mutated in approximately 1% of children with T-ALL. In 32 of 33 leukemias the deletion of MAP3K7 also included the adjacent CASP8AP2 gene. MAP3K7 deletions were associated with the occurrence of SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and outcome. Depletion of MAP3K7 expression in T-ALL cell lines by shRNAs slowed down proliferation and induced apoptosis, but neither changed protein levels of components of NF-κB signaling nor NF-κB target gene expression after stimulation with TNF-α. CONCLUSIONS This study revealed that the recurrent deletion of MAP3K7/CASP8AP2 is associated with SIL-TAL1 fusions and a mature immunophenotype, but not with response to treatment and risk of relapse. Homozygous deletions of MAP3K7 were not observed, and efficient depletion of MAP3K7 interfered with viability of T-ALL cells, indicating that a residual expression of MAP3K7 is indispensable for T-lymphoblasts.
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Affiliation(s)
- David M Cordas Dos Santos
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Juliane Eilers
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Alfonso Sosa Vizcaino
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Elena Orlova
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Martin Zimmermann
- Department of Pediatric Hematology and Oncology, MH Hannover, Hannover, Germany
| | - Martin Stanulla
- Department of Pediatric Hematology and Oncology, MH Hannover, Hannover, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,BioQuant Center, Heidelberg University, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,BioQuant Center, Heidelberg University, Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg University, Heidelberg, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Joachim B Kunz
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Children's Hospital, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.
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27
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Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference. Proc Natl Acad Sci U S A 2018; 115:E2696-E2705. [PMID: 29432194 DOI: 10.1073/pnas.1719565115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Small interfering RNA (siRNA) represents a promising class of inhibitors in both fundamental research and the clinic. Numerous delivery vehicles have been developed to facilitate siRNA delivery. Nevertheless, achieving highly potent RNA interference (RNAi) toward clinical translation requires efficient formation of RNA-induced gene-silencing complex (RISC) in the cytoplasm. Here we coencapsulate siRNA and the central RNAi effector protein Argonaute 2 (Ago2) via different delivery carriers as a platform to augment RNAi. The physical clustering between siRNA and Ago2 is found to be indispensable for enhanced RNAi. Moreover, by utilizing polyamines bearing the same backbone but distinct cationic side-group arrangements of ethylene diamine repeats as the delivery vehicles, we find that the molecular structure of these polyamines modulates the degree of siRNA/Ago2-mediated improvement of RNAi. We apply this strategy to silence the oncogene STAT3 and significantly prolong survival in mice challenged with melanoma. Our findings suggest a paradigm for RNAi via the synergistic coassembly of RNA with helper proteins.
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28
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Kunze C, Börner K, Kienle E, Orschmann T, Rusha E, Schneider M, Radivojkov-Blagojevic M, Drukker M, Desbordes S, Grimm D, Brack-Werner R. Synthetic AAV/CRISPR vectors for blocking HIV-1 expression in persistently infected astrocytes. Glia 2017; 66:413-427. [PMID: 29119608 DOI: 10.1002/glia.23254] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 10/04/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023]
Abstract
Astrocytes, the most abundant cells in the mammalian brain, perform key functions and are involved in several neurodegenerative diseases. The human immunodeficiency virus (HIV) can persist in astrocytes, contributing to the HIV burden and neurological dysfunctions in infected individuals. While a comprehensive approach to HIV cure must include the targeting of HIV-1 in astrocytes, dedicated tools for this purpose are still lacking. Here we report a novel Adeno-associated virus-based vector (AAV9P1) with a synthetic surface peptide for transduction of astrocytes. Analysis of AAV9P1 transduction efficiencies with single brain cell populations, including primary human brain cells, as well as human brain organoids demonstrated that AAV9P1 targeted terminally differentiated human astrocytes much more efficiently than neurons. We then investigated whether AAV9P1 can be used to deliver HIV-inhibitory genes to astrocytes. To this end we generated AAV9P1 vectors containing genes for HIV-1 proviral editing by CRISPR/Cas9. Latently HIV-1 infected astrocytes transduced with these vectors showed significantly diminished reactivation of proviruses, compared with untransduced cultures. Sequence analysis identified mutations/deletions in key HIV-1 transcriptional control regions. We conclude that AAV9P1 is a promising tool for gene delivery to astrocytes and may facilitate inactivation/destruction of persisting HIV-1 proviruses in astrocyte reservoirs.
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Affiliation(s)
- Christine Kunze
- Institute of Virology, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, 69120, Germany.,German Center for Infection Research (DZIF), Partner site Heidelberg, Heidelberg, 69120, Germany
| | - Eike Kienle
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, 69120, Germany
| | - Tanja Orschmann
- SCADEV, Institute of Developmental Genetics, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Ejona Rusha
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Martha Schneider
- Institute of Virology, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | | | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Sabrina Desbordes
- SCADEV, Institute of Developmental Genetics, Helmholtz Center Munich, Neuherberg, 85764, Germany
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, 69120, Germany.,German Center for Infection Research (DZIF), Partner site Heidelberg, Heidelberg, 69120, Germany
| | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Center Munich, Neuherberg, 85764, Germany
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29
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Herrera-Carrillo E, Berkhout B. Dicer-independent processing of small RNA duplexes: mechanistic insights and applications. Nucleic Acids Res 2017; 45:10369-10379. [PMID: 28977573 PMCID: PMC5737282 DOI: 10.1093/nar/gkx779] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) play a pivotal role in the regulation of cellular gene expression via the conserved RNA interference (RNAi) mechanism. Biogenesis of the unusual miR-451 does not require Dicer. This molecule is instead processed by the Argonaute 2 (Ago2) enzyme. Similarly, unconventional short hairpin RNA (shRNA) molecules have been designed as miR-451 mimics that rely exclusively on Ago2 for maturation. We will review recent progress made in the understanding of this alternative processing route. Next, we describe different Dicer-independent shRNA designs that have been developed and discuss their therapeutic advantages and disadvantages. As an example, we will present the route towards development of a durable gene therapy against HIV-1.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
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30
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Grosse S, Penaud-Budloo M, Herrmann AK, Börner K, Fakhiri J, Laketa V, Krämer C, Wiedtke E, Gunkel M, Ménard L, Ayuso E, Grimm D. Relevance of Assembly-Activating Protein for Adeno-associated Virus Vector Production and Capsid Protein Stability in Mammalian and Insect Cells. J Virol 2017; 91:e01198-17. [PMID: 28768875 PMCID: PMC5625497 DOI: 10.1128/jvi.01198-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/28/2017] [Indexed: 12/16/2022] Open
Abstract
The discovery that adeno-associated virus 2 (AAV2) encodes an eighth protein, called assembly-activating protein (AAP), transformed our understanding of wild-type AAV biology. Concurrently, it raised questions about the role of AAP during production of recombinant vectors based on natural or molecularly engineered AAV capsids. Here, we show that AAP is indeed essential for generation of functional recombinant AAV2 vectors in both mammalian and insect cell-based vector production systems. Surprisingly, we observed that AAV2 capsid proteins VP1 to -3 are unstable in the absence of AAP2, likely due to rapid proteasomal degradation. Inhibition of the proteasome led to an increase of intracellular VP1 to -3 but neither triggered assembly of functional capsids nor promoted nuclear localization of the capsid proteins. Together, this underscores the crucial and unique role of AAP in the AAV life cycle, where it rapidly chaperones capsid assembly, thus preventing degradation of free capsid proteins. An expanded analysis comprising nine alternative AAV serotypes (1, 3 to 9, and rh10) showed that vector production always depends on the presence of AAP, with the exceptions of AAV4 and AAV5, which exhibited AAP-independent, albeit low-level, particle assembly. Interestingly, AAPs from all 10 serotypes could cross-complement AAP-depleted helper plasmids during vector production, despite there being distinct intracellular AAP localization patterns. These were most pronounced for AAP4 and AAP5, congruent with their inability to rescue an AAV2/AAP2 knockout. We conclude that AAP is key for assembly of genuine capsids from at least 10 different AAV serotypes, which has implications for vectors derived from wild-type or synthetic AAV capsids.IMPORTANCE Assembly of adeno-associated virus 2 (AAV2) is regulated by the assembly-activating protein (AAP), whose open reading frame overlaps with that of the viral capsid proteins. As the majority of evidence was obtained using virus-like particles composed solely of the major capsid protein VP3, AAP's role in and relevance for assembly of genuine AAV capsids have remained largely unclear. Thus, we established a trans-complementation assay permitting assessment of AAP functionality during production of recombinant vectors based on complete AAV capsids and derived from any serotype. We find that AAP is indeed a critical factor not only for AAV2, but also for generation of vectors derived from nine other AAV serotypes. Moreover, we identify a new role of AAP in maintaining capsid protein stability in mammalian and insect cells. Thereby, our study expands our current understanding of AAV/AAP biology, and it concomitantly provides insights into the importance of AAP for AAV vector production.
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Affiliation(s)
- Stefanie Grosse
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Magalie Penaud-Budloo
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Anne-Kathrin Herrmann
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Partner Site Heidelberg, Heidelberg, Germany
| | - Julia Fakhiri
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- German Center for Infection Research, Partner Site Heidelberg, Heidelberg, Germany
| | - Chiara Krämer
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Ellen Wiedtke
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Manuel Gunkel
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
- CellNetworks Advanced Biological Screening Facility, University of Heidelberg, Heidelberg, Germany
| | - Lucie Ménard
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Eduard Ayuso
- INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Partner Site Heidelberg, Heidelberg, Germany
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31
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Park JH, Shin SY, Shin C. Non-canonical targets destabilize microRNAs in human Argonautes. Nucleic Acids Res 2017; 45:1569-1583. [PMID: 28119422 PMCID: PMC5389725 DOI: 10.1093/nar/gkx029] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/15/2017] [Indexed: 01/06/2023] Open
Abstract
Although much is known about microRNA (miRNA) biogenesis and the mechanism by which miRNAs regulate their targets, little is known about the regulation of miRNA stability. Mature miRNAs are stabilized by binding to Argonaute (Ago) proteins, the core components of the RNA-induced silencing complex (RISC). Recent studies suggest that interactions between miRNAs and their highly complementary target RNAs promote release of miRNAs from Ago proteins, and this in turn can lead to destabilization of miRNAs. However, the physiological triggers of miRNA destabilization with molecular mechanisms remain largely unknown. Here, using an in vitro system that consists of a minimal human Ago2-RISC in HEK293T cell lysates, we sought to understand how miRNAs are destabilized by their targets. Strikingly, we showed that miRNA destabilization is dramatically enhanced by an interaction with seedless, non-canonical targets. We then showed that this process entails not only unloading of miRNAs from Ago, but also 3΄ end destabilization of miRNAs occurred within Ago. Furthermore, our mutation analysis indicates that conformational changes in the hinge region of the Ago PAZ domain are likely to be the main driving force of the miRNA destabilization. Our collective results suggest that non-canonical targets may provide a stability control mechanism in the regulation of miRNAs in humans.
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Affiliation(s)
- June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang-Yoon Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
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32
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Rezvani M, Español-Suñer R, Malato Y, Dumont L, Grimm AA, Kienle E, Bindman JG, Wiedtke E, Hsu BY, Naqvi SJ, Schwabe RF, Corvera CU, Grimm D, Willenbring H. In Vivo Hepatic Reprogramming of Myofibroblasts with AAV Vectors as a Therapeutic Strategy for Liver Fibrosis. Cell Stem Cell 2017; 18:809-816. [PMID: 27257763 DOI: 10.1016/j.stem.2016.05.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 03/22/2016] [Accepted: 05/09/2016] [Indexed: 12/21/2022]
Abstract
Liver fibrosis, a form of scarring, develops in chronic liver diseases when hepatocyte regeneration cannot compensate for hepatocyte death. Initially, collagen produced by myofibroblasts (MFs) functions to maintain the integrity of the liver, but excessive collagen accumulation suppresses residual hepatocyte function, leading to liver failure. As a strategy to generate new hepatocytes and limit collagen deposition in the chronically injured liver, we developed in vivo reprogramming of MFs into hepatocytes using adeno-associated virus (AAV) vectors expressing hepatic transcription factors. We first identified the AAV6 capsid as effective in transducing MFs in a mouse model of liver fibrosis. We then showed in lineage-tracing mice that AAV6 vector-mediated in vivo hepatic reprogramming of MFs generates hepatocytes that replicate function and proliferation of primary hepatocytes, and reduces liver fibrosis. Because AAV vectors are already used for liver-directed human gene therapy, our strategy has potential for clinical translation into a therapy for liver fibrosis.
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Affiliation(s)
- Milad Rezvani
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Regina Español-Suñer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yann Malato
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laure Dumont
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew A Grimm
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eike Kienle
- Department of Infectious Diseases, Heidelberg University Hospital, Cluster of Excellence CellNetworks, BioQuant BQ0030, D-69120 Heidelberg, Germany
| | - Jay G Bindman
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ellen Wiedtke
- Department of Infectious Diseases, Heidelberg University Hospital, Cluster of Excellence CellNetworks, BioQuant BQ0030, D-69120 Heidelberg, Germany
| | - Bernadette Y Hsu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Syed J Naqvi
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert F Schwabe
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Carlos U Corvera
- Department of Surgery, Division of Hepatobiliary and Pancreas Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dirk Grimm
- Department of Infectious Diseases, Heidelberg University Hospital, Cluster of Excellence CellNetworks, BioQuant BQ0030, D-69120 Heidelberg, Germany
| | - Holger Willenbring
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Surgery, Division of Transplantation, University of California, San Francisco, San Francisco, CA 94143, USA; Liver Center, University of California, San Francisco, San Francisco, CA 94110, USA.
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33
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Valdmanis PN, Kay MA. Future of rAAV Gene Therapy: Platform for RNAi, Gene Editing, and Beyond. Hum Gene Ther 2017; 28:361-372. [PMID: 28073291 PMCID: PMC5399734 DOI: 10.1089/hum.2016.171] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
The use of recombinant adeno-associated viruses (rAAVs) ushered in a new millennium of gene transfer for therapeutic treatment of a number of conditions, including congenital blindness, hemophilia, and spinal muscular atrophy. rAAV vectors have remarkable staying power from a therapeutic standpoint, withstanding several ebbs and flows. As new technologies such as clustered regularly interspaced short palindromic repeat genome editing emerge, it is now the delivery tool-the AAV vector-that is the stalwart. The long-standing safety of this vector in a multitude of clinical settings makes rAAV a selling point in the advancement of approaches for gene replacement, gene knockdown, gene editing, and genome modification/engineering. The research community is building on these advances to develop more tailored delivery approaches and to tweak the genome in new and unique ways. Intertwining these approaches with newly engineered rAAV vectors is greatly expanding the available tools to manipulate gene expression with a therapeutic intent.
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Affiliation(s)
- Paul N. Valdmanis
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California
| | - Mark A. Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California
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34
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Günther A, Luczak V, Abel T, Baumann A. Caspase-3 and GFAP as early markers for apoptosis and astrogliosis in shRNA-induced hippocampal cytotoxicity. ACTA ACUST UNITED AC 2017; 220:1400-1404. [PMID: 28167801 DOI: 10.1242/jeb.154583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/01/2017] [Indexed: 01/12/2023]
Abstract
Genetic manipulation of cells and tissue by RNA interference has significantly contributed to the functional characterization of individual proteins and their role in physiological processes. Despite its versatility, RNA interference can have detrimental side effects, including reduced cell viability. We applied recombinant adeno-associated viruses by stereotaxic injection into the murine hippocampus to express different short hairpin RNA (shRNA) constructs along with eGFP. Tissue responses were assessed immunohistochemically for up to 8 weeks post-infection. Strong hippocampal degeneration and tissue atrophy was observed, most likely induced by high shRNA expression. The effect was entirely absent in mice injected with vectors driving only expression of eGFP. Active caspase-3 (Casp-3) and glial fibrillary acidic protein (GFAP) were identified as molecular markers and early indicators of adverse tissue responses. Our findings also demonstrate that detrimental effects of high shRNA expression in hippocampal tissue can be monitored even before the onset of tissue degeneration.
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Affiliation(s)
- Anne Günther
- Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Vince Luczak
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arnd Baumann
- Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum Jülich, Jülich 52425, Germany
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35
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Plasmodium berghei EXP-1 interacts with host Apolipoprotein H during Plasmodium liver-stage development. Proc Natl Acad Sci U S A 2017; 114:E1138-E1147. [PMID: 28137845 DOI: 10.1073/pnas.1606419114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first, obligatory replication phase of malaria parasite infections is characterized by rapid expansion and differentiation of single parasites in liver cells, resulting in the formation and release of thousands of invasive merozoites into the bloodstream. Hepatic Plasmodium development occurs inside a specialized membranous compartment termed the parasitophorous vacuole (PV). Here, we show that, during the parasite's hepatic replication, the C-terminal region of the parasitic PV membrane protein exported protein 1 (EXP-1) binds to host Apolipoprotein H (ApoH) and that this molecular interaction plays a pivotal role for successful Plasmodium liver-stage development. Expression of a truncated EXP-1 protein, missing the specific ApoH interaction site, or down-regulation of ApoH expression in either hepatic cells or mouse livers by RNA interference resulted in impaired intrahepatic development. Furthermore, infection of mice with sporozoites expressing a truncated version of EXP-1 resulted in both a significant reduction of liver burden and delayed blood-stage patency, leading to a disease outcome different from that generally induced by infection with wild-type parasites. This study identifies a host-parasite protein interaction during the hepatic stage of infection by Plasmodium parasites. The identification of such vital interactions may hold potential toward the development of novel malaria prevention strategies.
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Phosphorylation-Dependent Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA Screening. Mol Cell 2017; 65:403-415.e8. [PMID: 28132841 DOI: 10.1016/j.molcel.2016.12.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 09/28/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022]
Abstract
Cell-autonomous induction of type I interferon must be stringently regulated. Rapid induction is key to control virus infection, whereas proper limitation of signaling is essential to prevent immunopathology and autoimmune disease. Using unbiased kinome-wide RNAi screening followed by thorough validation, we identified 22 factors that regulate RIG-I/IRF3 signaling activity. We describe a negative-feedback mechanism targeting RIG-I activity, which is mediated by death associated protein kinase 1 (DAPK1). RIG-I signaling triggers DAPK1 kinase activation, and active DAPK1 potently inhibits RIG-I stimulated IRF3 activity and interferon-beta production. DAPK1 phosphorylates RIG-I in vitro at previously reported as well as other sites that limit 5'ppp-dsRNA sensing and virtually abrogate RIG-I activation.
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Michler T, Große S, Mockenhaupt S, Röder N, Stückler F, Knapp B, Ko C, Heikenwalder M, Protzer U, Grimm D. Blocking sense-strand activity improves potency, safety and specificity of anti-hepatitis B virus short hairpin RNA. EMBO Mol Med 2016; 8:1082-98. [PMID: 27473329 PMCID: PMC5009812 DOI: 10.15252/emmm.201506172] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is a promising target for therapies based on RNA interference (RNAi) since it replicates via RNA transcripts that are vulnerable to RNAi silencing. Clinical translation of RNAi technology, however, requires improvements in potency, specificity and safety. To this end, we systematically compared different strategies to express anti-HBV short hairpin RNA (shRNA) in a pre-clinical immunocompetent hepatitis B mouse model. Using recombinant Adeno-associated virus (AAV) 8 vectors for delivery, we either (i) embedded the shRNA in an artificial mi(cro)RNA under a liver-specific promoter; (ii) co-expressed Argonaute-2, a rate-limiting cellular factor whose saturation with excess RNAi triggers can be toxic; or (iii) co-delivered a decoy ("TuD") directed against the shRNA sense strand to curb off-target gene regulation. Remarkably, all three strategies minimised adverse side effects as compared to a conventional shRNA vector that caused weight loss, liver damage and dysregulation of > 100 hepatic genes. Importantly, the novel AAV8 vector co-expressing anti-HBV shRNA and TuD outperformed all other strategies regarding efficiency and persistence of HBV knock-down, thus showing substantial promise for clinical translation.
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Affiliation(s)
- Thomas Michler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany German Center for Infection Research (DZIF), partner site München, München, Germany
| | - Stefanie Große
- Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, Heidelberg University Hospital, Heidelberg, Germany BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Stefan Mockenhaupt
- Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, Heidelberg University Hospital, Heidelberg, Germany BioQuant, University of Heidelberg, Heidelberg, Germany
| | - Natalie Röder
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
| | - Ferdinand Stückler
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bettina Knapp
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Chunkyu Ko
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, München, Germany German Center for Infection Research (DZIF), partner site München, München, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Cluster of Excellence CellNetworks, Heidelberg University Hospital, Heidelberg, Germany BioQuant, University of Heidelberg, Heidelberg, Germany
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Hentzschel F, Herrmann AK, Mueller AK, Grimm D. Plasmodium meets AAV-the (un)likely marriage of parasitology and virology, and how to make the match. FEBS Lett 2016; 590:2027-45. [PMID: 27117587 DOI: 10.1002/1873-3468.12187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/24/2016] [Accepted: 04/21/2016] [Indexed: 01/21/2023]
Abstract
The increasing use of screening technologies in malaria research has substantially expanded our knowledge on cellular factors hijacked by the Plasmodium parasite in the infected host, including those that participate in the clinically silent liver stage. This rapid gain in our understanding of the hepatic interaction partners now requires a means to validate and further disentangle parasite-host networks in physiologically relevant liver model systems. Here, we outline seminal work that contributed to our present knowledge on the intrahepatic Plasmodium host factors, followed by a discussion of surrogate models of mammalian livers or hepatocytes. We finally describe how Adeno-associated viruses could be engineered and used as hepatotropic tools to dissect Plasmodium-host interactions, and to deliberately control these networks for antimalaria vaccination or therapy.
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Affiliation(s)
- Franziska Hentzschel
- Department of Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Germany.,Department of Virology, Center for Infectious Diseases, Heidelberg University Hospital, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Anne-Kathrin Herrmann
- Department of Virology, Center for Infectious Diseases, Heidelberg University Hospital, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Ann-Kristin Mueller
- Department of Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Germany
| | - Dirk Grimm
- Department of Virology, Center for Infectious Diseases, Heidelberg University Hospital, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg, Germany
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He J, Huang L, Qiu H, Li J, Luo L, Li Y, Tian S, Kang K, Luo J, Liu L, Gou D. A new design of a lentiviral shRNA vector with inducible co-expression of ARGONAUTE 2 for enhancing gene silencing efficiency. Cell Biosci 2015; 5:67. [PMID: 26649169 PMCID: PMC4672530 DOI: 10.1186/s13578-015-0058-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/19/2015] [Indexed: 12/13/2022] Open
Abstract
Background RNA interference (RNAi) is a robust tool for inhibiting specific gene expression, but it is limited by the uncertain efficiency of siRNA or shRNA constructs. It has been shown that the overexpression of ARGONAUTE 2 (AGO2) protein increases silencing efficiency. However, the key elements required for AGO2-mediated enhancement of gene silencing in lentiviral vector has not been well studied. Results To explore the application of AGO2-based shRNA system in mammalian cells, we designed shRNA vectors targeting the EGFP reporter gene and evaluated the effects of various factors on silencing efficiency including stem length, loop sequence, antisense location as well as the ratio between AGO2 and shRNA. We found that 19 ~ 21-bp stem and 6- or 9-nt loop structure in the sense-loop-antisense (S-L-AS) orientation was an optimal design in the AGO2-shRNA system. Then, we constructed a single lentiviral vector co-expressing shRNA and AGO2 and demonstrated that the simultaneous expression of shRNA and AGO2 can achieve robust silencing of exogenous DsRed2 and endogenous ID1 and P65 genes. However, the titers of packaged lentivirus from constitutive expression of AGO2 vector were extremely low, severely limiting its broad application. For the first time, we demonstrated that the problem can be significantly improved by using the inducible expression of AGO2 lentiviral system. Conclusions We reported a novel lentiviral vector with an optimal design of shRNA and inducible AGO2 overexpression which provides a new tool for RNAi research.
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Affiliation(s)
- Jiening He
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Lian Huang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Huiling Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Jiexuan Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Lan Luo
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Yanjiao Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Shengli Tian
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
| | - Kang Kang
- Department of Physiology, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Jun Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Lin Liu
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078 USA
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences, Shenzhen University, Nanhai Ave 3688, Shenzhen, 518060 Guangdong China
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Nishi K, Takahashi T, Suzawa M, Miyakawa T, Nagasawa T, Ming Y, Tanokura M, Ui-Tei K. Control of the localization and function of a miRNA silencing component TNRC6A by Argonaute protein. Nucleic Acids Res 2015; 43:9856-73. [PMID: 26446993 PMCID: PMC4787778 DOI: 10.1093/nar/gkv1026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/28/2015] [Indexed: 12/12/2022] Open
Abstract
GW182 family proteins play important roles in microRNA (miRNA)-mediated RNA silencing. They directly interact with Argonaute (Ago) proteins in processing bodies (P bodies), cytoplasmic foci involved in mRNA degradation and storage. Recently, we revealed that a human GW182 family protein, TNRC6A, is a nuclear-cytoplasmic shuttling protein, and its subcellular localization is regulated by its own nuclear localization signal and nuclear export signal. Regarding the further controlling mechanism of TNRC6A subcellular localization, we found that TNRC6A protein is tethered in P bodies by direct interaction with Ago2 under Ago2 overexpression condition in HeLa cells. Furthermore, it was revealed that such Ago proteins might be strongly tethered in the P bodies through Ago-bound small RNAs. Thus, our results indicate that TNRC6A subcellular localization is substantially controlled by the interaction with Ago proteins. Furthermore, it was also revealed that the TNRC6A subcellular localization affects the RNA silencing activity.
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Affiliation(s)
- Kenji Nishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Masataka Suzawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Tatsuya Nagasawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Yvelt Ming
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba-ken 277-8651, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba-ken 277-8651, Japan
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Miura H, Inoko H, Tanaka M, Nakaoka H, Kimura M, Gurumurthy CB, Sato M, Ohtsuka M. Assessment of Artificial MiRNA Architectures for Higher Knockdown Efficiencies without the Undesired Effects in Mice. PLoS One 2015; 10:e0135919. [PMID: 26285215 PMCID: PMC4540464 DOI: 10.1371/journal.pone.0135919] [Citation(s) in RCA: 6] [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: 12/06/2014] [Accepted: 07/27/2015] [Indexed: 01/08/2023] Open
Abstract
RNAi-based strategies have been used for hypomorphic analyses. However, there are technical challenges to achieve robust, reproducible knockdown effect. Here we examined the artificial microRNA (amiRNA) architectures that could provide higher knockdown efficiencies. Using transient and stable transfection assays in cells, we found that simple amiRNA-expression cassettes, that did not contain a marker gene (−MG), displayed higher amiRNA expression and more efficient knockdown than those that contained a marker gene (+MG). Further, we tested this phenomenon in vivo, by analyzing amiRNA-expressing mice that were produced by the pronuclear injection-based targeted transgenesis (PITT) method. While we observed significant silencing of the target gene (eGFP) in +MG hemizygous mice, obtaining −MG amiRNA expression mice, even hemizygotes, was difficult and the animals died perinatally. We obtained only mosaic mice having both “−MG amiRNA” cells and “amiRNA low-expression” cells but they exhibited growth retardation and cataracts, and they could not transmit the –MG amiRNA allele to the next generation. Furthermore, +MG amiRNA homozygotes could not be obtained. These results suggested that excessive amiRNAs transcribed by −MG expression cassettes cause deleterious effects in mice, and the amiRNA expression level in hemizygous +MG amiRNA mice is near the upper limit, where mice can develop normally. In conclusion, the PITT-(+MG amiRNA) system demonstrated here can generate knockdown mouse models that reliably express highest and tolerable levels of amiRNAs.
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Affiliation(s)
- Hiromi Miura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259–1193, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259–1193, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259–1193, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411–8540, Japan
| | - Minoru Kimura
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259–1193, Japan
| | - Channabasavaiah B. Gurumurthy
- Mouse Genome Engineering Core Facility, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, 68198, United States of America
| | - Masahiro Sato
- Section of Gene Expression Regulation, Frontier Science Research Center, Kagoshima University, 1-21-20 Korimoto, Kagoshima, Kagoshima 890–0065, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259–1193, Japan
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259–1193, Japan
- * E-mail:
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Ye Z, Jin H, Qian Q. Argonaute 2: A Novel Rising Star in Cancer Research. J Cancer 2015; 6:877-82. [PMID: 26284139 PMCID: PMC4532985 DOI: 10.7150/jca.11735] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/15/2015] [Indexed: 12/18/2022] Open
Abstract
AGO2 (Argonaute 2, EIF2C2) is the only member in AGO family with catalytic activity and of extreme importance during small RNAs guided gene silencing processes. The structural investigations have provided insights into details and functional mechanisms of the four major domains within AGO2. As a multifunction player, AGO2 has been revealed involved in tumorgenesis through miRNAs-dependent or independent ways. And nowadays, AGO2 has also been more importantly found ectopically over-expressed in carcinomas and closely associated with aspects of cancers in means of interacting with well-known tumor factors. Here, we provide a review on structural insights, functional mechanisms, novel roles and relationship with carcinomas of AGO2.
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Affiliation(s)
- ZhenLong Ye
- Laboratory of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - HuaJun Jin
- Laboratory of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - QiJun Qian
- Laboratory of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
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Alleviation of off-target effects from vector-encoded shRNAs via codelivered RNA decoys. Proc Natl Acad Sci U S A 2015; 112:E4007-16. [PMID: 26170322 DOI: 10.1073/pnas.1510476112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Exogenous RNAi triggers such as shRNAs ideally exert their activities exclusively via the antisense strand that binds and silences designated target mRNAs. However, in principle, the sense strand also possesses silencing capacity that may contribute to adverse RNAi side effects including off-target gene regulation. Here, we address this concern with a novel strategy that reduces sense strand activity of vector-encoded shRNAs via codelivery of inhibitory tough decoy (TuD) RNAs. Using various shRNAs for proof of concept, we validate that coexpression of TuDs can sequester and inactivate shRNA sense strands in human cells selectively without affecting desired antisense activities from the same shRNAs. Moreover, we show how coexpressed TuDs can alleviate shRNA-mediated perturbation of global gene expression by specifically de-repressing off-target transcripts carrying seed matches to the shRNA sense strand. Our combination of shRNA and TuD in a single bicistronic gene transfer vector derived from Adeno-associated virus (AAV) enables a wide range of applications, including gene therapies. To this end, we engineered our constructs in a modular fashion and identified simple hairpin design rules permitting adaptation to preexisting or new shRNAs. Finally, we demonstrate the power of our vectors for combinatorial RNAi strategies by showing robust suppression of hepatitis C virus (HCV) with an AAV expressing a bifunctional TuD against an anti-HCV shRNA sense strand and an HCV-related cellular miRNA. The data and tools reported here represent an important step toward the next generation of RNAi triggers with increased specificity and thus ultimately safety in humans.
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Störchel PH, Thümmler J, Siegel G, Aksoy-Aksel A, Zampa F, Sumer S, Schratt G. A large-scale functional screen identifies Nova1 and Ncoa3 as regulators of neuronal miRNA function. EMBO J 2015; 34:2237-54. [PMID: 26105073 DOI: 10.15252/embj.201490643] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/20/2015] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of neuronal development, network connectivity, and synaptic plasticity. While many neuronal miRNAs were previously shown to modulate neuronal morphogenesis, little is known regarding the regulation of miRNA function. In a large-scale functional screen, we identified two novel regulators of neuronal miRNA function, Nova1 and Ncoa3. Both proteins are expressed in the nucleus and the cytoplasm of developing hippocampal neurons. We found that Nova1 and Ncoa3 stimulate miRNA function by different mechanisms that converge on Argonaute (Ago) proteins, core components of the miRNA-induced silencing complex (miRISC). While Nova1 physically interacts with Ago proteins, Ncoa3 selectively promotes the expression of Ago2 at the transcriptional level. We further show that Ncoa3 regulates dendritic complexity and dendritic spine maturation of hippocampal neurons in a miRNA-dependent fashion. Importantly, both the loss of miRNA activity and increased dendrite complexity upon Ncoa3 knockdown were rescued by Ago2 overexpression. Together, we uncovered two novel factors that control neuronal miRISC function at the level of Ago proteins, with possible implications for the regulation of synapse development and plasticity.
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Affiliation(s)
- Peter H Störchel
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Juliane Thümmler
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Gabriele Siegel
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Ayla Aksoy-Aksel
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Federico Zampa
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Simon Sumer
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
| | - Gerhard Schratt
- Institute for Physiological Chemistry Biochemical-Pharmacological Center Marburg Philipps-University Marburg, Marburg, Germany
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Wei J, Ouyang Y, Li X, Zhu B, Yang J, Cui Y, Chen X, Lin F, Long M, Yang A, Dong K, Zhang H. Early growth response gene 1, a TRBP binding protein, is involved in miRNA activity of miR-125a-3p in human cells. Cell Signal 2015; 27:1120-8. [PMID: 25725290 DOI: 10.1016/j.cellsig.2015.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/28/2015] [Accepted: 02/16/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) are key regulators of many cellular pathways. However, the picture for components or regulators involved in the process of miRNA biogenesis and function remains to be further elucidated. Early growth response gene 1 (Egr1) has long been considered as tumor suppressor and transcriptional factor involved in cell proliferation and regulation of apoptosis. RESULTS Here we show that Egr1 is able to modulate guide strand loading of certain miRNAs or siRNAs in human HEK293 and A549 cells, which is related with thermodynamic parameters of miRNA or siRNA. Further, we found that Egr1 modulates the silencing activity of miR-125a-3p in vivo. Immunoprecipitation experiment demonstrated that Egr1 could bind miRNA biogenesis protein TAR RNA-binding protein2 (TRBP2), and knockdown TRBP by RNAi abolished the regulating effects of Egr1 on miR-125a-3p efficiency. Further experiments revealed that deleting sequence 97-227aa containing dsRBD B domain of TRBP eliminated the binding phenomenon between Egr1 and TRBP and impaired the effect of Egr1 on miR-125a-3p efficiency. CONCLUSIONS Taken together, our study has demonstrated that Egr1 is able to regulate miRNA activity of miR-125a-3p in human cells through binding TRBP, which highlights an unexpected function of Egr1 in miRNA pathway.
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Affiliation(s)
- Junxia Wei
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yongri Ouyang
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xia Li
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Baoyi Zhu
- Department of Ophthalmology, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jie Yang
- Department of Nephroloogy, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ying Cui
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xi Chen
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Fang Lin
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Min Long
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Angang Yang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Ke Dong
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.
| | - Huizhong Zhang
- Department of Clinical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
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Identification of RISC-associated adenoviral microRNAs, a subset of their direct targets, and global changes in the targetome upon lytic adenovirus 5 infection. J Virol 2014; 89:1608-27. [PMID: 25410853 DOI: 10.1128/jvi.02336-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
UNLABELLED Adenoviruses encode a set of highly abundant microRNAs (mivaRNAs), which are generated by Dicer-mediated cleavage of the larger noncoding virus-associated RNAs (VA RNAs) I and II. We performed deep RNA sequencing to thoroughly investigate the relative abundance of individual single strands of mivaRNA isoforms in human A549 cells lytically infected with human adenovirus 5 (Ad5) at physiologically relevant multiplicities of infection (MOIs). In addition, we investigated their relative abundance in the endogenous RNA-induced silencing complexes (RISCs). The occupation of endogenous RISCs by mivaRNAs turned out to be pronounced but not as dominant as previously inferred from experiments with AGO2-overexpressing cells infected at high MOIs. In parallel, levels of RISC-incorporated mRNAs were investigated as well. Analysis of mRNAs enriched in RISCs in Ad5-infected cells revealed that only mRNAs with complementarity to the seed sequences of mivaRNAs derived from VA RNAI but not VA RNAII were overrepresented among them, indicating that only mivaRNAs derived from VA RNAI are likely to contribute substantially to the posttranscriptional downregulation of host gene expression. Furthermore, to generate a comprehensive picture of the entire transcriptome/targetome in lytically infected cells, we determined changes in cellular miRNA levels in both total RNA and RISC RNA as well, and bioinformatical analysis of mRNAs of total RNA/RISC fractions revealed a general, genome-wide trend toward detargeting of cellular mRNAs upon infection. Lastly, we identified the direct targets of both single strands of a VA RNAI-derived mivaRNA that constituted one of the two most abundant isoforms in RISCs of lytically infected A549 cells. IMPORTANCE Viral and cellular miRNAs have been recognized as important players in virus-host interactions. This work provides the currently most comprehensive picture of the entire mRNA/miRNA transcriptome and of the complete RISC targetome during lytic adenovirus infection and thus represents the basis for a deeper understanding of the interplay between the virus and the cellular RNA interference machinery. Our data suggest that, at least in the model system that was employed, lytic infection by Ad5 is accompanied by a measurable global net detargeting effect on cellular mRNAs, and analysis of RISC-associated viral small RNAs revealed that the VA RNAs are the only source of virus-encoded miRNAs. Moreover, this work allows to assess the power of individual viral miRNAs to regulate cellular gene expression and provides a list of proven and putative direct targets of these miRNAs, which is of importance, given the fact that information about validated targets of adenovirus-encoded miRNAs is scarce.
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Senís E, Fatouros C, Große S, Wiedtke E, Niopek D, Mueller AK, Börner K, Grimm D. CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. Biotechnol J 2014; 9:1402-12. [PMID: 25186301 DOI: 10.1002/biot.201400046] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/12/2014] [Accepted: 09/02/2014] [Indexed: 12/18/2022]
Abstract
Its remarkable ease and efficiency make the CRISPR (clustered regularly interspaced short palindromic repeats) DNA editing machinery highly attractive as a new tool for experimental gene annotation and therapeutic genome engineering in eukaryotes. Here, we report a versatile set of plasmids and vectors derived from adeno-associated virus (AAV) that allow robust and specific delivery of the two essential CRISPR components - Cas9 and chimeric g(uide)RNA - either alone or in combination. All our constructs share a modular design that enables simple and stringent guide RNA (gRNA) cloning as well as rapid exchange of promoters driving Cas9 or gRNA. Packaging into potent synthetic AAV capsids permits CRISPR delivery even into hard-to-transfect targets, as shown for human T-cells. Moreover, we demonstrate the feasibility to direct Cas9 expression to or away from hepatocytes, using a liver-specific promoter or a hepatic miRNA binding site, respectively. We also report a streamlined and economical protocol for detection of CRISPR-induced mutations in less than 3 h. Finally, we provide original evidence that AAV/CRISPR vectors can be exploited for gene engineering in vivo, as exemplified in the liver of adult mice. Our new tools and protocols should foster the broad application of CRISPR technology in eukaryotic cells and organisms, and accelerate its clinical translation into humans.
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Affiliation(s)
- Elena Senís
- Heidelberg University Hospital, Cluster of Excellence CellNetworks, Centre for Infectious Diseases, Virology, Heidelberg, Germany
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AAV8-mediated in vivo overexpression of miR-155 enhances the protective capacity of genetically attenuated malarial parasites. Mol Ther 2014; 22:2130-2141. [PMID: 25189739 DOI: 10.1038/mt.2014.172] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 08/25/2014] [Indexed: 12/17/2022] Open
Abstract
Malaria, caused by protozoan Plasmodium parasites, remains a prevalent infectious human disease due to the lack of an efficient and safe vaccine. This is directly related to the persisting gaps in our understanding of the parasite's interactions with the infected host, especially during the clinically silent yet essential liver stage of Plasmodium development. Previously, we and others showed that genetically attenuated parasites (GAP) that arrest in the liver induce sterile immunity, but only upon multiple administrations. Here, we comprehensively studied hepatic gene and miRNA expression in GAP-injected mice, and found both a broad activation of IFNγ-associated pathways and a significant increase of murine microRNA-155 (miR-155), that was especially pronounced in non-parenchymal cells including liver-resident macrophages (Kupffer cells). Remarkably, ectopic upregulation of this miRNA in the liver of mice using robust hepatotropic adeno-associated virus 8 (AAV8) vectors enhanced GAP's protective capacity substantially. In turn, this AAV8-mediated miR-155 expression permitted a reduction of GAP injections needed to achieve complete protection against infectious parasite challenge from previously three to only one. Our study highlights a crucial role of mammalian miRNAs in Plasmodium liver infection in vivo and concurrently implies their great potential as future immune-augmenting agents in improved vaccination regimes against malaria and other diseases.
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Evers B, Bernards R, Beijersbergen RL. The Good, the Bad, and the Ugly: in search of gold standards for assessing functional genetic screen quality. Mol Syst Biol 2014; 10:738. [PMID: 24987117 PMCID: PMC4299495 DOI: 10.15252/msb.20145372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Variable screen quality, off-target effects, and unclear false discovery rates often hamper
large-scale functional genomic screens in mammalian cells. Hart et al (2014)
introduce gold standard reference sets of essential and non-essential genes, aiming at standardizing
the analysis of genome-wide screens. This work provides a framework to compare both the quality and
analysis methods of functional genetic screens.
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Affiliation(s)
- Bastiaan Evers
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rene Bernards
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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