1
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Frericks N, Brown RJP, Reinecke BM, Herrmann M, Brüggemann Y, Todt D, Miskey C, Vondran FWR, Steinmann E, Pietschmann T, Sheldon J. Unraveling the dynamics of hepatitis C virus adaptive mutations and their impact on antiviral responses in primary human hepatocytes. J Virol 2024; 98:e0192123. [PMID: 38319104 PMCID: PMC10949430 DOI: 10.1128/jvi.01921-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Hepatitis C virus (HCV) infection progresses to chronicity in the majority of infected individuals. Its high intra-host genetic variability enables HCV to evade the continuous selection pressure exerted by the host, contributing to persistent infection. Utilizing a cell culture-adapted HCV population (p100pop) which exhibits increased replicative capacity in various liver cell lines, this study investigated virus and host determinants that underlie enhanced viral fitness. Characterization of a panel of molecular p100 clones revealed that cell culture adaptive mutations optimize a range of virus-host interactions, resulting in expanded cell tropism, altered dependence on the cellular co-factor micro-RNA 122 and increased rates of virus spread. On the host side, comparative transcriptional profiling of hepatoma cells infected either with p100pop or its progenitor virus revealed that enhanced replicative fitness correlated with activation of endoplasmic reticulum stress signaling and the unfolded protein response. In contrast, infection of primary human hepatocytes with p100pop led to a mild attenuation of virion production which correlated with a greater induction of cell-intrinsic antiviral defense responses. In summary, long-term passage experiments in cells where selective pressure from innate immunity is lacking improves multiple virus-host interactions, enhancing HCV replicative fitness. However, this study further indicates that HCV has evolved to replicate at low levels in primary human hepatocytes to minimize innate immune activation, highlighting that an optimal balance between replicative fitness and innate immune induction is key to establish persistence. IMPORTANCE Hepatitis C virus (HCV) infection remains a global health burden with 58 million people currently chronically infected. However, the detailed molecular mechanisms that underly persistence are incompletely defined. We utilized a long-term cell culture-adapted HCV, exhibiting enhanced replicative fitness in different human liver cell lines, in order to identify molecular principles by which HCV optimizes its replication fitness. Our experimental data revealed that cell culture adaptive mutations confer changes in the host response and usage of various host factors. The latter allows functional flexibility at different stages of the viral replication cycle. However, increased replicative fitness resulted in an increased activation of the innate immune system, which likely poses boundary for functional variation in authentic hepatocytes, explaining the observed attenuation of the adapted virus population in primary hepatocytes.
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Affiliation(s)
- Nicola Frericks
- Institute for Experimental Virology, TWINCORE, Hannover, Germany
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Richard J. P. Brown
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
- Division of Veterinary Medicine, Paul Ehrlich Institute, Langen, Germany
| | | | - Maike Herrmann
- Division of Veterinary Medicine, Paul Ehrlich Institute, Langen, Germany
| | - Yannick Brüggemann
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Florian W. R. Vondran
- Department for General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany
- Clinic for General, Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Thomas Pietschmann
- Institute for Experimental Virology, TWINCORE, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Julie Sheldon
- Institute for Experimental Virology, TWINCORE, Hannover, Germany
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2
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Bagato O, Balkema-Buschmann A, Todt D, Weber S, Gömer A, Qu B, Miskey C, Ivics Z, Mettenleiter TC, Finke S, Brown RJP, Breithaupt A, Ushakov DS. Spatiotemporal analysis of SARS-CoV-2 infection reveals an expansive wave of monocyte-derived macrophages associated with vascular damage and virus clearance in hamster lungs. Microbiol Spectr 2024; 12:e0246923. [PMID: 38009950 PMCID: PMC10782978 DOI: 10.1128/spectrum.02469-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE We present the first study of the 3D kinetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the early host response in a large lung volume using a combination of tissue imaging and transcriptomics. This approach allowed us to make a number of important findings: Spatially restricted antiviral response is shown, including the formation of monocytic macrophage clusters and upregulation of the major histocompatibility complex II in infected epithelial cells. The monocyte-derived macrophages are linked to SARS-CoV-2 clearance, and the appearance of these cells is associated with post-infection endothelial damage; thus, we shed light on the role of these cells in infected tissue. An early onset of tissue repair occurring simultaneously with inflammatory and necrotizing processes provides the basis for longer-term alterations in the lungs.
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Affiliation(s)
- Ola Bagato
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Water Pollution Research Department, Dokki, Giza, Egypt
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Saskia Weber
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - André Gömer
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Bingqian Qu
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems, Germany
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Richard J. P. Brown
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Dmitry S. Ushakov
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
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3
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Frericks N, Brown RJP, Reinecke BM, Herrmann M, Brüggemann Y, Todt D, Miskey C, Vondran FWR, Steinmann E, Pietschmann T, Sheldon J. Hepatitis C virus cell culture adaptive mutations enhance cell culture propagation by multiple mechanisms but boost antiviral responses in primary human hepatocytes. bioRxiv 2023:2023.11.22.568224. [PMID: 38045248 PMCID: PMC10690267 DOI: 10.1101/2023.11.22.568224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Hepatitis C virus (HCV) infection progresses to chronicity in the majority of infected individuals. Its high intra-host genetic variability enables HCV to evade the continuous selection pressure exerted by the host, contributing to persistent infection. Utilizing a cell culture adapted HCV population (p100pop) which exhibits increased replicative capacity in various liver cell lines, this study investigated virus and host determinants which underlie enhanced viral fitness. Characterization of a panel of molecular p100 clones revealed that cell culture adaptive mutations optimize a range of virus-host interactions, resulting in expanded cell tropism, altered dependence on the cellular co-factor micro-RNA 122 and increased rates of virus spread. On the host side, comparative transcriptional profiling of hepatoma cells infected either with p100pop or its progenitor virus revealed that enhanced replicative fitness correlated with activation of endoplasmic reticulum stress signaling and the unfolded protein response. In contrast, infection of primary human hepatocytes with p100pop led to a mild attenuation of virion production which correlated with a greater induction of cell-intrinsic antiviral defense responses. In summary, long-term passage experiments in cells where selective pressure from innate immunity is lacking improves multiple virus-host interactions, enhancing HCV replicative fitness. However, this study further indicates that HCV has evolved to replicate at low levels in primary human hepatocytes to minimize innate immune activation, highlighting that an optimal balance between replicative fitness and innate immune induction is key to establishing persistence. Author Summary HCV infection remains a global health burden with 58 million people currently chronically infected. However, the detailed molecular mechanisms which underly persistence are incompletely defined. We utilized a long-term cell culture adapted HCV, exhibiting enhanced replicative fitness in different human liver cell lines, in order to identify molecular principles by which HCV optimizes its replication fitness. Our experimental data revealed that cell culture adaptive mutations confer changes in the host response and usage of various host factors. The latter allows functional flexibility at different stages of the viral replication cycle. However, increased replicative fitness resulted in an increased activation of the innate immune system, which likely poses boundary for functional variation in authentic hepatocytes, explaining the observed attenuation of the adapted virus population in primary hepatocytes.
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Kovač A, Miskey C, Ivics Z. Sleeping Beauty Transposon Insertions into Nucleolar DNA by an Engineered Transposase Localized in the Nucleolus. Int J Mol Sci 2023; 24:14978. [PMID: 37834425 PMCID: PMC10573994 DOI: 10.3390/ijms241914978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Transposons are nature's gene delivery vehicles that can be harnessed for experimental and therapeutic purposes. The Sleeping Beauty (SB) transposon shows efficient transposition and long-term transgene expression in human cells, and is currently under clinical development for gene therapy. SB transposition occurs into the human genome in a random manner, which carries a risk of potential genotoxic effects associated with transposon integration. Here, we evaluated an experimental strategy to manipulate SB's target site distribution by preferentially compartmentalizing the SB transposase to the nucleolus, which contains repetitive ribosomal RNA (rRNA) genes. We generated a fusion protein composed of the nucleolar protein nucleophosmin (B23) and the SB100X transposase, which was found to retain almost full transposition activity as compared to unfused transposase and to be predominantly localized to nucleoli in transfected human cells. Analysis of transposon integration sites generated by B23-SB100X revealed a significant enrichment into the p-arms of chromosomes containing nucleolus organizing regions (NORs), with preferential integration into the p13 and p11.2 cytobands directly neighboring the NORs. This bias in the integration pattern was accompanied by an enrichment of insertions into nucleolus-associated chromatin domains (NADs) at the periphery of nucleolar DNA and into lamina-associated domains (LADs). Finally, sub-nuclear targeting of the transposase resulted in preferential integration into chromosomal domains associated with the Upstream Binding Transcription Factor (UBTF) that plays a critical role in the transcription of 47S rDNA gene repeats of the NORs by RNA Pol I. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Research Centre of the Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, Paul Ehrlich Str. 51–59, D-63225 Langen, Germany; (A.K.); (C.M.)
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Magnani CF, Myburgh R, Brunn S, Chambovey M, Ponzo M, Volta L, Manfredi F, Pellegrino C, Pascolo S, Miskey C, Sandoval-Villegas N, Ivics Z, Shizuru JA, Neri D, Manz MG. Erratum: Anti-CD117 CAR T cells incorporating a safety switch eradicate human acute myeloid leukemia and hematopoietic stem cells. Mol Ther Oncolytics 2023; 30:150. [PMID: 37654971 PMCID: PMC10465849 DOI: 10.1016/j.omto.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
[This corrects the article DOI: 10.1016/j.omto.2023.07.003.].
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Magnani CF, Myburgh R, Brunn S, Chambovey M, Ponzo M, Volta L, Manfredi F, Pellegrino C, Pascolo S, Miskey C, Ivics Z, Shizuru JA, Neri D, Manz MG. Anti-CD117 CAR T cells incorporating a safety switch eradicate human acute myeloid leukemia and hematopoietic stem cells. Mol Ther Oncolytics 2023; 30:56-71. [PMID: 37583386 PMCID: PMC10424000 DOI: 10.1016/j.omto.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Discrimination between hematopoietic stem cells and leukemic stem cells remains a major challenge for acute myeloid leukemia immunotherapy. CAR T cells specific for the CD117 antigen can deplete malignant and healthy hematopoietic stem cells before consolidation with allogeneic hematopoietic stem cell transplantation in absence of cytotoxic conditioning. Here we exploit non-viral technology to achieve early termination of CAR T cell activity to prevent incoming graft rejection. Transient expression of an anti-CD117 CAR by mRNA conferred T cells the ability to eliminate CD117+ targets in vitro and in vivo. As an alternative approach, we used a Sleeping Beauty transposon vector for the generation of CAR T cells incorporating an inducible Caspase 9 safety switch. Stable CAR expression was associated with high proportion of T memory stem cells, low levels of exhaustion markers, and potent cellular cytotoxicity. Anti-CD117 CAR T cells mediated depletion of leukemic cells and healthy hematopoietic stem cells in NSG mice reconstituted with human leukemia or CD34+ cord blood cells, respectively, and could be terminated in vivo. The use of a non-viral technology to control CAR T cell pharmacokinetic properties is attractive for a first-in-human study in patients with acute myeloid leukemia prior to hematopoietic stem cell transplantation.
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Affiliation(s)
- Chiara F. Magnani
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Renier Myburgh
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Silvan Brunn
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Morgane Chambovey
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Marianna Ponzo
- Tettamanti Center, Fondazione IRCCS San Gerardo Dei Tintori, 20900 Monza, Italy
| | - Laura Volta
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Francesco Manfredi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Christian Pellegrino
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Judith A. Shizuru
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, 8093 ETH Zurich, Switzerland
| | - Markus G. Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), 8091 Zurich, Switzerland
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Wang S, Gao B, Miskey C, Guan Z, Sang Y, Chen C, Wang X, Ivics Z, Song C. Passer, a highly active transposon from a fish genome, as a potential new robust genetic manipulation tool. Nucleic Acids Res 2023; 51:1843-1858. [PMID: 36688327 PMCID: PMC9976928 DOI: 10.1093/nar/gkad005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
The discovery of new, active DNA transposons can expand the range of genetic tools and provide more options for genomic manipulation. In this study, a bioinformatics analysis suggested that Passer (PS) transposons, which are members of the pogo superfamily, show signs of recent and current activity in animals and may be active in some species. Cell-based transposition assays revealed that the native PS transposases from Gasterosteus aculeatus and Danio rerio displayed very high activity in human cells relative to the Sleeping Beauty transposon. A typical overproduction inhibition phenomenon was observed for PS, and transposition capacity was decreased by ∼12% with each kilobase increase in the insertion size. Furthermore, PS exhibited a pronounced integration preference for genes and their transcriptional regulatory regions. We further show that two domesticated human proteins derived from PS transposases have lost their transposition activity. Overall, PS may represent an alternative with a potentially efficient genetic manipulation tool for transgenesis and mutagenesis applications.
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Affiliation(s)
- Saisai Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, D-63225 Langen, Germany
| | - Zhongxia Guan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, D-63225 Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
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Himmelsbach K, Mueller S, Kress J, Fiedler SA, Miskey C, Ivics Z, Patek A, Chudy M. Second hepatitis C virus transmission by blood components since introduction of mandatory NAT screening in Germany. Transfusion 2023; 63:339-347. [PMID: 36515262 DOI: 10.1111/trf.17224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Viral safety of blood products in Germany has improved significantly over the last two decades. We describe the second documented transfusion-transmitted (TT) episode for the hepatitis C virus (HCV) in Germany since mandatory nucleic acid amplification techniques (NAT) screening was introduced in 1999. STUDY DESIGN AND METHODS When a repeat donor who had tested negative for anti-HCV tested positive for HCV RNA by NAT in a minipool (MP) of eight, a look-back procedure was initiated. Qualitative, quantitative and genotyping assays were used to investigate the titers of the quarantined fresh frozen plasma (FFP) from the donor and a serum sample from the recipient of the pooled platelet concentrate (PPC). Amplified products of 5'UTR and HVR1 were used for sequence comparison to characterize the HCV genomic identity of donor and recipient samples. RESULTS All NAT tests utilized in this procedure were able to detect a low HCV RNA titer (~15 IU/ml) in the FFP from the donation. Dilution of FFP by factor 8 was performed to mimic an MP, and the detection rate correlated well with the claimed sensitivity of the tests. Analysis of donor and recipient samples revealed genotype 3a viral transmission confirmed by sequence analysis. CONCLUSION This TT HCV case could have been prevented by individual donation (ID) NAT. However, a low titer blood donation in the window period (WP) is very rare. Residual risk calculation for TT HCV in the WP revealed that, compared to MP-NAT testing, ID-NAT would improve blood safety only marginally.
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Affiliation(s)
| | - Susanne Mueller
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institut, Langen, Germany
| | - Julia Kress
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Sarah A Fiedler
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institut, Langen, Germany
| | - Csaba Miskey
- Department of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Zoltan Ivics
- Department of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Alexander Patek
- Blood Donation Service Saar-Pfalz, Klinikum Saarbruecken, Saarbruecken, Germany
| | - Michael Chudy
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
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Mattern L, Otten K, Miskey C, Fuest M, Izsvák Z, Ivics Z, Walter P, Thumann G, Johnen S. Molecular and Functional Characterization of BDNF-Overexpressing Human Retinal Pigment Epithelial Cells Established by Sleeping Beauty Transposon-Mediated Gene Transfer. Int J Mol Sci 2022; 23:12982. [PMID: 36361771 PMCID: PMC9656812 DOI: 10.3390/ijms232112982] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/30/2022] [Accepted: 10/25/2022] [Indexed: 04/12/2024] Open
Abstract
More and more patients suffer from multifactorial neurodegenerative diseases, such as age-related macular degeneration (AMD). However, their pathological mechanisms are still poorly understood, which complicates the development of effective therapies. To improve treatment of multifactorial diseases, cell-based gene therapy can be used to increase the expression of therapeutic factors. To date, there is no approved therapy for dry AMD, including late-stage geographic atrophy. We present a treatment option for dry AMD that transfers the brain-derived neurotrophic factor (BDNF) gene into retinal pigment epithelial (RPE) cells by electroporation using the plasmid-based Sleeping Beauty (SB) transposon system. ARPE-19 cells and primary human RPE cells were co-transfected with two plasmids encoding the SB100X transposase and the transposon carrying a BDNF transcription cassette. We demonstrated efficient expression and secretion of BDNF in both RPE cell types, which were further increased in ARPE-19 cell cultures exposed to hydrogen peroxide. BDNF-transfected cells exhibited lower apoptosis rates and stimulated neurite outgrowth in human SH-SY5Y cells. This study is an important step in the development of a cell-based BDNF gene therapy that could be applied as an advanced therapy medicinal product to treat dry AMD or other degenerative retinal diseases.
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Affiliation(s)
- Larissa Mattern
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Katrin Otten
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Matthias Fuest
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Peter Walter
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Gabriele Thumann
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
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10
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Rommel MG, Walz L, Fotopoulou F, Kohlscheen S, Schenk F, Miskey C, Botezatu L, Krebs Y, Voelker IM, Wittwer K, Holland-Letz T, Ivics Z, von Messling V, Essers MA, Milsom MD, Pfaller CK, Modlich U. Influenza A virus infection instructs hematopoiesis to megakaryocyte-lineage output. Cell Rep 2022; 41:111447. [DOI: 10.1016/j.celrep.2022.111447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022] Open
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11
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Ebenig A, Muraleedharan S, Kazmierski J, Todt D, Auste A, Anzaghe M, Gömer A, Postmus D, Gogesch P, Niles M, Plesker R, Miskey C, Gellhorn Serra M, Breithaupt A, Hörner C, Kruip C, Ehmann R, Ivics Z, Waibler Z, Pfaender S, Wyler E, Landthaler M, Kupke A, Nouailles G, Goffinet C, Brown RJP, Mühlebach MD. Vaccine-associated enhanced respiratory pathology in COVID-19 hamsters after TH2-biased immunization. Cell Rep 2022; 40:111214. [PMID: 35952673 PMCID: PMC9346010 DOI: 10.1016/j.celrep.2022.111214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/17/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022] Open
Abstract
Vaccine-associated enhanced respiratory disease (VAERD) is a severe complication for some respiratory infections. To investigate the potential for VAERD induction in coronavirus disease 2019 (COVID-19), we evaluate two vaccine leads utilizing a severe hamster infection model: a T helper type 1 (TH1)-biased measles vaccine-derived candidate and a TH2-biased alum-adjuvanted, non-stabilized spike protein. The measles virus (MeV)-derived vaccine protects the animals, but the protein lead induces VAERD, which can be alleviated by dexamethasone treatment. Bulk transcriptomic analysis reveals that our protein vaccine prepares enhanced host gene dysregulation in the lung, exclusively up-regulating mRNAs encoding the eosinophil attractant CCL-11, TH2-driving interleukin (IL)-19, or TH2 cytokines IL-4, IL-5, and IL-13. Single-cell RNA sequencing (scRNA-seq) identifies lung macrophages or lymphoid cells as sources, respectively. Our findings imply that VAERD is caused by the concerted action of hyperstimulated macrophages and TH2 cytokine-secreting lymphoid cells and potentially links VAERD to antibody-dependent enhancement (ADE). In summary, we identify the cytokine drivers and cellular contributors that mediate VAERD after TH2-biased vaccination.
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Affiliation(s)
- Aileen Ebenig
- Product Testing of IVMPs, Div. of Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Samada Muraleedharan
- Product Testing of IVMPs, Div. of Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Julia Kazmierski
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr-University, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany
| | - Arne Auste
- Product Testing of IVMPs, Div. of Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany; German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Martina Anzaghe
- Div. of Immunology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - André Gömer
- Department for Molecular and Medical Virology, Ruhr-University, 44801 Bochum, Germany; Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Dylan Postmus
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Patricia Gogesch
- Div. of Immunology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Marc Niles
- Div. of Immunology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Roland Plesker
- Animal Facilities, Div. Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Csaba Miskey
- Div. of Medical Biotechnology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | | | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Cindy Hörner
- Product Testing of IVMPs, Div. of Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany; German Center for Infection Research, Gießen-Marburg-Langen, Germany
| | - Carina Kruip
- Product Testing of IVMPs, Div. of Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Rosina Ehmann
- Institute for Microbiology, Bundeswehr, 80937 München, Germany
| | - Zoltan Ivics
- Div. of Medical Biotechnology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Zoe Waibler
- Div. of Immunology, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Stephanie Pfaender
- Department for Molecular and Medical Virology, Ruhr-University, 44801 Bochum, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115 Berlin, Germany; IRI Life Sciences, Institute for Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Alexandra Kupke
- German Center for Infection Research, Gießen-Marburg-Langen, Germany; Institute for Virology, Phillipps-University, 35043 Marburg, Germany
| | - Geraldine Nouailles
- Division of Pulmonary Inflammation, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Richard J P Brown
- Virus Tropism and Immunogenicity, Div. of Veterinary Medicine, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Michael D Mühlebach
- Product Testing of IVMPs, Div. of Veterinary Medicines, Paul-Ehrlich-Institut, 63225 Langen, Germany; German Center for Infection Research, Gießen-Marburg-Langen, Germany.
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12
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Miskey C, Botezatu L, Temiz NA, Gogol-Doring A, Bartha A, Gyorffy B, Largaespada DA, Ivics Z, Sebe A. In Vitro Insertional Mutagenesis Screen Identifies Novel Genes Driving Breast Cancer Metastasis. Mol Cancer Res 2022; 20:1502-1515. [PMID: 35687718 DOI: 10.1158/1541-7786.mcr-21-0772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/07/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Metastasis, a complex, multistep process, is responsible for the overwhelming majority of cancer-related deaths. Despite its devastating consequences, it is not possible to effectively treat cancer that has spread to vital organs, the mechanisms leading to metastasis are still poorly understood and the catalogue of metastasis promoting genes is still incomprehensive. To identify new driver genes of metastasis development, we performed an in vitro Sleeping Beauty transposon-based forward genetic screen in non-metastatic SKBR3 human breast cancer cells. Boyden chamber- based matrix invasion assays were used to harvest cells that acquired a de novo invasive phenotype. Using targeted RNA-sequencing data from eighteen pools of invasive cells, we carried out a gene-centric candidate gene prediction and identified established and novel metastasis driver genes. Analysis of these genes revealed their association with metastasis related processes and we further established their clinical relevance in metastatic breast cancer. Two novel candidate genes, GIT2 and MUSK, were functionally validated as metastasis driver genes in a series of in vitro and in vivo experimental metastasis models. We propose that our robust and scalable approach will be a useful addition to the toolkit of methodological resources used to identify genes driving cancer metastasis. Implications: Novel metastasis drivers were identified in a human breast cancer cell line by performing an in vitro, Sleeping Beauty transposon-based forward genetic screen and an RNA fusion-based candidate gene prediction.
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Affiliation(s)
| | | | - Nuri A Temiz
- University of Minnesota, Minneapolis, MN, United States
| | | | | | - Balazs Gyorffy
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Budapest, Hungary
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13
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Bexte T, Botezatu L, Miskey C, Reindl LM, Campe J, Mertlitz S, Gebel V, Schubert R, Cremer A, Rettinger E, Prommersberger S, Penack O, Wels WS, Hudecek M, Ivics Z, Ullrich E. High antileukemic efficiency of CD19-CAR NK cells engineered with
Sleeping Beauty transposon vectors. KLINISCHE PADIATRIE 2022. [DOI: 10.1055/s-0042-1748751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- T Bexte
- Experimental Immunology, Department for Children and Adolescents
Medicine, Hospital of the Goethe University Frankfurt, 60590,
Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main,
Germany
- University Cancer Center (UCT) Frankfurt-Marburg
| | - L Botezatu
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen,
Germany
| | - C Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen,
Germany
| | - LM Reindl
- Experimental Immunology, Department for Children and Adolescents
Medicine, Hospital of the Goethe University Frankfurt, 60590,
Germany
| | - J Campe
- Experimental Immunology, Department for Children and Adolescents
Medicine, Hospital of the Goethe University Frankfurt, 60590,
Germany
| | - S Mertlitz
- Charité Universitätsmedizin Berlin, Berlin,
Germany
| | - V Gebel
- Experimental Immunology, Department for Children and Adolescents
Medicine, Hospital of the Goethe University Frankfurt, 60590,
Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main,
Germany
- University Cancer Center (UCT) Frankfurt-Marburg
| | - R Schubert
- Department for Children and Adolescents, University Hospital,
Goethe-University, Frankfurt, Germany
| | - A Cremer
- Department of Hematology and Oncology, Johann Wolfgang Goethe
University, Frankfurt, Germany
| | - E Rettinger
- Division of Stem Cell Transplantation and Immunology, Department of
Children and Adolescent Medicine, Hospital of the Goethe University Frankfurt,
60590, Germany
| | - S Prommersberger
- Department of Internal Medicine II, University Hospital
Würzburg, Würzburg, Germany
| | - O Penack
- Charité Universitätsmedizin Berlin, Berlin,
Germany
| | - WS Wels
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main,
Germany
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental
Therapy, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz,
Frankfurt am Main, Germany
| | - M Hudecek
- Department of Internal Medicine II, University Hospital
Würzburg, Würzburg, Germany
| | - Z Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen,
Germany
| | - E Ullrich
- Experimental Immunology, Department for Children and Adolescents
Medicine, Hospital of the Goethe University Frankfurt, 60590,
Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main,
Germany
- University Cancer Center (UCT) Frankfurt-Marburg
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz,
Frankfurt am Main, Germany
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14
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Prommersberger S, Monjezi R, Botezatu L, Miskey C, Amberger M, Mestermann K, Hudecek M, Ivics Z. Generation of CAR-T Cells with Sleeping Beauty Transposon Gene Transfer. Methods Mol Biol 2022; 2521:41-66. [PMID: 35732992 DOI: 10.1007/978-1-0716-2441-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Human T lymphocytes that transgenically express a chimeric antigen receptor (CAR) have proven efficacy and safety in gene- and cell-based immunotherapy of certain hematological cancers. Appropriate gene vectors and methods of genetic engineering are required for therapeutic cell products to be biologically potent and their manufacturing to be economically viable. Transposon-based gene transfer satisfies these needs, and is currently being evaluated in clinical trials. In this protocol we describe the basic Sleeping Beauty (SB) transposon vector components required for stable gene integration in human cells, with special emphasis on minicircle DNA vectors and the use of synthetic mRNA. We provide a protocol for functional validation of the vector components in cultured human cell lines on the basis of fluorescent reporter gene expression. Finally, we provide a protocol for CAR-T cell engineering and describe assays that address transgene expression, biological potency and genomic vector copy numbers in polyclonal cell populations. Because transposons allow virus-free gene transfer with naked nucleic acids, the protocol can be adopted by any laboratory equipped with biological safety level S1 facilities.
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Affiliation(s)
| | - Razieh Monjezi
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | | | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | | | - Katrin Mestermann
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Michael Hudecek
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
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15
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Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
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Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
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16
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Lapaillerie D, Lelandais B, Mauro E, Lagadec F, Tumiotto C, Miskey C, Ferran G, Kuschner N, Calmels C, Métifiot M, Rooryck C, Ivics Z, Ruff M, Zimmer C, Lesbats P, Toutain J, Parissi V. Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75. Nucleic Acids Res 2021; 49:11241-11256. [PMID: 34634812 PMCID: PMC8565322 DOI: 10.1093/nar/gkab886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
The stable insertion of the retroviral genome into the host chromosomes requires the association between integration complexes and cellular chromatin via the interaction between retroviral integrase and the nucleosomal target DNA. This final association may involve the chromatin-binding properties of both the retroviral integrase and its cellular cofactor LEDGF/p75. To investigate this and better understand the LEDGF/p75-mediated chromatin tethering of HIV-1 integrase, we used a combination of biochemical and chromosome-binding assays. Our study revealed that retroviral integrase has an intrinsic ability to bind and recognize specific chromatin regions in metaphase even in the absence of its cofactor. Furthermore, this integrase chromatin-binding property was modulated by the interaction with its cofactor LEDGF/p75, which redirected the enzyme to alternative chromosome regions. We also better determined the chromatin features recognized by each partner alone or within the functional intasome, as well as the chronology of efficient LEDGF/p75-mediated targeting of HIV-1 integrase to chromatin. Our data support a new chromatin-binding function of integrase acting in concert with LEDGF/p75 for the optimal association with the nucleosomal substrate. This work also provides additional information about the behavior of retroviral integration complexes in metaphase chromatin and the mechanism of action of LEDGF/p75 in this specific context.
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Affiliation(s)
- Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Benoît Lelandais
- Imaging and modeling unit, Computational Biology Department, Institut Pasteur, Paris, France
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Floriane Lagadec
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Camille Tumiotto
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Csaba Miskey
- Paul-Ehrlich-Institute, division of medical biotechnology, Langen, Germany
| | | | | | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Mathieu Métifiot
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | | | - Zoltan Ivics
- Paul-Ehrlich-Institute, division of medical biotechnology, Langen, Germany
| | - Marc Ruff
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale intégrative, UDS, U596 INSERM, UMR7104, CNRS, Strasbourg, France
| | - Christophe Zimmer
- Imaging and modeling unit, Computational Biology Department, Institut Pasteur, Paris, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Jérôme Toutain
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
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Zahn T, Mhedhbi I, Hein S, Raupach J, Miskey C, Husria Y, Bayanga K, Bartel D, Vieths S, Ivics Z, Oberle D, Keller‐Stanislawski B, Herrlein M, Maier TJ, Hildt E. Persistence of infectious SARS-CoV-2 particles for up to 37 days in patients with mild COVID-19. Allergy 2021; 77:2053-2066. [PMID: 34637150 PMCID: PMC8652783 DOI: 10.1111/all.15138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/19/2021] [Accepted: 10/01/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND People suffering from COVID-19 are typically considered non-infectious 14 days after diagnosis if symptoms have disappeared for at least 48 h. We describe three patients who independently acquired their infection. These three patients experienced mild COVID-19 and completely recovered symptomatically within 10 days, but remained PCR-positive in deep pharyngeal samples for at least 38 days. We attempted to isolate virus from pharyngeal swabs to investigate whether these patients still carried infectious virus. METHODS Infectious virus was amplified in Vero E6 cells and characterized by electron microscopy and WGS. The immune response was investigated by ELISA and peptide arrays. RESULTS In all three cases, infectious and replication-competent virus was isolated and amplified in Vero E6 cells. Virus replication was detected by RT-PCR and immunofluorescence microscopy. Electron microscopy confirmed the formation of intact SARS-CoV-2 particles. For a more detailed analysis, all three isolates were characterized by whole-genome sequencing (WGS). The sequence data revealed that the isolates belonged to the 20A or 20C clade, and two mutations in ORF8 were identified among other mutations that could be relevant for establishing a long-term infection. Characterization of the humoral immune response in comparison to patients that had fully recovered from mild COVID-19 revealed a lack of antibodies binding to sequential epitopes of the receptor-binding domain (RBD) for the long-term infected patients. CONCLUSION Thus, a small portion of COVID-19 patients displays long-term infectivity and termination of quarantine periods after 14 days, without PCR-based testing, should be reconsidered critically.
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Affiliation(s)
- Tobias Zahn
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Ines Mhedhbi
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Sascha Hein
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Jan Raupach
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Csaba Miskey
- Division of Medical Biotechnology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Younes Husria
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Kathrin Bayanga
- Division of Transfusion Medicine Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Detlef Bartel
- Division of Allergology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Stefan Vieths
- Management board Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Doris Oberle
- Division of Pharmacovigilance Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Brigitte Keller‐Stanislawski
- Division of Pharmacovigilance Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Marie‐Luise Herrlein
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Thorsten Jürgen Maier
- Division of Pharmacovigilance Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
| | - Eberhard Hildt
- Division of Virology Paul‐Ehrlich‐InstitutFederal Institute for Vaccines and Biomedicines Langen Germany
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18
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Miskei M, Horváth A, Viola L, Varga L, Nagy É, Feró O, Karányi Z, Roszik J, Miskey C, Ivics Z, Székvölgyi L. Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome. Comput Struct Biotechnol J 2021; 19:4032-4041. [PMID: 34377368 PMCID: PMC8327481 DOI: 10.1016/j.csbj.2021.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Throughout evolution, DNA transposons provide a recurrent supply of genetic information to give rise to novel gene functions by fusion of their transposase domain to various domains of host-encoded proteins. One of these "domesticated", transposase-derived factors is SETMAR/Metnase which is a naturally occurring fusion protein that consists of a histone-lysine methyltransferase domain and an HsMar1 transposase. To elucidate the biological role of SETMAR, it is crucial to identify genomic targets to which SETMAR specifically binds and link these sites to the regulation of gene expression. Herein, we mapped the genomic landscape of SETMAR binding in a near-haploid human leukemia cell line (HAP1) in order to identify on-target and off-target binding sites at high resolution and to elucidate their role in terms of gene expression. Our analysis revealed a perfect correlation between SETMAR and inverted terminal repeats (ITRs) of HsMar1 transposon remnants, which are considered as natural target sites for SETMAR binding. However, we did not detect any untargeted events at non-ITR sequences, calling into question previously proposed off-target binding sites. We identified sequence fidelity of the ITR motif as a key factor for determining the binding affinity of SETMAR for chromosomes, as higher conservation of ITR sequences resulted in increased affinity for chromatin and stronger repression of SETMAR-bound gene loci. These associations highlight how SETMAR's chromatin binding fine-tune gene regulatory networks in human tumour cells.
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Affiliation(s)
- Márton Miskei
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Adrienn Horváth
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Lívia Viola
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Laura Varga
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Éva Nagy
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Orsolya Feró
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Zsolt Karányi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
- Department of Internal Medicine, Faculty of Medicine, University of Debrecen, Hungary
| | - Jason Roszik
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Centre, University of Texas, USA
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen D-63225, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen D-63225, Germany
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
- Faculty of Pharmacy, University of Debrecen, Hungary
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19
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Shen D, Gao B, Miskey C, Chen C, Sang Y, Zong W, Wang S, Wang Y, Wang X, Ivics Z, Song C. Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates. Genome Biol Evol 2021; 12:1060-1073. [PMID: 32602886 DOI: 10.1093/gbe/evaa135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.
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Affiliation(s)
- Dan Shen
- College of Animal Science & Technology, Yangzhou University, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, China
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, China
| | - Saisai Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, China
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20
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Shen D, Song C, Miskey C, Chan S, Guan Z, Sang Y, Wang Y, Chen C, Wang X, Müller F, Ivics Z, Gao B. A native, highly active Tc1/mariner transposon from zebrafish (ZB) offers an efficient genetic manipulation tool for vertebrates. Nucleic Acids Res 2021; 49:2126-2140. [PMID: 33638993 PMCID: PMC7913693 DOI: 10.1093/nar/gkab045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
New genetic tools and strategies are currently under development to facilitate functional genomics analyses. Here, we describe an active member of the Tc1/mariner transposon superfamily, named ZB, which invaded the zebrafish genome very recently. ZB exhibits high activity in vertebrate cells, in the range of those of the widely used transposons piggyBac (PB), Sleeping Beauty (SB) and Tol2. ZB has a similar structural organization and target site sequence preference to SB, but a different integration profile with respect to genome-wide preference among mammalian functional annotation features. Namely, ZB displays a preference for integration into transcriptional regulatory regions of genes. Accordingly, we demonstrate the utility of ZB for enhancer trapping in zebrafish embryos and in the mouse germline. These results indicate that ZB may be a powerful tool for genetic manipulation in vertebrate model species.
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Affiliation(s)
- Dan Shen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Shuheng Chan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhongxia Guan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen 63225, Germany
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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21
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Gao B, Zong W, Miskey C, Ullah N, Diaby M, Chen C, Wang X, Ivics Z, Song C. Intruder (DD38E), a recently evolved sibling family of DD34E/Tc1 transposons in animals. Mob DNA 2020; 11:32. [PMID: 33303022 PMCID: PMC7731502 DOI: 10.1186/s13100-020-00227-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A family of Tc1/mariner transposons with a characteristic DD38E triad of catalytic amino acid residues, named Intruder (IT), was previously discovered in sturgeon genomes, but their evolutionary landscapes remain largely unknown. RESULTS Here, we comprehensively investigated the evolutionary profiles of ITs, and evaluated their cut-and-paste activities in cells. ITs exhibited a narrow taxonomic distribution pattern in the animal kingdom, with invasions into two invertebrate phyla (Arthropoda and Cnidaria) and three vertebrate lineages (Actinopterygii, Agnatha, and Anura): very similar to that of the DD36E/IC family. Some animal orders and species seem to be more hospitable to Tc1/mariner transposons, one order of Amphibia and seven Actinopterygian orders are the most common orders with horizontal transfer events and have been invaded by all four families (DD38E/IT, DD35E/TR, DD36E/IC and DD37E/TRT) of Tc1/mariner transposons, and eight Actinopterygii species were identified as the major hosts of these families. Intact ITs have a total length of 1.5-1.7 kb containing a transposase gene flanked by terminal inverted repeats (TIRs). The phylogenetic tree and sequence identity showed that IT transposases were most closely related to DD34E/Tc1. ITs have been involved in multiple events of horizontal transfer in vertebrates and have invaded most lineages recently (< 5 million years ago) based on insertion age analysis. Accordingly, ITs presented high average sequence identity (86-95%) across most vertebrate species, suggesting that some are putatively active. ITs can transpose in human HeLa cells, and the transposition efficiency of consensus TIRs was higher than that of the TIRs of natural isolates. CONCLUSIONS We conclude that DD38E/IT originated from DD34E/Tc1 and can be detected in two invertebrate phyla (Arthropoda and Cnidaria), and in three vertebrate lineages (Actinopterygii, Agnatha and Anura). IT has experienced multiple HT events in animals, dominated by recent amplifications in most species and has high identity among vertebrate taxa. Our reconstructed IT transposon vector designed according to the sequence from the "cat" genome showed high cut-and-paste activity. The data suggest that IT has been acquired recently and is active in many species. This study is meaningful for understanding the evolution of the Tc1/mariner superfamily members and their hosts.
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Affiliation(s)
- Bo Gao
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Numan Ullah
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Mohamed Diaby
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, 225009, Jiangsu, China.
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22
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Brown RJP, Tegtmeyer B, Sheldon J, Khera T, Anggakusuma, Todt D, Vieyres G, Weller R, Joecks S, Zhang Y, Sake S, Bankwitz D, Welsch K, Ginkel C, Engelmann M, Gerold G, Steinmann E, Yuan Q, Ott M, Vondran FWR, Krey T, Ströh LJ, Miskey C, Ivics Z, Herder V, Baumgärtner W, Lauber C, Seifert M, Tarr AW, McClure CP, Randall G, Baktash Y, Ploss A, Thi VLD, Michailidis E, Saeed M, Verhoye L, Meuleman P, Goedecke N, Wirth D, Rice CM, Pietschmann T. Liver-expressed Cd302 and Cr1l limit hepatitis C virus cross-species transmission to mice. Sci Adv 2020; 6:eabd3233. [PMID: 33148654 PMCID: PMC7673688 DOI: 10.1126/sciadv.abd3233] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/21/2020] [Indexed: 12/06/2023]
Abstract
Hepatitis C virus (HCV) has no animal reservoir, infecting only humans. To investigate species barrier determinants limiting infection of rodents, murine liver complementary DNA library screening was performed, identifying transmembrane proteins Cd302 and Cr1l as potent restrictors of HCV propagation. Combined ectopic expression in human hepatoma cells impeded HCV uptake and cooperatively mediated transcriptional dysregulation of a noncanonical program of immunity genes. Murine hepatocyte expression of both factors was constitutive and not interferon inducible, while differences in liver expression and the ability to restrict HCV were observed between the murine orthologs and their human counterparts. Genetic ablation of endogenous Cd302 expression in human HCV entry factor transgenic mice increased hepatocyte permissiveness for an adapted HCV strain and dysregulated expression of metabolic process and host defense genes. These findings highlight human-mouse differences in liver-intrinsic antiviral immunity and facilitate the development of next-generation murine models for preclinical testing of HCV vaccine candidates.
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Affiliation(s)
- Richard J P Brown
- Division of Veterinary Medicine, Paul Ehrlich Institute, 63225 Langen, Germany.
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Birthe Tegtmeyer
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Julie Sheldon
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Tanvi Khera
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Department of Gastroenterology and Hepatology, Faculty of Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Anggakusuma
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Department of Research and Development, uniQure Biopharma, BV, Amsterdam, Netherlands
| | - Daniel Todt
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Ruhr University Bochum, Faculty of Medicine, Department for Molecular and Medical Virology, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany
| | - Gabrielle Vieyres
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Romy Weller
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Sebastian Joecks
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Yudi Zhang
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Svenja Sake
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Dorothea Bankwitz
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Kathrin Welsch
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Corinne Ginkel
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Michael Engelmann
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Ruhr University Bochum, Faculty of Medicine, Department for Molecular and Medical Virology, Bochum, Germany
| | - Gisa Gerold
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
- Department of Clinical Microbiology, Virology and Wallenberg Center for Molecular Medicine (WCMM), Umeå University, 901 85 Umeå, Sweden
| | - Eike Steinmann
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Ruhr University Bochum, Faculty of Medicine, Department for Molecular and Medical Virology, Bochum, Germany
| | - Qinggong Yuan
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
- Twincore Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30625 Hannover, Germany
- Twincore Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
| | - Florian W R Vondran
- Department of General, Visceral, and Transplant Surgery, Hannover Medical School, 30625 Hannover, Germany
- German Centre for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Thomas Krey
- German Centre for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Luisa J Ströh
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany
| | - Vanessa Herder
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Chris Lauber
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Alexander W Tarr
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
- School of Life Sciences and NIHR Nottingham BRC, University of Nottingham, Nottingham, UK
| | - C Patrick McClure
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
- School of Life Sciences and NIHR Nottingham BRC, University of Nottingham, Nottingham, UK
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, IL 60439, USA
| | - Yasmine Baktash
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Parc Científic de Barcelona, Carrer del Catedràtic Agustín Escardino 9, 46980 Paterna, Valencia, Spain
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Viet Loan Dao Thi
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Schaller Research Group at Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Eleftherios Michailidis
- Schaller Research Group at Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Department of Biochemistry, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Lieven Verhoye
- Laboratory of Liver Infectious Diseases, Ghent University, Ghent, Belgium
| | - Philip Meuleman
- Laboratory of Liver Infectious Diseases, Ghent University, Ghent, Belgium
| | - Natascha Goedecke
- Helmholtz Centre for Infection Research, Division Model Systems for Infection and Immunity, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Dagmar Wirth
- Helmholtz Centre for Infection Research, Division Model Systems for Infection and Immunity, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Pietschmann
- Institute for Experimental Virology, Centre for Experimental and Clinical Infection Research, Twincore, Feodor-Lynen-Strasse 7, 30625 Hannover, Germany.
- German Centre for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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23
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Kesselring L, Miskey C, Zuliani C, Querques I, Kapitonov V, Laukó A, Fehér A, Palazzo A, Diem T, Lustig J, Sebe A, Wang Y, Dinnyés A, Izsvák Z, Barabas O, Ivics Z. A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming. Nucleic Acids Res 2020; 48:316-331. [PMID: 31777924 PMCID: PMC6943129 DOI: 10.1093/nar/gkz1119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
The Sleeping Beauty (SB) transposon is an advanced tool for genetic engineering and a useful model to investigate cut-and-paste DNA transposition in vertebrate cells. Here, we identify novel SB transposase mutants that display efficient and canonical excision but practically unmeasurable genomic re-integration. Based on phylogenetic analyses, we establish compensating amino acid replacements that fully rescue the integration defect of these mutants, suggesting epistasis between these amino acid residues. We further show that the transposons excised by the exc+/int− transposase mutants form extrachromosomal circles that cannot undergo a further round of transposition, thereby representing dead-end products of the excision reaction. Finally, we demonstrate the utility of the exc+/int− transposase in cassette removal for the generation of reprogramming factor-free induced pluripotent stem cells. Lack of genomic integration and formation of transposon circles following excision is reminiscent of signal sequence removal during V(D)J recombination, and implies that cut-and-paste DNA transposition can be converted to a unidirectional process by a single amino acid change.
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Affiliation(s)
- Lisa Kesselring
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Vladimir Kapitonov
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | | | - Anita Fehér
- BioTalentum Ltd, Gödöllő, 2100 Gödöllő, Hungary
| | - Antonio Palazzo
- Department of Biology, University of Bari 'Aldo Moro', Italy
| | - Tanja Diem
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Janna Lustig
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Attila Sebe
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Yongming Wang
- Mobile DNA, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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24
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Kovač A, Miskey C, Menzel M, Grueso E, Gogol-Döring A, Ivics Z. RNA-guided retargeting of S leeping Beauty transposition in human cells. eLife 2020; 9:e53868. [PMID: 32142408 PMCID: PMC7077980 DOI: 10.7554/elife.53868] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
An ideal tool for gene therapy would enable efficient gene integration at predetermined sites in the human genome. Here we demonstrate biased genome-wide integration of the Sleeping Beauty (SB) transposon by combining it with components of the CRISPR/Cas9 system. We provide proof-of-concept that it is possible to influence the target site selection of SB by fusing it to a catalytically inactive Cas9 (dCas9) and by providing a single guide RNA (sgRNA) against the human Alu retrotransposon. Enrichment of transposon integrations was dependent on the sgRNA, and occurred in an asymmetric pattern with a bias towards sites in a relatively narrow, 300 bp window downstream of the sgRNA targets. Our data indicate that the targeting mechanism specified by CRISPR/Cas9 forces integration into genomic regions that are otherwise poor targets for SB transposition. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
- Adrian Kovač
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
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25
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Zhang W, Muck-Hausl M, Wang J, Sun C, Gebbing M, Miskey C, Ivics Z, Izsvak Z, Ehrhardt A. Correction: Integration Profile and Safety of an Adenovirus Hybrid-Vector Utilizing Hyperactive Sleeping Beauty Transposase for Somatic Integration. PLoS One 2020; 15:e0228902. [PMID: 32017798 PMCID: PMC6999872 DOI: 10.1371/journal.pone.0228902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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26
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Hernandez M, Recalde S, Garcia-Garcia L, Bezunartea J, Miskey C, Johnen S, Diarra S, Sebe A, Rodriguez-Madoz JR, Pouillot S, Marie C, Izsvák Z, Scherman D, Kropp M, Prosper F, Thumann G, Ivics Z, Garcia-Layana A, Fernandez-Robredo P. Preclinical Evaluation of a Cell-Based Gene Therapy Using the Sleeping Beauty Transposon System in Choroidal Neovascularization. Mol Ther Methods Clin Dev 2019; 15:403-417. [PMID: 31890733 PMCID: PMC6909167 DOI: 10.1016/j.omtm.2019.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 01/05/2023]
Abstract
Age-related macular degeneration (AMD) is a progressive retinal disorder characterized by imbalanced pro- and antiangiogenic signals. The aim of this study was to evaluate the effect of ex vivo cell-based gene therapy with stable expression of human pigment epithelium-derived factor (PEDF) release using the non-viral Sleeping Beauty (SB100X) transposon system delivered by miniplasmids free of antibiotic resistance markers (pFAR4). Retinal pigment epithelial (RPE) cells and iris pigment epithelial (IPE) cells were co-transfected with pFAR4-inverted terminal repeats (ITRs) CMV-PEDF-BGH and pFAR4-CMV-SB100X-SV40 plasmids. Laser-induced choroidal neovascularization (CNV) was performed in rats, and transfected primary cells (transfected RPE [tRPE] and transfected IPE [tIPE] cells) were injected into the subretinal space. The leakage and CNV areas, vascular endothelial growth factor (VEGF), PEDF protein expression, metalloproteinases 2 and 9 (MMP-2/9), and microglial/macrophage markers were measured. Injection with tRPE/IPE cells significantly reduced the leakage area at 7 and 14 days and the CNV area at 7 days. There was a significant increase in PEDF and the PEDF/VEGF ratio with tRPE cells and a reduction in the MMP-2 activity. Our data demonstrated that ex vivo non-viral gene therapy reduces CNV and could be an effective and safe therapeutic option for angiogenic retinal diseases.
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Affiliation(s)
- Maria Hernandez
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Sergio Recalde
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Laura Garcia-Garcia
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Jaione Bezunartea
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Sabine Diarra
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Attila Sebe
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Juan Roberto Rodriguez-Madoz
- Regenerative Medicine Program, Center for Applied Medical Research (CIMA), University of Navarra, IdiSNA, Pamplona 31008, Spain
| | | | - Corinne Marie
- Université de Paris, UTCBS, CNRS, INSERM, F-75006 Paris, France
- Chimie ParisTech, PSL Research University, F-75005 Paris, France
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Daniel Scherman
- Université de Paris, UTCBS, CNRS, INSERM, F-75006 Paris, France
| | - Martina Kropp
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Felipe Prosper
- Regenerative Medicine Program, Center for Applied Medical Research (CIMA), University of Navarra, IdiSNA, Pamplona 31008, Spain
- Area of Cell Therapy, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona 31008, Spain
| | - Gabriele Thumann
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Alfredo Garcia-Layana
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Patricia Fernandez-Robredo
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
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27
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Querques I, Mades A, Zuliani C, Miskey C, Alb M, Grueso E, Machwirth M, Rausch T, Einsele H, Ivics Z, Hudecek M, Barabas O. A highly soluble Sleeping Beauty transposase improves control of gene insertion. Nat Biotechnol 2019; 37:1502-1512. [PMID: 31685959 PMCID: PMC6894935 DOI: 10.1038/s41587-019-0291-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/13/2019] [Indexed: 12/21/2022]
Abstract
The Sleeping Beauty (SB) transposon system is an efficient non-viral gene transfer tool in mammalian cells but its broad use has been hampered by uncontrolled transposase gene activity from DNA vectors, posing a risk for genome instability, and by the inability to use transposase protein directly. Here, we used rational protein design based on the crystal structure of the hyperactive SB100X variant to create an SB transposase (hsSB) with enhanced solubility and stability. We demonstrate that hsSB can be delivered with transposon DNA to genetically modify cell lines and embryonic, hematopoietic and induced pluripotent stem cells (iPSCs), overcoming uncontrolled transposase activity. We used hsSB to generate chimeric antigen receptor (CAR) T-cells, which exhibit potent anti-tumor activity in vitro and in xenograft mice. We found that hsSB spontaneously penetrates cells, enabling modification of iPSCs and generation of CAR-T cells without the use of transfection reagents. Titration of hsSB to modulate genomic integration frequency achieved as few as two integrations per genome.
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Affiliation(s)
- Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Mades
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Miriam Alb
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Esther Grueso
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Markus Machwirth
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Tobias Rausch
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Michael Hudecek
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany.
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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28
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Clauss J, Obenaus M, Miskey C, Ivics Z, Izsvák Z, Uckert W, Bunse M. Efficient Non-Viral T-Cell Engineering by Sleeping Beauty Minicircles Diminishing DNA Toxicity and miRNAs Silencing the Endogenous T-Cell Receptors. Hum Gene Ther 2019; 29:569-584. [PMID: 29562762 DOI: 10.1089/hum.2017.136] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transposon-based vectors have entered clinical trials as an alternative to viral vectors for genetic engineering of T cells. However, transposon vectors require DNA transfection into T cells, which were found to cause adverse effects. T-cell viability was decreased in a dose-dependent manner, and DNA-transfected T cells showed a delayed response upon T-cell receptor (TCR) stimulation with regard to blast formation, proliferation, and surface expression of CD25 and CD28. Gene expression analysis demonstrated a DNA-dependent induction of a type I interferon response and interferon-β upregulation. By combining Sleeping Beauty transposon minicircle vectors with SB100X transposase-encoding RNA, it was possible to reduce the amount of total DNA required, and stable expression of therapeutic TCRs was achieved in >50% of human T cells without enrichment. The TCR-engineered T cells mediated effective tumor cell killing and cytokine secretion upon antigen-specific stimulation. Additionally, the Sleeping Beauty transposon system was further improved by miRNAs silencing the endogenous TCR chains. These miRNAs increased the surface expression of the transgenic TCR, diminished mispairing with endogenous TCR chains, and enhanced antigen-specific T-cell functionality. This approach facilitates the rapid non-viral generation of highly functional, engineered T cells for immunotherapy.
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Affiliation(s)
- Julian Clauss
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Berlin, Germany
| | - Matthias Obenaus
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Berlin, Germany .,2 Charité Universitätsmedizin Berlin , Campus Virchow-Klinikum, Berlin, Germany
| | - Csaba Miskey
- 3 Division of Medical Biotechnology, Paul Ehrlich-Institut , Langen, Germany
| | - Zoltán Ivics
- 3 Division of Medical Biotechnology, Paul Ehrlich-Institut , Langen, Germany
| | - Zsuzsanna Izsvák
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Berlin, Germany .,4 Berlin Institute of Health , Berlin, Germany
| | - Wolfgang Uckert
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Berlin, Germany .,4 Berlin Institute of Health , Berlin, Germany .,5 Institute of Biology, Humboldt-Universität zu Berlin , Berlin, Germany
| | - Mario Bunse
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association , Berlin, Germany
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29
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Palazzo A, Lorusso P, Miskey C, Walisko O, Gerbino A, Marobbio CMT, Ivics Z, Marsano RM. Transcriptionally promiscuous "blurry" promoters in Tc1/ mariner transposons allow transcription in distantly related genomes. Mob DNA 2019; 10:13. [PMID: 30988701 PMCID: PMC6446368 DOI: 10.1186/s13100-019-0155-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/26/2019] [Indexed: 12/04/2022] Open
Abstract
Background We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined “blurry”, able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and bacteria. In order to clarify whether the blurry promoter is a specific feature of the Bari transposon family, we have extended this study to promoters isolated from three additional DNA transposon and from two additional LTR retrotransposons. Results Here we show that the blurry promoter is also a feature of two vertebrate transposable elements, Sleeping Beauty and Hsmar1, belonging to the Tc1/mariner superfamily. In contrast, this feature is not shared by the promoter of the hobo transposon, which belongs to the hAT superfamily, nor by LTR retrotransposon-derived promoters, which, in general, do not activate transcription when introduced into non-related genomes. Conclusions Our results suggest that the blurry promoter could be a shared feature of the members of the Tc1/mariner superfamily with possible evolutionary and biotechnological implications. Electronic supplementary material The online version of this article (10.1186/s13100-019-0155-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Palazzo
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy.,Present address: Laboratory of Translational Nanotechnology, "Istituto Tumori Giovanni Paolo II" I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy
| | - Patrizio Lorusso
- 1Department of Biology, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | - Csaba Miskey
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Oliver Walisko
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Andrea Gerbino
- 3Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, 70125 Bari, Italy
| | | | - Zoltán Ivics
- 2Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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30
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Guan S, Munder A, Hedtfeld S, Braubach P, Glage S, Zhang L, Lienenklaus S, Schultze A, Hasenpusch G, Garrels W, Stanke F, Miskey C, Johler SM, Kumar Y, Tümmler B, Rudolph C, Ivics Z, Rosenecker J. Self-assembled peptide-poloxamine nanoparticles enable in vitro and in vivo genome restoration for cystic fibrosis. Nat Nanotechnol 2019; 14:287-297. [PMID: 30692673 DOI: 10.1038/s41565-018-0358-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Developing safe and efficient non-viral delivery systems remains a major challenge for in vivo applications of gene therapy, especially in cystic fibrosis. Unlike conventional cationic polymers or lipids, the emerging poloxamine-based copolymers display promising in vivo gene delivery capabilities. However, poloxamines are invalid for in vitro applications and their in vivo transfection efficiency is still low compared with viral vectors. Here, we show that peptides developed by modular design approaches can spontaneously form compact and monodisperse nanoparticles with poloxamines and nucleic acids via self-assembly. Both messenger RNA and plasmid DNA expression mediated by peptide-poloxamine nanoparticles are greatly boosted in vitro and in the lungs of cystic fibrosis mice with negligible toxicity. Peptide-poloxamine nanoparticles containing integrating vectors enable successful in vitro and in vivo long-term restoration of cystic fibrosis transmembrane conductance regulator deficiency with a safe integration profile. Our dataset provides a new framework for designing non-viral gene delivery systems qualified for in vivo genetic modifications.
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Affiliation(s)
- Shan Guan
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Antje Munder
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
| | - Silke Hedtfeld
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Peter Braubach
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Silke Glage
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Longgui Zhang
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Stefan Lienenklaus
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Anja Schultze
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Wiebke Garrels
- Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Frauke Stanke
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Sarah M Johler
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Burkhard Tümmler
- Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover, German Center for Lung Research, Hannover, Germany
| | - Carsten Rudolph
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
- Ethris, Planegg, Germany
| | - Zoltan Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Joseph Rosenecker
- Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany.
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31
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Barabas O, Querques I, Zuliani C, Voigt F, Wiedemann L, Miskey C, Ivics Z. Structural and mechanistic insights into DNA transposition facilitate genetic tool development. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318094974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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32
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Holstein M, Mesa-Nuñez C, Miskey C, Almarza E, Poletti V, Schmeer M, Grueso E, Ordóñez Flores JC, Kobelt D, Walther W, Aneja MK, Geiger J, Bonig HB, Izsvák Z, Schleef M, Rudolph C, Mavilio F, Bueren JA, Guenechea G, Ivics Z. Efficient Non-viral Gene Delivery into Human Hematopoietic Stem Cells by Minicircle Sleeping Beauty Transposon Vectors. Mol Ther 2018; 26:1137-1153. [PMID: 29503198 PMCID: PMC6079369 DOI: 10.1016/j.ymthe.2018.01.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 01/08/2018] [Accepted: 01/12/2018] [Indexed: 12/26/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a non-viral gene delivery platform that combines simplicity, inexpensive manufacture, and favorable safety features in the context of human applications. However, efficient correction of hematopoietic stem and progenitor cells (HSPCs) with non-viral vector systems, including SB, demands further refinement of gene delivery techniques. We set out to improve SB gene transfer into hard-to-transfect human CD34+ cells by vectorizing the SB system components in the form of minicircles that are devoid of plasmid backbone sequences and are, therefore, significantly reduced in size. As compared to conventional plasmids, delivery of the SB transposon system as minicircle DNA is ∼20 times more efficient, and it is associated with up to a 50% reduction in cellular toxicity in human CD34+ cells. Moreover, providing the SB transposase in the form of synthetic mRNA enabled us to further increase the efficacy and biosafety of stable gene delivery into hematopoietic progenitors ex vivo. Genome-wide insertion site profiling revealed a close-to-random distribution of SB transposon integrants, which is characteristically different from gammaretroviral and lentiviral integrations in HSPCs. Transplantation of gene-marked CD34+ cells in immunodeficient mice resulted in long-term engraftment and hematopoietic reconstitution, which was most efficient when the SB transposase was supplied as mRNA and nucleofected cells were maintained for 4–8 days in culture before transplantation. Collectively, implementation of minicircle and mRNA technologies allowed us to further refine the SB transposon system in the context of HSPC gene delivery to ultimately meet clinical demands of an efficient and safe non-viral gene therapy protocol.
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Affiliation(s)
- Marta Holstein
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cristina Mesa-Nuñez
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Elena Almarza
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | | | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Juan Carlos Ordóñez Flores
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Dennis Kobelt
- Translational Oncology, Experimental and Clinical Research Center, Charité University Medicine, Berlin, Germany
| | - Wolfgang Walther
- Translational Oncology, Experimental and Clinical Research Center, Charité University Medicine, Berlin, Germany
| | | | | | - Halvard B Bonig
- Department of Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe Universität, Frankfurt, Germany
| | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - Carsten Rudolph
- ethris GmbH, Planegg, Germany; Department of Pediatrics, Ludwig Maximilian University, Munich, Germany
| | - Fulvio Mavilio
- Genethon, Evry, France; Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Juan A Bueren
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | - Guillermo Guenechea
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain; Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM) Madrid, Spain
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany.
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33
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Benleulmi MS, Matysiak J, Robert X, Miskey C, Mauro E, Lapaillerie D, Lesbats P, Chaignepain S, Henriquez DR, Calmels C, Oladosu O, Thierry E, Leon O, Lavigne M, Andreola ML, Delelis O, Ivics Z, Ruff M, Gouet P, Parissi V. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails. Retrovirology 2017; 14:54. [PMID: 29179726 PMCID: PMC5704366 DOI: 10.1186/s12977-017-0378-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/20/2017] [Indexed: 01/28/2023] Open
Abstract
Background Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein–protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. Results We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Conclusions Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin. Electronic supplementary material The online version of this article (10.1186/s12977-017-0378-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed S Benleulmi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Julien Matysiak
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Xavier Robert
- MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Stéphane Chaignepain
- UMR CNRS 5248 CBMN (Chimie Biologie des Membranes et Nanoobjets), Université de Bordeaux, 33076, Bordeaux, France
| | - Daniel R Henriquez
- Virology Program, ICBM, Faculty of Medicine, University of Chile, Santiago of Chile, Chile
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Oyindamola Oladosu
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France
| | | | - Oscar Leon
- Virology Program, ICBM, Faculty of Medicine, University of Chile, Santiago of Chile, Chile
| | - Marc Lavigne
- Dpt de Virologie, UMR 3569, CNRS, Institut Pasteur, Paris, France.,Institut Cochin-Inserm U1016-CNRS UMR8104-Université Paris Descartes, Paris, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Marie-Line Andreola
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Olivier Delelis
- LBPA, UMR8113, CNRS, ENS-Cachan, 94235, Cachan, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Marc Ruff
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Patrice Gouet
- MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, Bordeaux Cedex, France. .,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS, University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France. .,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France.
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34
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Thumann G, Harmening N, Prat-Souteyrand C, Marie C, Pastor M, Sebe A, Miskey C, Hurst LD, Diarra S, Kropp M, Walter P, Scherman D, Ivics Z, Izsvák Z, Johnen S. Engineering of PEDF-Expressing Primary Pigment Epithelial Cells by the SB Transposon System Delivered by pFAR4 Plasmids. Mol Ther Nucleic Acids 2017; 6:302-314. [PMID: 28325297 PMCID: PMC5363513 DOI: 10.1016/j.omtn.2017.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 01/14/2023]
Abstract
Neovascular age-related macular degeneration (nvAMD) is characterized by choroidal blood vessels growing into the subretinal space, leading to retinal pigment epithelial (RPE) cell degeneration and vision loss. Vessel growth results from an imbalance of pro-angiogenic (e.g., vascular endothelial growth factor [VEGF]) and anti-angiogenic factors (e.g., pigment epithelium-derived factor [PEDF]). Current treatment using intravitreal injections of anti-VEGF antibodies improves vision in about 30% of patients but may be accompanied by side effects and non-compliance. To avoid the difficulties posed by frequent intravitreal injections, we have proposed the transplantation of pigment epithelial cells modified to overexpress human PEDF. Stable transgene integration and expression is ensured by the hyperactive Sleeping Beauty transposon system delivered by pFAR4 miniplasmids, which have a backbone free of antibiotic resistance markers. We demonstrated efficient expression of the PEDF gene and an optimized PEDF cDNA sequence in as few as 5 × 103 primary cells. At 3 weeks post-transfection, PEDF secretion was significantly elevated and long-term follow-up indicated a more stable secretion by cells transfected with the optimized PEDF transgene. Analysis of transgene insertion sites in human RPE cells showed an almost random genomic distribution. The results represent an important contribution toward a clinical trial aiming at a non-viral gene therapy of nvAMD.
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Affiliation(s)
- Gabriele Thumann
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland; Laboratory of Ophthalmology, University of Geneva, 1205 Geneva, Switzerland.
| | - Nina Harmening
- Laboratory of Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
| | | | - Corinne Marie
- CNRS, Unité de Technologies Chimiques et Biologiques pour la Santé UMR 8258, 75006 Paris, France; Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS, 75006 Paris, France; INSERM, UTCBS U 1022, 75006 Paris, France; Chimie ParisTech, PSL Research University, UTCBS, 75005 Paris, France
| | - Marie Pastor
- CNRS, Unité de Technologies Chimiques et Biologiques pour la Santé UMR 8258, 75006 Paris, France; Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS, 75006 Paris, France; INSERM, UTCBS U 1022, 75006 Paris, France; Chimie ParisTech, PSL Research University, UTCBS, 75005 Paris, France
| | - Attila Sebe
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, BA2 7AY Bath, UK
| | - Sabine Diarra
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Martina Kropp
- Laboratory of Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
| | - Peter Walter
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Daniel Scherman
- CNRS, Unité de Technologies Chimiques et Biologiques pour la Santé UMR 8258, 75006 Paris, France; Université Paris Descartes, Sorbonne-Paris-Cité, UTCBS, 75006 Paris, France; INSERM, UTCBS U 1022, 75006 Paris, France; Chimie ParisTech, PSL Research University, UTCBS, 75005 Paris, France
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13092 Berlin, Germany
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
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Zhou MB, Hu H, Miskey C, Lazarow K, Ivics Z, Kunze R, Yang G, Izsvák Z, Tang DQ. Transposition of the bamboo Mariner-like element Ppmar1 in yeast. Mol Phylogenet Evol 2017; 109:367-374. [PMID: 28189615 DOI: 10.1016/j.ympev.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 12/30/2022]
Abstract
The moso bamboo genome contains the two structurally intact and thus potentially functional mariner-like elements Ppmar1 and Ppmar2. Both elements contain perfect terminal inverted repeats (TIRs) and a full-length intact transposase gene. Here we investigated whether Ppmar1 is functional in yeast (Saccharomyces cerevisiae). We have designed a two-component system consisting of a transposase expression cassette and a non-autonomous transposon on two separate plasmids. We demonstrate that the Ppmar1 transposase Pptpase1 catalyses excision of the non-autonomous Ppmar1NA element from the plasmid and reintegration at TA dinucleotide sequences in the yeast chromosomes. In addition, we generated 14 hyperactive Ppmar1 transposase variants by systematic single amino acid substitutions. The most active transposase variant, S171A, induces 10-fold more frequent Ppmar1NA excisions in yeast than the wild type transposase. The Ppmar1 transposon is a promising tool for insertion mutagenesis in moso bamboo and may be used in other plants as an alternative to the established transposon tagging systems.
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Affiliation(s)
- Ming-Bing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Hui Hu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China
| | - Csaba Miskey
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Katina Lazarow
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Zoltán Ivics
- Paul Ehrlich Institute, Paul Ehrlich Str. 51-59, 63225 Langen, Germany
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Freie Universität Berlin, 14195 Berlin, Germany
| | - Guojun Yang
- Department of Biology, University of Toronto, Mississauga, ON, Canada
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany.
| | - Ding-Qin Tang
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, China.
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Monjezi R, Miskey C, Gogishvili T, Schleef M, Schmeer M, Wegner J, Einsele H, Ivics Z, Hudecek M. 73. Enhanced Engineering of Chimeric Antigen Receptor (CAR)-Modified T Cells Using Non-Viral Sleeping Beauty Transposition from Minicircle Vectors. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)32882-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Zhang W, Muck-Hausl M, Wang J, Sun C, Gebbing M, Miskey C, Ivics Z, Izsvak Z, Ehrhardt A. Integration profile and safety of an adenovirus hybrid-vector utilizing hyperactive sleeping beauty transposase for somatic integration. PLoS One 2013; 8:e75344. [PMID: 24124483 PMCID: PMC3790794 DOI: 10.1371/journal.pone.0075344] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/11/2013] [Indexed: 12/18/2022] Open
Abstract
We recently developed adenovirus/transposase hybrid-vectors utilizing the previously described hyperactive Sleeping Beauty (SB) transposase HSB5 for somatic integration and we could show stabilized transgene expression in mice and a canine model for hemophilia B. However, the safety profile of these hybrid-vectors with respect to vector dose and genotoxicity remains to be investigated. Herein, we evaluated this hybrid-vector system in C57Bl/6 mice with escalating vector dose settings. We found that in all mice which received the hyperactive SB transposase, transgene expression levels were stabilized in a dose-dependent manner and that the highest vector dose was accompanied by fatalities in mice. To analyze potential genotoxic side-effects due to somatic integration into host chromosomes, we performed a genome-wide integration site analysis using linker-mediated PCR (LM-PCR) and linear amplification-mediated PCR (LAM-PCR). Analysis of genomic DNA samples obtained from HSB5 treated female and male mice revealed a total of 1327 unique transposition events. Overall the chromosomal distribution pattern was close-to-random and we observed a random integration profile with respect to integration into gene and non-gene areas. Notably, when using the LM-PCR protocol, 27 extra-chromosomal integration events were identified, most likely caused by transposon excision and subsequent transposition into the delivered adenoviral vector genome. In total, this study provides a careful evaluation of the safety profile of adenovirus/Sleeping Beauty transposase hybrid-vectors. The obtained information will be useful when designing future preclinical studies utilizing hybrid-vectors in small and large animal models.
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Affiliation(s)
- Wenli Zhang
- Max von Pettenkofer-Institute, Department of Virology, Ludwig-Maximilians-University Munich, Munich, Germany
- Northwest Agriculture and Forestry University, Yangling, China
| | - Martin Muck-Hausl
- Max von Pettenkofer-Institute, Department of Virology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jichang Wang
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chuanbo Sun
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Csaba Miskey
- Paul-Ehrlich-Institute, Division of Medical Biotechnology, Langen, Germany
| | - Zoltan Ivics
- Paul-Ehrlich-Institute, Division of Medical Biotechnology, Langen, Germany
| | | | - Anja Ehrhardt
- Max von Pettenkofer-Institute, Department of Virology, Ludwig-Maximilians-University Munich, Munich, Germany
- Institute for Virology and Microbiology, Center for Biomedical Education and Research, Department of Human Medicine, Faculty of Health, University Witten/Herdecke, Witten, Germany
- * E-mail:
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Jursch T, Miskey C, Izsvák Z, Ivics Z. Regulation of DNA transposition by CpG methylation and chromatin structure in human cells. Mob DNA 2013; 4:15. [PMID: 23676100 PMCID: PMC3680223 DOI: 10.1186/1759-8753-4-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/19/2013] [Indexed: 12/25/2022] Open
Abstract
Background The activity of transposable elements can be regulated by different means. DNA CpG methylation is known to decrease or inhibit transpositional activity of diverse transposons. However, very surprisingly, it was previously shown that CpG methylation of the Sleeping Beauty (SB) transposon significantly enhanced transposition in mouse embryonic stem cells. Results In order to investigate the unexpected response of SB transposition to CpG methylation, related transposons from the Tc1/mariner superfamily, that is, Tc1, Himar1, Hsmar1, Frog Prince (FP) and Minos were tested to see how transposition was affected by CpG methylation. A significant increase of >20-fold in transposition of SB, FP and Minos was seen, whereas Tc1, Himar1 and Hsmar1 showed no difference in transposition upon CpG-methylation. The terminal inverted repeats (TIRs) of the SB, FP and Minos elements share a common structure, in which each TIR contains two functionally important binding sites for the transposase (termed the IR/DR structure). The group of IR/DR elements showed increased excision after CpG methylation compared to untreated transposon donor plasmids. We found that de novo CpG methylation is not required for transposition. A mutated FP donor plasmid with depleted CpG sites in both TIRs was as efficient in transposition as the wild-type transposon, indicating that CpG sites inside the TIRs are not responsible for altered binding of factors potentially modulating transposition. By using an in vivo one-hybrid DNA-binding assay in cultured human cells we found that CpG methylation had no appreciable effect on the affinity of SB transposase to its binding sites. However, chromatin immunoprecipitation indicated that CpG-methylated transposon donor plasmids are associated with a condensed chromatin structure characterized by trimethylated histone H3K9. Finally, DNA compaction by protamine was found to enhance SB transposition. Conclusions We have shown that DNA CpG methylation upregulates transposition of IR/DR elements in the Tc1/mariner superfamily. CpG methylation provokes the formation of a tight chromatin structure at the transposon DNA, likely aiding the formation of a catalytically active complex by facilitating synapsis of sites bound by the transposase.
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Affiliation(s)
- Tobias Jursch
- Max Delbrück Center for Molecular Medicine, D-13125, Berlin, Germany.
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Hozumi A, Mita K, Miskey C, Mates L, Izsvak Z, Ivics Z, Satake H, Sasakura Y. Germline transgenesis of the chordate Ciona intestinalis with hyperactive variants of sleeping beauty transposable element. Dev Dyn 2012; 242:30-43. [PMID: 23073965 DOI: 10.1002/dvdy.23891] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2012] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Transposon-mediated transgenesis is an excellent method for creating stable transgenic lines and insertional mutants. In the chordate Ciona intestinalis, Minos is the only transposon that has been used as the tool for germline transformation. Adding another transposon system in this organism enables us to conduct genetic techniques which can only be realized with the use of two transposons. RESULTS In the present study, we found that another Tc1/mariner superfamily transposon, sleeping beauty (SB), retains sufficient activity for germline transformation of C. intestinalis. SB shows efficiencies of germline transformation, insertion into gene coding regions, and enhancer detection comparable to those of Minos. We have developed a system for the remobilization of SB copies in the C. intestinalis genome by using transgenic lines expressing SB transposase in the germ cells. With this system, we examined the manner of SB mobilization in the C. intestinalis genome. SB shows intrachromosomal transposition more frequently than Minos. CONCLUSIONS SB-based germline transformation and the establishment of a new method that uses its frequent intrachromosomal transposition will result in breakthroughs in genetic approaches that use C. intestinalis together with Minos.
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Affiliation(s)
- Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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Ammar I, Gogol-Döring A, Miskey C, Chen W, Cathomen T, Izsvák Z, Ivics Z. Retargeting transposon insertions by the adeno-associated virus Rep protein. Nucleic Acids Res 2012; 40:6693-712. [PMID: 22523082 PMCID: PMC3413126 DOI: 10.1093/nar/gks317] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Sleeping Beauty (SB), piggyBac (PB) and Tol2 transposons are promising instruments for genome engineering. Integration site profiling of SB, PB and Tol2 in human cells showed that PB and Tol2 insertions were enriched in genes, whereas SB insertions were randomly distributed. We aimed to introduce a bias into the target site selection properties of the transposon systems by taking advantage of the locus-specific integration system of adeno-associated virus (AAV). The AAV Rep protein binds to Rep recognition sequences (RRSs) in the human genome, and mediates viral integration into nearby sites. A series of fusion constructs consisting of the N-terminal DNA-binding domain of Rep and the transposases or the N57 domain of SB were generated. A plasmid-based transposition assay showed that Rep/SB yielded a 15-fold enrichment of transposition at a particular site near a targeted RRS. Genome-wide insertion site analysis indicated that an approach based on interactions between the SB transposase and Rep/N57 enriched transgene insertions at RRSs. We also provide evidence of biased insertion of the PB and Tol2 transposons. This study provides a comparative insight into target site selection properties of transposons, as well as proof-of-principle for targeted chromosomal transposition by composite protein–protein and protein–DNA interactions.
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Affiliation(s)
- Ismahen Ammar
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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Moldt B, Miskey C, Staunstrup NH, Gogol-Döring A, Bak RO, Sharma N, Mátés L, Izsvák Z, Chen W, Ivics Z, Mikkelsen JG. Comparative genomic integration profiling of Sleeping Beauty transposons mobilized with high efficacy from integrase-defective lentiviral vectors in primary human cells. Mol Ther 2011; 19:1499-510. [PMID: 21468003 DOI: 10.1038/mt.2011.47] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It has been previously shown that integrase-defective HIV-1-based gene vectors can serve, with moderate efficiency, as substrate for DNA transposition by a transiently expressed Sleeping Beauty (SB) transposase. Here, we describe the enhanced gene transfer properties of a HIV-1/SB hybrid vector that allows efficient DNA transposition, facilitated by the hyperactive SB100X transposase, from vector DNA intermediates in primary human cells. Potent transposase-dependent integration of genetic cargo carried by the hybrid HIV-1/SB vector (up to 160-fold above background) is reported in human cell lines as well as in primary human fibroblasts and keratinocytes. The efficiency of transgene integration in context of the newly developed hybrid vector is comparable with that of conventional lentiviral vectors (LVs). Integration profiles of integrating HIV-1-derived vectors and SB transposons mobilized from LVs are investigated by deep sequencing of a large number of integration sites. A significant bias of lentiviral integrations in genes is reported, confirming that biological properties of the viral integration machinery facilitate preferred insertion into actively transcribed genomic regions. In sharp contrast, lentiviral insertions catalyzed by the SB100X transposase are far more random with respect to genes. Based on these properties, HIV-1/SB vectors may become valuable tools for genetic engineering and therapeutic gene transfer.
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Affiliation(s)
- Brian Moldt
- Department of Human Genetics, University of Aarhus, Aarhus, Denmark
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Mátés L, Chuah MKL, Belay E, Jerchow B, Manoj N, Acosta-Sanchez A, Grzela DP, Schmitt A, Becker K, Matrai J, Ma L, Samara-Kuko E, Gysemans C, Pryputniewicz D, Miskey C, Fletcher B, VandenDriessche T, Ivics Z, Izsvák Z. Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates. Nat Genet 2009; 41:753-61. [PMID: 19412179 DOI: 10.1038/ng.343] [Citation(s) in RCA: 654] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 02/02/2009] [Indexed: 01/12/2023]
Abstract
The Sleeping Beauty (SB) transposon is a promising technology platform for gene transfer in vertebrates; however, its efficiency of gene insertion can be a bottleneck in primary cell types. A large-scale genetic screen in mammalian cells yielded a hyperactive transposase (SB100X) with approximately 100-fold enhancement in efficiency when compared to the first-generation transposase. SB100X supported 35-50% stable gene transfer in human CD34(+) cells enriched in hematopoietic stem or progenitor cells. Transplantation of gene-marked CD34(+) cells in immunodeficient mice resulted in long-term engraftment and hematopoietic reconstitution. In addition, SB100X supported sustained (>1 year) expression of physiological levels of factor IX upon transposition in the mouse liver in vivo. Finally, SB100X reproducibly resulted in 45% stable transgenesis frequencies by pronuclear microinjection into mouse zygotes. The newly developed transposase yields unprecedented stable gene transfer efficiencies following nonviral gene delivery that compare favorably to stable transduction efficiencies with integrating viral vectors and is expected to facilitate widespread applications in functional genomics and gene therapy.
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Affiliation(s)
- Lajos Mátés
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Orbán TI, Apáti Á, Németh A, Varga N, Krizsik V, Schamberger A, Szebényi K, Erdei Z, Várady G, Karászi É, Homolya L, Német K, Gócza E, Miskey C, Mátés L, Ivics Z, Izsvák Z, Sarkadi B. Applying a “Double-Feature” Promoter to Identify Cardiomyocytes Differentiated from Human Embryonic Stem Cells Following Transposon-Based Gene Delivery. Stem Cells 2009; 27:1077-87. [DOI: 10.1002/stem.45] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Walisko O, Schorn A, Rolfs F, Devaraj A, Miskey C, Izsvák Z, Ivics Z. Transcriptional activities of the Sleeping Beauty transposon and shielding its genetic cargo with insulators. Mol Ther 2007; 16:359-69. [PMID: 18071335 DOI: 10.1038/sj.mt.6300366] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Sleeping Beauty (SB) transposable element shows efficient transposition in human cells, and provides long-term transgene expression in preclinical animal models. Random chromosomal insertion of SB vectors represents a safety issue in human gene therapeutic applications, due to potential genotoxic effects associated with transposon integration. We investigated the transcriptional activities of SB in order to assess its potential to alter host gene expression upon integration. The untranslated regions (UTRs) of the transposon direct convergent, inward-directed transcription. Transcription from the 5'-UTR of SB is upregulated by the host-encoded factor high-mobility group 2-like 1 (HMG2L1), and requires a 65-base pair (bp) region not present in commonly used SB vectors. The SB transposase antagonizes the effect of HMG2L1, suggesting that natural transposase expression is under a negative feedback regulation. SB transposon vectors lacking the 65-bp region associated with HMG2L1-dependent upregulation exhibit benign transcriptional activities, at a level up to 100-times lower than that of the murine leukemia virus (MLV) long terminal repeat (LTR). Incorporation of chicken beta-globin HS4 insulator sequences in SB-based vectors reduces the transactivation of model promoters by transposon-borne enhancers, and thus may lower the risk of transcriptional activation of host genes situated close to a transposon insertion site.
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Affiliation(s)
- Oliver Walisko
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Miskey C, Papp B, Mátés L, Sinzelle L, Keller H, Izsvák Z, Ivics Z. The ancient mariner sails again: transposition of the human Hsmar1 element by a reconstructed transposase and activities of the SETMAR protein on transposon ends. Mol Cell Biol 2007; 27:4589-600. [PMID: 17403897 PMCID: PMC1900042 DOI: 10.1128/mcb.02027-06] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hsmar1, one of the two subfamilies of mariner transposons in humans, is an ancient element that entered the primate genome lineage approximately 50 million years ago. Although Hsmar1 elements are inactive due to mutational damage, one particular copy of the transposase gene has apparently been under selection. This transposase coding region is part of the SETMAR gene, in which a histone methylatransferase SET domain is fused to an Hsmar1 transposase domain. A phylogenetic approach was taken to reconstruct the ancestral Hsmar1 transposase gene, which we named Hsmar1-Ra. The Hsmar1-Ra transposase efficiently mobilizes Hsmar1 transposons by a cut-and-paste mechanism in human cells and zebra fish embryos. Hsmar1-Ra can also mobilize short inverted-repeat transposable elements (MITEs) related to Hsmar1 (MiHsmar1), thereby establishing a functional relationship between an Hsmar1 transposase source and these MITEs. MiHsmar1 excision is 2 orders of magnitude more efficient than that of long elements, thus providing an explanation for their high copy numbers. We show that the SETMAR protein binds and introduces single-strand nicks into Hsmar1 inverted-repeat sequences in vitro. Pathway choices for DNA break repair were found to be characteristically different in response to transposon cleavage mediated by Hsmar1-Ra and SETMAR in vivo. Whereas nonhomologous end joining plays a dominant role in repairing excision sites generated by the Hsmar1-Ra transposase, DNA repair following cleavage by SETMAR predominantly follows a homology-dependent pathway. The novel transposon system can be a useful tool for genome manipulations in vertebrates and for investigations into the transpositional dynamics and the contributions of these elements to primate genome evolution.
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Affiliation(s)
- Csaba Miskey
- Max Delbrück Center for Molecular Medicine, Robert Rössle Str 10, Berlin, Germany
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Abstract
Genome sequences of many model organisms of developmental or agricultural importance are becoming available. The tremendous amount of sequence data is fuelling the next phases of challenging research: annotating all genes with functional information, and devising new ways for the experimental manipulation of vertebrate genomes. Transposable elements are known to be efficient carriers of foreign DNA into cells. Notably, members of the Tc1/mariner and the hAT transposon families retain their high transpositional activities in species other than their hosts. Indeed, several of these elements have been successfully used for transgenesis and insertional mutagenesis, expanding our abilities in genome manipulations in vertebrate model organisms. Transposon-based genetic tools can help scientists to understand mechanisms of embryonic development and pathogenesis, and will likely contribute to successful human gene therapy. We discuss the possibilities of transposon-based techniques in functional genomics, and review the latest results achieved by the most active DNA transposons in vertebrates. We put emphasis on the evolution and regulation of members of the best-characterized and most widely used Tc1/mariner family.
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Affiliation(s)
- C Miskey
- Max Delbrück Center for Molecular Medicine, Robert Rössle Str. 10, 13092, Berlin, Germany
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Miskey C, Izsvák Z, Plasterk RH, Ivics Z. The Frog Prince: a reconstructed transposon from Rana pipiens with high transpositional activity in vertebrate cells. Nucleic Acids Res 2004; 31:6873-81. [PMID: 14627820 PMCID: PMC290277 DOI: 10.1093/nar/gkg910] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog species Rana pipiens. The isolated clones were approximately 90% identical to a predicted transposase gene sequence from Xenopus laevis, but contained an unpredicted, approximately 180 bp region encoding the N-terminus of the putative transposase. None of these native genes was found to be active. Therefore, a consensus sequence of the transposase gene was derived. This engineered transposase and the transposon inverted repeats together constitute the components of a novel transposon system that we named Frog Prince (FP). FP has only approximately 50% sequence similarity to Sleeping Beauty (SB), and catalyzes efficient cut-and-paste transposition in fish, amphibian and mammalian cell lines. We demonstrate high-efficiency gene trapping in human cells using FP transposition. FP is the most efficient DNA-based transposon from vertebrates described to date, and shows approximately 70% higher activity in zebrafish cells than SB. Frog Prince can greatly extend our possibilities for genetic analyses in vertebrates.
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Affiliation(s)
- Csaba Miskey
- Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, D-13092 Berlin, Germany
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Ivics Z, Kaufman CD, Zayed H, Miskey C, Walisko O, Izsvák Z. The Sleeping Beauty transposable element: evolution, regulation and genetic applications. Curr Issues Mol Biol 2004; 6:43-55. [PMID: 14632258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrate species are inactive due to the accumulation of mutations. A representative of a subfamily of fish elements estimated to be last active > 10 million years ago has been reconstructed, and named Sleeping Beauty(SB). This element opened up new avenues for studies on DNA transposition in vertebrates, and for the development of transposon tools for genetic manipulation in important model species and in humans. Multiple transposase binding sites within the terminal inverted repeats, a transpositional enhancer sequence, unequal affinity of the transposase to the binding sites and the activity of the cellular HMGB1 protein all contribute to a highly regulated assembly of SB synaptic complexes, which is likely a requirement for the subsequent catalytic steps. Host proteins involved in double-strand DNA break repair are limiting factors of SB transposition in mammalian cells, underscoring evolutionary, structural and functional links between DNA transposition, retroviral integration and V(D)J recombination. SB catalyzes efficient cut-and-paste transposition in a wide range of vertebrate cells in tissue culture, and in somatic tissues as well as the germline of the mouse and zebrafish in vivo, indicating its usefulness as a vector for transgenesis and insertional mutagenesis.
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Affiliation(s)
- Zoltán Ivics
- Max Delbrück Center for Molecular Medicine, Robert Rössle Str. 10, D-13092, Berlin, Germany.
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