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Zelensky AN, Schimmel J, Kool H, Kanaar R, Tijsterman M. Inactivation of Pol θ and C-NHEJ eliminates off-target integration of exogenous DNA. Nat Commun 2017; 8:66. [PMID: 28687761 PMCID: PMC5501794 DOI: 10.1038/s41467-017-00124-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/01/2017] [Indexed: 11/09/2022] Open
Abstract
Off-target or random integration of exogenous DNA hampers precise genomic engineering and presents a safety risk in clinical gene therapy strategies. Genetic definition of random integration has been lacking for decades. Here, we show that the A-family DNA polymerase θ (Pol θ) promotes random integration, while canonical non-homologous DNA end joining plays a secondary role; cells double deficient for polymerase θ and canonical non-homologous DNA end joining are devoid of any integration events, demonstrating that these two mechanisms define random integration. In contrast, homologous recombination is not reduced in these cells and gene targeting is improved to 100% efficiency. Such complete reversal of integration outcome, from predominately random integration to exclusively gene targeting, provides a rational way forward to improve the efficacy and safety of DNA delivery and gene correction approaches.Random off-target integration events can impair precise gene targeting and poses a safety risk for gene therapy. Here the authors show that repression of polymerase θ and classical non-homologous recombination eliminates random integration.
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Affiliation(s)
- Alex N Zelensky
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam,, 3000 CA, The Netherlands
| | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam,, 3000 CA, The Netherlands.
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, PO Box 9600, Leiden,, 2300 RC, The Netherlands.
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Dutta RK, Kondeti VK, Sharma I, Chandel NS, Quaggin SE, Kanwar YS. Beneficial Effects of Myo-Inositol Oxygenase Deficiency in Cisplatin-Induced AKI. J Am Soc Nephrol 2017; 28:1421-1436. [PMID: 27895157 PMCID: PMC5407728 DOI: 10.1681/asn.2016070744] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/17/2016] [Indexed: 11/03/2022] Open
Abstract
Overexpression of the proximal tubular enzyme myo-inositol oxygenase (MIOX) induces oxidant stress in vitro However, the relevance of MIOX to tubular pathobiology remains enigmatic. To investigate the role of MIOX in cisplatin-induced tubular AKI, we generated conditional MIOX-overexpressing transgenic (MIOX-TG) mice and MIOX-knockout (MIOX-/-) mice with tubule-specific MIOX overexpression or knockout, respectively. Compared with cisplatin-treated wild-type (WT) mice, cisplatin-treated MIOX-TG mice had even greater increases in urea, creatinine, and KIM-1 levels and more tubular injury and apoptosis, but these effects were attenuated in cisplatin-treated MIOX-/- mice. Similarly, MIOX-TG mice had the highest and MIOX-/- mice had the lowest renal levels of Bax, cleaved caspase-3, and NADPH oxidase-4 expression and reactive oxygen species (ROS) generation after cisplatin treatment. In vitro, cisplatin dose-dependently increased ROS generation in LLC-PK1 cells. Furthermore, MIOX overexpression in these cells accentuated cisplatin-induced ROS generation and perturbations in the ratio of GSH to oxidized GSH, whereas MIOX-siRNA or N-acetyl cysteine treatment attenuated these effects. Additionally, the cisplatin-induced enhancement of p53 activation, NF-κB binding to DNA, and NF-κB nuclear translocation in WT mice was exacerbated in MIOX-TG mice but absent in MIOX-/- mice. In vitro, MIOX-siRNA or NAC treatment reduced the dose-dependent increase in p53 expression induced by cisplatin. We also observed a remarkable influx of inflammatory cells and upregulation of cytokines in kidneys of cisplatin-treated MIOX-TG mice. Finally, analysis of genomic DNA in WT mice revealed cisplatin-induced hypomethylation of the MIOX promoter. These data suggest that MIOX overexpression exacerbates, whereas MIOX gene disruption protects against, cisplatin-induced AKI.
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Affiliation(s)
| | | | | | | | | | - Yashpal S Kanwar
- Departments of Pathology and
- Medicine, Northwestern University, Chicago, Illinois
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Reuter M, Zelensky A, Smal I, Meijering E, van Cappellen WA, de Gruiter HM, van Belle GJ, van Royen ME, Houtsmuller AB, Essers J, Kanaar R, Wyman C. BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells. ACTA ACUST UNITED AC 2015; 207:599-613. [PMID: 25488918 PMCID: PMC4259808 DOI: 10.1083/jcb.201405014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Nuclear BRCA2 is oligomeric and associated with RAD51, possibly sequestering it until it is delivered to DNA damage sites. Genome maintenance by homologous recombination depends on coordinating many proteins in time and space to assemble at DNA break sites. To understand this process, we followed the mobility of BRCA2, a critical recombination mediator, in live cells at the single-molecule level using both single-particle tracking and fluorescence correlation spectroscopy. BRCA2-GFP and -YFP were compared to distinguish diffusion from fluorophore behavior. Diffusive behavior of fluorescent RAD51 and RAD54 was determined for comparison. All fluorescent proteins were expressed from endogenous loci. We found that nuclear BRCA2 existed in oligomeric clusters, and exhibited heterogeneous mobility. DNA damage increased BRCA2 transient binding, presumably including binding to damaged sites. Despite its very different size, RAD51 displayed mobility similar to BRCA2, which indicates physical interaction between these proteins both before and after induction of DNA damage. We propose that BRCA2-mediated sequestration of nuclear RAD51 serves to prevent inappropriate DNA interactions and that all RAD51 is delivered to DNA damage sites in association with BRCA2.
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Affiliation(s)
- Marcel Reuter
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Alex Zelensky
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Ihor Smal
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Erik Meijering
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Wiggert A van Cappellen
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - H Martijn de Gruiter
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Gijsbert J van Belle
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Martin E van Royen
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Jeroen Essers
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Claire Wyman
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
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Mao L, Zabel C, Herrmann M, Nolden T, Mertes F, Magnol L, Chabert C, Hartl D, Herault Y, Delabar JM, Manke T, Himmelbauer H, Klose J. Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks. PLoS One 2007; 2:e1218. [PMID: 18043732 PMCID: PMC2077926 DOI: 10.1371/journal.pone.0001218] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 11/01/2007] [Indexed: 11/25/2022] Open
Abstract
Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene dose alterations on the cellular proteome, we carried out a proteomic investigation on murine embryonic stem cells that either overexpressed individual genes or displayed aneuploidy over a genomic region encompassing 14 genes. The number of variant proteins detected per cell line ranged between 70 and 110, and did not correlate with the number of modified genes. In cell lines with single gene mutations, up and down-regulated proteins were always in balance in comparison to parental cell lines regarding number as well as concentration of differentially expressed proteins. In contrast, dose alteration of 14 genes resulted in an unequal number of up and down-regulated proteins, though the balance was kept at the level of protein concentration. We propose that the observed protein changes might partially be explained by a proteomic network response. Hence, we hypothesize the existence of a class of “balancer” proteins within the proteomic network, defined as proteins that buffer or cushion a system, and thus oppose multiple system disturbances. Through database queries and resilience analysis of the protein interaction network, we found that potential balancer proteins are of high cellular abundance, possess a low number of direct interaction partners, and show great allelic variation. Moreover, balancer proteins contribute more heavily to the network entropy, and thus are of high importance in terms of system resilience. We propose that the “elasticity” of the proteomic regulatory network mediated by balancer proteins may compensate for changes that occur under diseased conditions.
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Affiliation(s)
- Lei Mao
- Institute for Human Genetics, Charité-University Medicine Berlin, Germany.
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