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Lehle S, Emons J, Hack C, Heindl F, Hein A, Preuß C, Seitz K, Zahn AL, Fasching AP, Beckmann WM, Ruebner M, Huebner H. Vergleich automatisierter Methoden zur Extraktion zirkulierender
zell-freier DNA. Geburtshilfe Frauenheilkd 2022. [DOI: 10.1055/s-0042-1749030] [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: 10/18/2022] Open
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Dannenmann B, Lehle S, Lorscheid S, Huber SM, Essmann F, Schulze-Osthoff K. Simultaneous quantification of DNA damage and mitochondrial copy number by long-run DNA-damage quantification (LORD-Q). Oncotarget 2017; 8:112417-112425. [PMID: 29348835 PMCID: PMC5762520 DOI: 10.18632/oncotarget.20112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 06/19/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022] Open
Abstract
DNA damage and changes in the mitochondrial DNA content have been implicated in ageing and cancer development. To prevent genomic instability and tumorigenesis, cells must maintain the integrity of their nuclear and mitochondrial DNA. Advances in the research of DNA damage protection and genomic stability, however, also depend on the availability of techniques that can reliably quantify alterations of mitochondrial DNA copy numbers and DNA lesions in an accurate high-throughput manner. Unfortunately, no such method has been established yet. Here, we describe the high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) and its suitability to simultaneously measure DNA damage rates and mitochondrial DNA copy numbers in cultured cells and tissue samples. Using the LORD-Q multiplex assay, we exemplarily show that the mitochondrial DNA content does not directly affect DNA damage susceptibility, but influences the efficacy of certain anticancer drugs. Hence, LORD-Q provides a fast and precise method to assess DNA lesions, DNA repair and mtDNA replication as well as their role in a variety of pathological settings.
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Affiliation(s)
- Benjamin Dannenmann
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Simon Lehle
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Sebastian Lorscheid
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Stephan M Huber
- Department of Radiation Oncology, University of Tübingen, 72076 Tübingen, Germany
| | - Frank Essmann
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Klaus Schulze-Osthoff
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Dannenmann B, Lehle S, Essmann F, Schulze-Osthoff K. Genome surveillance in pluripotent stem cells: Low apoptosis threshold and efficient antioxidant defense. Mol Cell Oncol 2015; 3:e1052183. [PMID: 27308586 DOI: 10.1080/23723556.2015.1052183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 01/30/2023]
Abstract
Pluripotent stem cells must be endowed with efficient genome surveillance. Here we describe the multiple mechanisms that ensure their genome integrity, including high susceptibility to apoptosis and efficient prevention of DNA lesions. In induced pluripotent stem cells, apoptosis hypersensitivity is mediated by increased expression of proapoptotic BCL-2 protein, whereas DNA damage is prevented by the upregulation of several antioxidant enzymes. Antioxidants might be therefore employed for safer stem cell therapies.
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Affiliation(s)
- Benjamin Dannenmann
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen , Tübingen, Germany
| | - Simon Lehle
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen , Tübingen, Germany
| | - Frank Essmann
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen , Tübingen, Germany
| | - Klaus Schulze-Osthoff
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen, Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Dannenmann B, Lehle S, Hildebrand DG, Kübler A, Grondona P, Schmid V, Holzer K, Fröschl M, Essmann F, Rothfuss O, Schulze-Osthoff K. High glutathione and glutathione peroxidase-2 levels mediate cell-type-specific DNA damage protection in human induced pluripotent stem cells. Stem Cell Reports 2015; 4:886-98. [PMID: 25937369 PMCID: PMC4437487 DOI: 10.1016/j.stemcr.2015.04.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 04/03/2015] [Accepted: 04/03/2015] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells must strictly maintain genomic integrity to prevent transmission of mutations. In human induced pluripotent stem cells (iPSCs), we found that genome surveillance is achieved via two ways, namely, a hypersensitivity to apoptosis and a very low accumulation of DNA lesions. The low apoptosis threshold was mediated by constitutive p53 expression and a marked upregulation of proapoptotic p53 target genes of the BCL-2 family, ensuring the efficient iPSC removal upon genotoxic insults. Intriguingly, despite the elevated apoptosis sensitivity, both mitochondrial and nuclear DNA lesions induced by genotoxins were less frequent in iPSCs compared to fibroblasts. Gene profiling identified that mRNA expression of several antioxidant proteins was considerably upregulated in iPSCs. Knockdown of glutathione peroxidase-2 and depletion of glutathione impaired protection against DNA lesions. Thus, iPSCs ensure genomic integrity through enhanced apoptosis induction and increased antioxidant defense, contributing to protection against DNA damage. The iPSCs maintain genomic integrity by DNA damage protection and rapid apoptosis Apoptosis hypersensitivity is mediated by p53 and proapoptotic BCL-2 proteins The iPSCs also display a strongly elevated antioxidant defense Depletion of glutathione and GPX2 impairs DNA damage protection in iPSCs
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Affiliation(s)
- Benjamin Dannenmann
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Simon Lehle
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Dominic G Hildebrand
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Ayline Kübler
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Paula Grondona
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Vera Schmid
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Katharina Holzer
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Mirjam Fröschl
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Frank Essmann
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Oliver Rothfuss
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Klaus Schulze-Osthoff
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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Lehle S, Hildebrand DG, Merz B, Malak PN, Becker MS, Schmezer P, Essmann F, Schulze-Osthoff K, Rothfuss O. LORD-Q: a long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis. Nucleic Acids Res 2013; 42:e41. [PMID: 24371283 PMCID: PMC3973301 DOI: 10.1093/nar/gkt1349] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA damage is tightly associated with various biological and pathological processes, such as aging and tumorigenesis. Although detection of DNA damage is attracting increasing attention, only a limited number of methods are available to quantify DNA lesions, and these techniques are tedious or only detect global DNA damage. In this study, we present a high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) in both the mitochondrial and nuclear genome. While most conventional methods are of low-sensitivity or restricted to abundant mitochondrial DNA samples, we established a protocol that enables the accurate sequence-specific quantification of DNA damage in >3-kb probes for any mitochondrial or nuclear DNA sequence. In order to validate the sensitivity of this method, we compared LORD-Q with a previously published qPCR-based method and the standard single-cell gel electrophoresis assay, demonstrating a superior performance of LORD-Q. Exemplarily, we monitored induction of DNA damage and repair processes in human induced pluripotent stem cells and isogenic fibroblasts. Our results suggest that LORD-Q provides a sequence-specific and precise method to quantify DNA damage, thereby allowing the high-throughput assessment of DNA repair, genotoxicity screening and various other processes for a wide range of life science applications.
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Affiliation(s)
- Simon Lehle
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen, 72076 Tübingen, Germany, Division of Immunogenetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Hildebrand DG, Lehle S, Borst A, Haferkamp S, Essmann F, Schulze-Osthoff K. α-Fucosidase as a novel convenient biomarker for cellular senescence. Cell Cycle 2013; 12:1922-7. [PMID: 23673343 DOI: 10.4161/cc.24944] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [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: 01/16/2023] Open
Abstract
Due to its role in aging and antitumor defense, cellular senescence has recently attracted increasing interest. However, there is currently no single specific marker that can unequivocally detect senescent cells. Here, we identified α-L-fucosidase (α-Fuc) as a novel sensitive biomarker for cellular senescence. Regardless of the stress stimulus and cell type, α-Fuc activity was induced in all canonical types of cellular senescence, including replicative, DNA damage- and oncogene-induced senescence. Strikingly, in most models the degree of α-Fuc upregulation was higher than the induction of senescence-associated β-galactosidase (SA-β-Gal), the current gold standard for senescence detection. As α-Fuc is convenient and easy to measure, we suggest its utility as a valuable marker, in particular in cells with low SA-β-Gal activity.
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Affiliation(s)
- Dominic G Hildebrand
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
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Hildebrand DG, Alexander E, Hörber S, Lehle S, Obermayer K, Münck NA, Rothfuss O, Frick JS, Morimatsu M, Schmitz I, Roth J, Ehrchen JM, Essmann F, Schulze-Osthoff K. IκBζ is a transcriptional key regulator of CCL2/MCP-1. J Immunol 2013; 190:4812-20. [PMID: 23547114 DOI: 10.4049/jimmunol.1300089] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
CCL2, also referred to as MCP-1, is critically involved in directing the migration of blood monocytes to sites of inflammation. Consequently, excessive CCL2 secretion has been linked to many inflammatory diseases, whereas a lack of expression severely impairs immune responsiveness. We demonstrate that IκBζ, an atypical IκB family member and transcriptional coactivator required for the selective expression of a subset of NF-κB target genes, is a key activator of the Ccl2 gene. IκBζ-deficient macrophages exhibited impaired secretion of CCL2 when challenged with diverse inflammatory stimuli, such as LPS or peptidoglycan. These findings were reflected at the level of Ccl2 gene expression, which was tightly coupled to the presence of IκBζ. Moreover, mechanistic insights acquired by chromatin immunoprecipitation demonstrate that IκBζ is directly recruited to the proximal promoter region of the Ccl2 gene and is required for transcription-enhancing histone H3 at lysine-4 trimethylation. Finally, IκBζ-deficient mice showed significantly impaired CCL2 secretion and monocyte infiltration in an experimental model of peritonitis. Together, these findings suggest a distinguished role of IκBζ in mediating the targeted recruitment of monocytes in response to local inflammatory events.
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Affiliation(s)
- Dominic G Hildebrand
- Interfaculty Institute for Biochemistry, Eberhard Karls University, D-72076 Tübingen, Germany
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Shanmugasundararaj S, Lehle S, Yamodo HI, Husain SS, Tseng C, Nguyen K, Addona GH, Miller KW. The location and nature of general anesthetic binding sites on the active conformation of firefly luciferase; a time resolved photolabeling study. PLoS One 2012; 7:e29854. [PMID: 22272253 PMCID: PMC3260189 DOI: 10.1371/journal.pone.0029854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 10/06/2011] [Accepted: 12/05/2011] [Indexed: 11/18/2022] Open
Abstract
Firefly luciferase is one of the few soluble proteins that is acted upon by a wide variety of general anesthetics and alcohols; they inhibit the ATP–driven production of light. We have used time–resolved photolabeling to locate the binding sites of alcohols during the initial light output, some 200 ms after adding ATP. The photolabel 3-azioctanol inhibited the initial light output with an IC50 of 200 µM, close to its general anesthetic potency. Photoincorporation of [3H]3-azioctanol into luciferase was saturable but weak. It was enhanced 200 ms after adding ATP but was negligible minutes later. Sequencing of tryptic digests by HPLC–MSMS revealed a similar conformation–dependence for photoincorporation of 3-azioctanol into Glu-313, a residue that lines the bottom of a deep cleft (vestibule) whose outer end binds luciferin. An aromatic diazirine analog of benzyl alcohol with broader side chain reactivity reported two sites. First, it photolabeled two residues in the vestibule, Ser-286 and Ile-288, both of which are implicated with Glu-313 in the conformation change accompanying activation. Second, it photolabeled two residues that contact luciferin, Ser-316 and Ser-349. Thus, time resolved photolabeling supports two mechanisms of action. First, an allosteric one, in which anesthetics bind in the vestibule displacing water molecules that are thought to be involved in light output. Second, a competitive one, in which anesthetics bind isosterically with luciferin. This work provides structural evidence that supports the competitive and allosteric actions previously characterized by kinetic studies.
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Affiliation(s)
| | - Simon Lehle
- Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Herve I. Yamodo
- Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - S. Shaukat Husain
- Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Claire Tseng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Khanh Nguyen
- Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - George H. Addona
- Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Keith W. Miller
- Department of Anesthesia and Critical Care, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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