1
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Velavalapalli VM, Maddipati V, Gurská S, Annadurai N, Lišková B, Katari NK, Džubák P, Hajdúch M, Das V, Gundla R. Novel 5-Substituted Oxindole Derivatives as Bruton's Tyrosine Kinase Inhibitors: Design, Synthesis, Docking, Molecular Dynamics Simulation, and Biological Evaluation. ACS OMEGA 2024; 9:8067-8081. [PMID: 38405484 PMCID: PMC10882696 DOI: 10.1021/acsomega.3c08343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/07/2024] [Accepted: 01/23/2024] [Indexed: 02/27/2024]
Abstract
Bruton's tyrosine kinase (BTK) is a non-RTK cytoplasmic kinase predominantly expressed by hemopoietic lineages, particularly B-cells. A new oxindole-based focused library was designed to identify potent compounds targeting the BTK protein as anticancer agents. This study used rational approaches like structure-based pharmacophore modeling, docking, and ADME properties to select compounds. Molecular dynamics simulations carried out at 20 ns supported the stability of compound 9g within the binding pocket. All the compounds were synthesized and subjected to biological screening on two BTK-expressing cancer cell lines, RAMOS and K562; six non-BTK cancer cell lines, A549, HCT116 (parental and p53-/-), U2OS, JURKAT, and CCRF-CEM; and two non-malignant fibroblast lines, BJ and MRC-5. This study resulted in the identification of four new compounds, 9b, 9f, 9g, and 9h, possessing free binding energies of -10.8, -11.1, -11.3, and -10.8 kcal/mol, respectively, and displaying selective cytotoxicity against BTK-high RAMOS cells. Further analysis demonstrated the antiproliferative activity of 9h in RAMOS cells through selective inhibition of pBTK (Tyr223) without affecting Lyn and Syk, upstream proteins in the BCR signaling pathway. In conclusion, we identified a promising oxindole derivative (9h) that shows specificity in modulating BTK signaling pathways.
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Affiliation(s)
- Vani Madhuri Velavalapalli
- GITAM
School of Pharmacy, GITAM Deemed to Be University, Hyderabad, Telangana 502329, India
- Department
of Chemistry, GITAM School of Science, GITAM
Deemed to Be University, Hyderabad, Telangana 502329, India
| | | | - Soňa Gurská
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital
Olomouc, Hněvotínská
1333/5, Olomouc 77900, Czech Republic
- Czech
Advanced Technologies and Research Institute (CATRIN), Institute of
Molecular and Translational Medicine, Palacký
University Olomouc, Olomouc 77900, Czech Republic
| | - Narendran Annadurai
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital
Olomouc, Hněvotínská
1333/5, Olomouc 77900, Czech Republic
| | - Barbora Lišková
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital
Olomouc, Hněvotínská
1333/5, Olomouc 77900, Czech Republic
| | - Naresh Kumar Katari
- Department
of Chemistry, GITAM School of Science, GITAM
Deemed to Be University, Hyderabad, Telangana 502329, India
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital
Olomouc, Hněvotínská
1333/5, Olomouc 77900, Czech Republic
- Czech
Advanced Technologies and Research Institute (CATRIN), Institute of
Molecular and Translational Medicine, Palacký
University Olomouc, Olomouc 77900, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital
Olomouc, Hněvotínská
1333/5, Olomouc 77900, Czech Republic
- Czech
Advanced Technologies and Research Institute (CATRIN), Institute of
Molecular and Translational Medicine, Palacký
University Olomouc, Olomouc 77900, Czech Republic
| | - Viswanath Das
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital
Olomouc, Hněvotínská
1333/5, Olomouc 77900, Czech Republic
- Czech
Advanced Technologies and Research Institute (CATRIN), Institute of
Molecular and Translational Medicine, Palacký
University Olomouc, Olomouc 77900, Czech Republic
| | - Rambabu Gundla
- Department
of Chemistry, GITAM School of Science, GITAM
Deemed to Be University, Hyderabad, Telangana 502329, India
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2
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Lu M, Billerbeck S. Improving homology-directed repair by small molecule agents for genetic engineering in unconventional yeast?-Learning from the engineering of mammalian systems. Microb Biotechnol 2024; 17:e14398. [PMID: 38376092 PMCID: PMC10878012 DOI: 10.1111/1751-7915.14398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 02/21/2024] Open
Abstract
The ability to precisely edit genomes by deleting or adding genetic information enables the study of biological functions and the building of efficient cell factories. In many unconventional yeasts, such as those promising new hosts for cell factory design but also human pathogenic yeasts and food spoilers, this progress has been limited by the fact that most yeasts favour non-homologous end joining (NHEJ) over homologous recombination (HR) as a DNA repair mechanism, impairing genetic access to these hosts. In mammalian cells, small molecules that either inhibit proteins involved in NHEJ, enhance protein function in HR, or arrest the cell cycle in HR-dominant phases are regarded as promising agents for the simple and transient increase of HR-mediated genome editing without the need for a priori host engineering. Only a few of these chemicals have been applied to the engineering of yeast, although the targeted proteins are mostly conserved, making chemical agents a yet-underexplored area for enhancing yeast engineering. Here, we consolidate knowledge of the available small molecules that have been used to improve HR efficiency in mammalian cells and the few ones that have been used in yeast. We include available high-throughput-compatible NHEJ/HR quantification assays that could be used to screen for and isolate yeast-specific inhibitors.
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Affiliation(s)
- Min Lu
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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3
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Koraboina CP, Maddipati VC, Annadurai N, Gurská S, Džubák P, Hajdúch M, Das V, Gundla R. Synthesis and Biological Evaluation of Oxindole Sulfonamide Derivatives as Bruton's Tyrosine Kinase Inhibitors. ChemMedChem 2024; 19:e202300511. [PMID: 37916435 DOI: 10.1002/cmdc.202300511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/03/2023]
Abstract
Bruton's tyrosine kinase (BTK) is a promising molecular target for several human B-cell-related autoimmune disorders, inflammation, and haematological malignancies. The pathogenic alterations in various cancer tissues depend on mutant BTK for cell proliferation and survival, and BTK is also overexpressed in a range of hematopoietic cells. Due to this, BTK is emerging as a potential drug target to treat various human diseases, and several reversible and irreversible inhibitors have been developed and are being developed. As a result, BTK inhibition, clinically validated as an anticancer treatment, is finding great interest in B-cell malignancies and solid tumours. This study focuses on the design and synthesis of new oxindole sulfonamide derivatives as promising inhibitors of BTK with negligible off-target effects. The most cytotoxic compounds with greater basicity were PID-4 (2.29±0.52 μM), PID-6 (9.37±2.47 μM), and PID-19 (2.64±0.88 μM). These compounds caused a selective inhibition of Burkitt's lymphoma RAMOS cells without significant cytotoxicity in non-BTK cancerous and non-cancerous cell lines. Further, PID-4 showed promising activity in inhibiting BTK and downstream signalling cascades. As a potent inhibitor of Burkitt's lymphoma cells, PID-4 is a promising lead for developing novel chemotherapeutics.
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Affiliation(s)
- Chandra Prakash Koraboina
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad, Telangana, 502 329, India
| | | | - Narendran Annadurai
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Křížkovského 511/8, 77900, Olomouc, Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Křížkovského 511/8, 77900, Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Křížkovského 511/8, 77900, Olomouc, Czech Republic
| | - Viswanath Das
- Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry, Palacký University and University Hospital Olomouc, Hněvotínská 1333/5, 77900, Olomouc, Czech Republic
- Czech Advanced Technologies and Research Institute (CATRIN), Institute of Molecular and Translational Medicine, Palacký University Olomouc, Křížkovského 511/8, 77900, Olomouc, Czech Republic
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM (Deemed to be University), Hyderabad, Telangana, 502 329, India
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4
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Dutta A, Mitra J, Hegde PM, Mitra S, Hegde ML. Characterizing the Repair of DNA Double-Strand Breaks: A Review of Surrogate Plasmid-Based Reporter Methods. Methods Mol Biol 2023; 2701:173-182. [PMID: 37574482 DOI: 10.1007/978-1-0716-3373-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
DNA double-strand breaks (DSBs) are the most lethal genomic lesions that are induced endogenously during physiological reactions as well as by external stimuli and genotoxicants. DSBs are repaired in mammalian cells via one of three well-studied pathways depending on the cell cycle status and/or the nature of the break. First, the homologous recombination (HR) pathway utilizes the duplicated sister chromatid as a template in S/G2 cells. Second, the nonhomologous end-joining (NHEJ) is the predominant DSB repair pathway throughout the cell cycle. The third pathway, microhomology-mediated/alternative end-joining (MMEJ/Alt-EJ), is a specialized backup pathway that works not only in the S phase but also in G0/G1 cells that constitute the bulk of human tissues. In vitro experimental methods to recapitulate the repair of physiologically relevant DSBs pose a challenge. Commonly employed plasmid- or oligonucleotide-based substrates contain restriction enzyme-cleaved DSB mimics, which undoubtedly do not mimic DSB ends generated by ionizing radiation (IR), chemotherapeutics, and reactive oxygen species (ROS). DSBs can also be indirectly generated by reactive oxygen species (ROS). All such DSBs invariably contain blocked termini. In this methodology chapter, we describe a method to recapitulate the DSB repair mechanism using in cellulo and in vitro cell-free systems. This methodology enables researchers to assess the contribution of NHEJ vs. Alt-EJ using a reporter plasmid containing DSB lesions with non-ligatable termini. Limitations and challenges of prevailing methods are also addressed.
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Affiliation(s)
- Arijit Dutta
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Joy Mitra
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Pavana M Hegde
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Sankar Mitra
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research, Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Neurosciences, Weill Cornell Medical College, New York, NY, USA.
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5
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Tatin X, Muggiolu G, Sauvaigo S, Breton J. Evaluation of DNA double-strand break repair capacity in human cells: Critical overview of current functional methods. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108388. [PMID: 34893153 DOI: 10.1016/j.mrrev.2021.108388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/05/2023]
Abstract
DNA double-strand breaks (DSBs) are highly deleterious lesions, responsible for mutagenesis, chromosomal translocation or cell death. DSB repair (DSBR) is therefore a critical part of the DNA damage response (DDR) to restore molecular and genomic integrity. In humans, this process is achieved through different pathways with various outcomes. The balance between DSB repair activities varies depending on cell types, tissues or individuals. Over the years, several methods have been developed to study variations in DSBR capacity. Here, we mainly focus on functional techniques, which provide dynamic information regarding global DSB repair proficiency or the activity of specific pathways. These methods rely on two kinds of approaches. Indirect techniques, such as pulse field gel electrophoresis (PFGE), the comet assay and immunofluorescence (IF), measure DSB repair capacity by quantifying the time-dependent decrease in DSB levels after exposure to a DNA-damaging agent. On the other hand, cell-free assays and reporter-based methods directly track the repair of an artificial DNA substrate. Each approach has intrinsic advantages and limitations and despite considerable efforts, there is currently no ideal method to quantify DSBR capacity. All techniques provide different information and can be regarded as complementary, but some studies report conflicting results. Parameters such as the type of biological material, the required equipment or the cost of analysis may also limit available options. Improving currently available methods measuring DSBR capacity would be a major step forward and we present direct applications in mechanistic studies, drug development, human biomonitoring and personalized medicine, where DSBR analysis may improve the identification of patients eligible for chemo- and radiotherapy.
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Affiliation(s)
- Xavier Tatin
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France; LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | | | - Sylvie Sauvaigo
- LXRepair, 5 Avenue du Grand Sablon, 38700 La Tronche, France
| | - Jean Breton
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, 38000 Grenoble, France.
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6
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Eki R, She J, Parlak M, Benamar M, Du KP, Kumar P, Abbas T. A robust CRISPR-Cas9-based fluorescent reporter assay for the detection and quantification of DNA double-strand break repair. Nucleic Acids Res 2020; 48:e126. [PMID: 33068408 PMCID: PMC7708081 DOI: 10.1093/nar/gkaa897] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 12/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic lesions that can lead to chromosome rearrangements, genomic instability and cell death. Consequently, cells have evolved multiple mechanisms to efficiently repair DSBs to preserve genomic integrity. We have developed a DSB repair assay system, designated CDDR (CRISPR-Cas9-based Dual-fluorescent DSB Repair), that enables the detection and quantification of DSB repair outcomes in mammalian cells with high precision. CDDR is based on the introduction and subsequent resolution of one or two DSB(s) in an intrachromosomal fluorescent reporter following the expression of Cas9 and sgRNAs targeting the reporter. CDDR can discriminate between high-fidelity (HF) and error-prone non-homologous end-joining (NHEJ), as well as between proximal and distal NHEJ repair. Furthermore, CDDR can detect homology-directed repair (HDR) with high sensitivity. Using CDDR, we found HF-NHEJ to be strictly dependent on DNA Ligase IV, XRCC4 and XLF, members of the canonical branch of NHEJ pathway (c-NHEJ). Loss of these genes also stimulated HDR, and promoted error-prone distal end-joining. Deletion of the DNA repair kinase ATM, on the other hand, stimulated HF-NHEJ and suppressed HDR. These findings demonstrate the utility of CDDR in characterizing the effect of repair factors and in elucidating the balance between competing DSB repair pathways.
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Affiliation(s)
- Rebeka Eki
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Jane She
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA
| | - Mahmut Parlak
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA
| | - Mouadh Benamar
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Kang-Ping Du
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Tarek Abbas
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22908, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.,Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA.,Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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7
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Chen Y, Geng A, Zhang W, Qian Z, Wan X, Jiang Y, Mao Z. Fight to the bitter end: DNA repair and aging. Ageing Res Rev 2020; 64:101154. [PMID: 32977059 DOI: 10.1016/j.arr.2020.101154] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/05/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
DNA carries the genetic information that directs complex biological processes; thus, maintaining a stable genome is critical for individual growth and development and for human health. DNA repair is a fundamental and conserved mechanism responsible for mending damaged DNA and restoring genomic stability, while its deficiency is closely related to multiple human disorders. In recent years, remarkable progress has been made in the field of DNA repair and aging. Here, we will extensively discuss the relationship among DNA damage, DNA repair, aging and aging-associated diseases based on the latest research. In addition, the possible role of DNA repair in several potential rejuvenation strategies will be discussed. Finally, we will also review the emerging methods that may facilitate future research on DNA repair.
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8
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Degenhardt S, Dreffke K, Schötz U, Petersen C, Engenhart-Cabillic R, Rothkamm K, Dahm-Daphi J, Dikomey E, Mansour WY. Establishment of a Transformation Coupled in vitro End Joining Assay to Estimate Radiosensitivity in Tumor Cells. Front Oncol 2020; 10:1480. [PMID: 32974177 PMCID: PMC7468517 DOI: 10.3389/fonc.2020.01480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/10/2020] [Indexed: 11/25/2022] Open
Abstract
Here, we present a modified in vitro end-joining (EJ) assay to quantify EJ capacity, accuracy as well as pathway switch to alternative end-joining (Alt-EJ) or single strand annealing (SSA). A novel transformation assay was established to specifically measure circular repair products, which correlate with classical EJ efficiency. The EJ assay was validated using EJ-deficient mammalian cell lines (Ku80, DNA-PKcs, LigIV, or XRCC4 mutants). A pathway switch to Alt-EJ and SSA was seen exclusively in Ku-deficient cells. Circular EJ product formation correlated with cell survival and DSB repair capacity after X-irradiation. Investigation of 14 HNSCC cell lines revealed differences in the total EJ capacity but a broader variation in the amount of circular repair products. Sequencing of repair junctions in HNSCC cells demonstrated a predominance of high-fidelity EJ and an avoidance of both Alt-EJ and SSA. A significant correlation was observed between the amount of circular repair products, repair of IR-induced DSB and radiosensitivity. Collectively, these data indicate that the presented in vitro-EJ-assay can not only estimate the repair capacity of cancer cells to enable the stratification into radiosensitive or radioresistant, but can also identify repair pathway deregulation such as a switch to Alt-EJ or SSA, which enables tumor targeting.
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Affiliation(s)
- Sarah Degenhardt
- Laboratory of Radiobiology and Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristin Dreffke
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Marburg, Germany
| | - Urlike Schötz
- Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Marburg, Germany
| | - Cordula Petersen
- Department of Radiotherapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Kai Rothkamm
- Laboratory of Radiobiology and Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jochen Dahm-Daphi
- Laboratory of Radiobiology and Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Marburg, Germany
| | - Ekkehard Dikomey
- Laboratory of Radiobiology and Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Radiotherapy and Radiooncology, Philipps-University Marburg, Marburg, Germany
| | - Wael Yassin Mansour
- Laboratory of Radiobiology and Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Tumor Biology, National Cancer Institute, Cairo University, Cairo, Egypt
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9
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Bartnik K, Barth A, Pilo-Pais M, Crevenna AH, Liedl T, Lamb DC. A DNA Origami Platform for Single-Pair Förster Resonance Energy Transfer Investigation of DNA-DNA Interactions and Ligation. J Am Chem Soc 2020; 142:815-825. [PMID: 31800234 DOI: 10.1021/jacs.9b09093] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA double-strand breaks (DSBs) pose an everyday threat to the conservation of genetic information and therefore life itself. Several pathways have evolved to repair these cytotoxic lesions by rejoining broken ends, among them the nonhomologous end-joining mechanism that utilizes a DNA ligase. Here, we use a custom-designed DNA origami nanostructure as a model system to specifically mimic a DNA DSB, enabling us to study the end-joining of two fluorescently labeled DNA with the T4 DNA ligase on the single-molecule level. The ligation reaction is monitored by Förster resonance energy transfer (FRET) experiments both in solution and on surface-anchored origamis. Due to the modularity of DNA nanotechnology, DNA double strands with different complementary overhang lengths can be studied using the same DNA origami design. We show that the T4 DNA ligase repairs sticky ends more efficiently than blunt ends and that the ligation efficiency is influenced by both DNA sequence and the incubation conditions. Before ligation, dynamic fluctuations of the FRET signal are observed due to transient binding of the sticky overhangs. After ligation, the FRET signal becomes static. Thus, we can directly monitor the ligation reaction through the transition from dynamic to static FRET signals. Finally, we revert the ligation process using a restriction enzyme digestion and religate the resulting blunt ends. The here-presented DNA origami platform is thus suited to study complex multistep reactions occurring over several cycles of enzymatic treatment.
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Affiliation(s)
- Kira Bartnik
- Department of Chemistry, Center for Nanoscience (CeNS), Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM) , Ludwig-Maximilians-Universität München , 81377 Munich , Germany
| | - Anders Barth
- Department of Chemistry, Center for Nanoscience (CeNS), Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM) , Ludwig-Maximilians-Universität München , 81377 Munich , Germany
| | - Mauricio Pilo-Pais
- Department of Physics and Center for Nanoscience (CeNS) , Ludwig-Maximilians-Universität , 80539 Munich , Germany
| | - Alvaro H Crevenna
- Department of Chemistry, Center for Nanoscience (CeNS), Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM) , Ludwig-Maximilians-Universität München , 81377 Munich , Germany
| | - Tim Liedl
- Department of Physics and Center for Nanoscience (CeNS) , Ludwig-Maximilians-Universität , 80539 Munich , Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nanoscience (CeNS), Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM) , Ludwig-Maximilians-Universität München , 81377 Munich , Germany
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10
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Savini C, Yang R, Savelyeva L, Göckel-Krzikalla E, Hotz-Wagenblatt A, Westermann F, Rösl F. Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes. Int J Mol Sci 2019; 20:ijms20051100. [PMID: 30836646 PMCID: PMC6429418 DOI: 10.3390/ijms20051100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 01/01/2023] Open
Abstract
Supplementation of micronutrients like folate is a double-edged sword in terms of their ambivalent role in cell metabolism. Although several epidemiological studies support a protective role of folate in carcinogenesis, there are also data arguing for an opposite effect. To address this issue in the context of human papillomavirus (HPV)-induced transformation, the molecular events of different folate availability on human keratinocytes immortalized by HPV16 E6 and E7 oncoproteins were examined. Several sublines were established: Control (4.5 µM folate), folate deficient (0.002 µM folate), and repleted cells (4.5 µM folate). Cells were analyzed in terms of oncogene expression, DNA damage and repair, karyotype changes, whole-genome sequencing, and transcriptomics. Here we show that folate depletion irreversibly induces DNA damage, impairment of DNA repair fidelity, and unique chromosomal alterations. Repleted cells additionally underwent growth advantage and enhanced clonogenicity, while the above mentioned impaired molecular properties became even more pronounced. Overall, it appears that a period of folate deficiency followed by repletion can shape immortalized cells toward an anomalous phenotype, thereby potentially contributing to carcinogenesis. These observations should elicit questions and inquiries for broader additional studies regarding folate fortification programs, especially in developing countries with micronutrient deficiencies and high HPV prevalence.
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Affiliation(s)
- Claudia Savini
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Ruwen Yang
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Larisa Savelyeva
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Elke Göckel-Krzikalla
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Agnes Hotz-Wagenblatt
- Omics IT and Data Management, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Frank Westermann
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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11
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Fujii N. Potential Strategies to Target Protein-Protein Interactions in the DNA Damage Response and Repair Pathways. J Med Chem 2017; 60:9932-9959. [PMID: 28654754 DOI: 10.1021/acs.jmedchem.7b00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review article discusses some insights about generating novel mechanistic inhibitors of the DNA damage response and repair (DDR) pathways by focusing on protein-protein interactions (PPIs) of the key DDR components. General requirements for PPI strategies, such as selecting the target PPI site on the basis of its functionality, are discussed first. Next, on the basis of functional rationale and biochemical feasibility to identify a PPI inhibitor, 26 PPIs in DDR pathways (BER, MMR, NER, NHEJ, HR, TLS, and ICL repair) are specifically discussed for inhibitor discovery to benefit cancer therapies using a DNA-damaging agent.
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Affiliation(s)
- Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
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12
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McCormick A, Donoghue P, Dixon M, O'Sullivan R, O'Donnell RL, Murray J, Kaufmann A, Curtin NJ, Edmondson RJ. Ovarian Cancers Harbor Defects in Nonhomologous End Joining Resulting in Resistance to Rucaparib. Clin Cancer Res 2017. [PMID: 27702817 DOI: 10.1158/1078-0432.ccr-16-0564] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purpose: DNA damage defects are common in ovarian cancer and can be used to stratify treatment. Although most work has focused on homologous recombination (HR), DNA double-strand breaks are repaired primarily by nonhomologous end joining (NHEJ). Defects in NHEJ have been shown to contribute to genomic instability and have been associated with the development of chemoresistance.Experimental Design: NHEJ was assessed in a panel of ovarian cancer cell lines and 47 primary ascetic-derived ovarian cancer cultures, by measuring the ability of cell extracts to end-join linearized plasmid monomers into multimers. mRNA and protein expression of components of NHEJ was determined using RT-qPCR and Western blotting. Cytotoxicities of cisplatin and the PARP inhibitor rucaparib were assessed using sulforhodamine B (SRB) assays. HR function was assessed using γH2AX/RAD51 foci assay.Results: NHEJ was defective (D) in four of six cell lines and 20 of 47 primary cultures. NHEJ function was independent of HR competence (C). NHEJD cultures were resistant to rucaparib (P = 0.0022). When HR and NHEJ functions were taken into account, only NHEJC/HRD cultures were sensitive to rucaparib (compared with NHEJC/HRC P = 0.034, NHEJD/HRC P = 0.0002, and NHEJD/HRD P = 0.0045). The DNA-PK inhibitor, NU7441, induced resistance to rucaparib (P = 0.014) and HR function recovery in a BRCA1-defective cell line.Conclusions: This study has shown that NHEJ is defective in 40% of ovarian cancers, which is independent of HR function and associated with resistance to PARP inhibitors in ex vivo primary cultures. Clin Cancer Res; 23(8); 2050-60. ©2016 AACR.
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Affiliation(s)
- Aiste McCormick
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Peter Donoghue
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Michelle Dixon
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Richard O'Sullivan
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Rachel L O'Donnell
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.,Northern Gynaecological Oncology Centre, Queen Elizabeth Hospital, Gateshead, United Kingdom
| | - James Murray
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Angelika Kaufmann
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.,Northern Gynaecological Oncology Centre, Queen Elizabeth Hospital, Gateshead, United Kingdom
| | - Nicola J Curtin
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.
| | - Richard J Edmondson
- Faculty Institute for Cancer Studies, University of Manchester, St Mary's Hospital, Oxford Road, Manchester, United Kingdom.
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13
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McCormick A, Donoghue P, Dixon M, O'Sullivan R, O'Donnell RL, Murray J, Kaufmann A, Curtin NJ, Edmondson RJ. Ovarian Cancers Harbor Defects in Nonhomologous End Joining Resulting in Resistance to Rucaparib. Clin Cancer Res 2017; 23:2050-2060. [PMID: 27702817 PMCID: PMC5393437 DOI: 10.1158/1078-0432.ccr-16-0564] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 11/16/2022]
Abstract
Purpose: DNA damage defects are common in ovarian cancer and can be used to stratify treatment. Although most work has focused on homologous recombination (HR), DNA double-strand breaks are repaired primarily by nonhomologous end joining (NHEJ). Defects in NHEJ have been shown to contribute to genomic instability and have been associated with the development of chemoresistance.Experimental Design: NHEJ was assessed in a panel of ovarian cancer cell lines and 47 primary ascetic-derived ovarian cancer cultures, by measuring the ability of cell extracts to end-join linearized plasmid monomers into multimers. mRNA and protein expression of components of NHEJ was determined using RT-qPCR and Western blotting. Cytotoxicities of cisplatin and the PARP inhibitor rucaparib were assessed using sulforhodamine B (SRB) assays. HR function was assessed using γH2AX/RAD51 foci assay.Results: NHEJ was defective (D) in four of six cell lines and 20 of 47 primary cultures. NHEJ function was independent of HR competence (C). NHEJD cultures were resistant to rucaparib (P = 0.0022). When HR and NHEJ functions were taken into account, only NHEJC/HRD cultures were sensitive to rucaparib (compared with NHEJC/HRC P = 0.034, NHEJD/HRC P = 0.0002, and NHEJD/HRD P = 0.0045). The DNA-PK inhibitor, NU7441, induced resistance to rucaparib (P = 0.014) and HR function recovery in a BRCA1-defective cell line.Conclusions: This study has shown that NHEJ is defective in 40% of ovarian cancers, which is independent of HR function and associated with resistance to PARP inhibitors in ex vivo primary cultures. Clin Cancer Res; 23(8); 2050-60. ©2016 AACR.
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Affiliation(s)
- Aiste McCormick
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Peter Donoghue
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Michelle Dixon
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Richard O'Sullivan
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Rachel L O'Donnell
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
- Northern Gynaecological Oncology Centre, Queen Elizabeth Hospital, Gateshead, United Kingdom
| | - James Murray
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Angelika Kaufmann
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
- Northern Gynaecological Oncology Centre, Queen Elizabeth Hospital, Gateshead, United Kingdom
| | - Nicola J Curtin
- Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.
| | - Richard J Edmondson
- Faculty Institute for Cancer Studies, University of Manchester, St Mary's Hospital, Oxford Road, Manchester, United Kingdom.
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14
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Zhu S, Peng A. Non-homologous end joining repair in Xenopus egg extract. Sci Rep 2016; 6:27797. [PMID: 27324260 PMCID: PMC4914968 DOI: 10.1038/srep27797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/25/2016] [Indexed: 11/09/2022] Open
Abstract
Non-homologous end joining (NHEJ) is a major DNA double-strand break (DSB) repair mechanism. We characterized here a series of plasmid-based DSB templates that were repaired in Xenopus egg extracts via the canonical, Ku-dependent NHEJ pathway. We showed that the template with compatible ends was efficiently repaired without end processing, in a manner that required the kinase activity of DNA-PKcs but not ATM. Moreover, non-compatible ends with blunt/3'-overhang, blunt/5'-overhang, and 3'-overhang/5'-overhang were predominantly repaired with fill-in and ligation without the removal of end nucleotides. In contrast, 3'-overhang/3'-overhang and 5'-overhang/5'-overhang templates were processed by resection of 3-5 bases and fill-in of 1-4 bases prior to end ligation. Therefore, the NHEJ machinery exhibited a strong preference for precise repair; the presence of neither non-compatible ends nor protruding single strand DNA sufficiently warranted the action of nucleases. ATM was required for the efficient repair of all non-compatible ends including those repaired without end processing by nucleases, suggesting its role beyond phosphorylation and regulation of Artemis. Finally, dephosphorylation of the 5'-overhang/3'-overhang template reduced the efficiency of DNA repair without increasing the risk of end resection, indicating that end protection via prompt end ligation is not the sole mechanism that suppresses the action of nucleases.
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Affiliation(s)
- Songli Zhu
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Aimin Peng
- Department of Oral Biology, College of Dentistry, University of Nebraska Medical Center, Lincoln, NE 68583, USA
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15
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Yuan Y, Britton S, Delteil C, Coates J, Jackson SP, Barboule N, Frit P, Calsou P. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein. Nucleic Acids Res 2015; 43:10264-76. [PMID: 26350212 PMCID: PMC4666393 DOI: 10.1093/nar/gkv894] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/26/2015] [Accepted: 08/26/2015] [Indexed: 11/17/2022] Open
Abstract
In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3' single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process.
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Affiliation(s)
- Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Sébastien Britton
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Christine Delteil
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN England, UK
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN England, UK
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
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16
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Abstract
Double-strand breaks (DSB) in genomic DNA are induced by ionizing radiation or radiomimetic drugs but also occur spontaneously during the cell cycle at quite significant frequencies. In vertebrate cells, nonhomologous DNA end joining (NHEJ) is considered the major pathway of DSB repair which is able to rejoin two broken DNA termini directly end-to-end irrespective of sequence and structure. Genetic studies in various radiosensitive and DSB repair-deficient cell lines yielded insight into the factors involved in NHEJ. Studies in cell-free systems derived from Xenopus eggs and mammalian cells allowed the dissection of the underlying mechanisms. In the present chapter, we describe a protocol for the preparation of whole cell extracts from mammalian cells and a plasmid-based in vitro assay which permits the easy analysis of the efficiency and fidelity of DSB repair via NHEJ in different cell types.
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17
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Wortmannin potentiates the combined effect of etoposide and cisplatin in human glioma cells. Int J Biochem Cell Biol 2014; 53:423-31. [DOI: 10.1016/j.biocel.2014.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 05/28/2014] [Accepted: 06/13/2014] [Indexed: 01/14/2023]
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18
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Shamanna RA, Singh DK, Lu H, Mirey G, Keijzers G, Salles B, Croteau DL, Bohr VA. RECQ helicase RECQL4 participates in non-homologous end joining and interacts with the Ku complex. Carcinogenesis 2014; 35:2415-24. [PMID: 24942867 DOI: 10.1093/carcin/bgu137] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RECQL4, a member of the RecQ helicase family, is a multifunctional participant in DNA metabolism. RECQL4 protein participates in several functions both in the nucleus and in the cytoplasm of the cell, and mutations in human RECQL4 are associated with three genetic disorders: Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. We previously reported that RECQL4 is recruited to laser-induced DNA double-strand breaks (DSB). Here, we have characterized the functional roles of RECQL4 in the non-homologous end joining (NHEJ) pathway of DSB repair. In an in vitro NHEJ assay that depends on the activity of DNA-dependent protein kinase (DNA-PK), extracts from RECQL4 knockdown cells display reduced end-joining activity on DNA substrates with cohesive and non-cohesive ends. Depletion of RECQL4 also reduced the end joining activity on a GFP reporter plasmid in vivo. Knockdown of RECQL4 increased the sensitivity of cells to γ-irradiation and resulted in accumulation of 53BP1 foci after irradiation, indicating defects in the processing of DSB. We find that RECQL4 interacts with the Ku70/Ku80 heterodimer, part of the DNA-PK complex, via its N-terminal domain. Further, RECQL4 stimulates higher order DNA binding of Ku70/Ku80 to a blunt end DNA substrate. Taken together, these results implicate that RECQL4 participates in the NHEJ pathway of DSB repair via a functional interaction with the Ku70/Ku80 complex. This is the first study to provide both in vitro and in vivo evidence for a role of a RecQ helicase in NHEJ.
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Affiliation(s)
- Raghavendra A Shamanna
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA, INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Dharmendra Kumar Singh
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA, INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Huiming Lu
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA, INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Gladys Mirey
- INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and
| | - Guido Keijzers
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Bernard Salles
- INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA, INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA, INRA, Université de Toulouse, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
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19
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Canugovi C, Shamanna RA, Croteau DL, Bohr VA. Base excision DNA repair levels in mitochondrial lysates of Alzheimer's disease. Neurobiol Aging 2014; 35:1293-300. [PMID: 24485507 PMCID: PMC5576885 DOI: 10.1016/j.neurobiolaging.2014.01.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 12/20/2013] [Accepted: 01/04/2014] [Indexed: 10/25/2022]
Abstract
Alzheimer's disease (AD) is a senile dementia with increased incidence in older subjects (age >65 years). One of the earliest markers of AD is oxidative DNA damage. Recently, it has been reported that preclinical AD patient brains show elevated levels of oxidative damage in both nuclear and mitochondrial nucleic acids. Moreover, different oxidative lesions in mitochondrial DNA are between 5- and 10-fold higher than in nuclear DNA in both control and AD postmortem brains. We previously showed that there is a significant loss of base excision repair (BER) components in whole tissue extracts of AD and mild cognitive impairment subjects relative to matched control subjects. However, comprehensive analysis of specific steps in BER levels in mitochondrial extracts of AD patient brains is not available. In this study, we mainly investigated various components of BER in mitochondrial extracts of AD and matched control postmortem brain samples. We found that the 5-hydroxyuracil incision and ligase activities are significantly lower in AD brains, whereas the uracil incision, abasic site cleavage, and deoxyribonucleotide triphosphate incorporation activities are normal in these samples.
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Affiliation(s)
- Chandrika Canugovi
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | | | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, Baltimore, MD, USA.
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20
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Rossner P, Rossnerova A, Beskid O, Tabashidze N, Libalova H, Uhlirova K, Topinka J, Sram RJ. Nonhomologous DNA end joining and chromosome aberrations in human embryonic lung fibroblasts treated with environmental pollutants. Mutat Res 2014; 763-764:28-38. [PMID: 24694657 DOI: 10.1016/j.mrfmmm.2014.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 02/25/2014] [Accepted: 03/07/2014] [Indexed: 06/03/2023]
Abstract
In order to evaluate the ability of a representative polycyclic aromatic hydrocarbon (PAH) and PAH-containing complex mixtures to induce double strand DNA breaks (DSBs) and repair of damaged DNA in human embryonic lung fibroblasts (HEL12469 cells), we investigated the effect of benzo[a]pyrene (B[a]P) and extractable organic matter (EOM) from ambient air particles <2.5μm (PM2.5) on nonhomologous DNA end joining (NHEJ) and induction of stable chromosome aberrations (CAs). PM2.5 was collected in winter and summer 2011 in two Czech cities differing in levels and sources of air pollutants. The cells were treated for 24h with the following concentrations of tested chemicals: B[a]P: 1μM, 10μM, 25μM; EOMs: 1μg/ml, 10μg/ml, 25μg/ml. We tested several endpoints representing key steps leading from DSBs to the formation of CAs including histone H2AX phosphorylation, levels of proteins Ku70, Ku80 and XRCC4 participating in NHEJ, in vitro ligation activity of nuclear extracts of the HEL12469 cells and the frequency of stable CAs assessed by whole chromosome painting of chromosomes 1, 2, 4, 5, 7 and 17 using fluorescence in situ hybridization. Our results show that 25μM of B[a]P and most of the tested doses of EOMs induced DSBs as indicated by H2AX phosphorylation. DNA damage was accompanied by induction of XRCC4 expression and an increased frequency of CAs. Translocations most frequently affected chromosome 7. We observed only a weak induction of Ku70/80 expression as well as ligation activity of nuclear extracts. In summary, our data suggest the induction of DSBs and NHEJ after treatment of human embryonic lung fibroblasts with B[a]P and complex mixtures containing PAHs.
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Affiliation(s)
- Pavel Rossner
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic.
| | - Andrea Rossnerova
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
| | - Olena Beskid
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
| | - Nana Tabashidze
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
| | - Helena Libalova
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
| | - Katerina Uhlirova
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
| | - Jan Topinka
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
| | - Radim J Sram
- Department of Genetic Ecotoxicology, Institute of Experimental Medicine AS CR, Prague, Czech Republic
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21
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Frit P, Barboule N, Yuan Y, Gomez D, Calsou P. Alternative end-joining pathway(s): bricolage at DNA breaks. DNA Repair (Amst) 2014; 17:81-97. [PMID: 24613763 DOI: 10.1016/j.dnarep.2014.02.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/01/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
To cope with DNA double strand break (DSB) genotoxicity, cells have evolved two main repair pathways: homologous recombination which uses homologous DNA sequences as repair templates, and non-homologous Ku-dependent end-joining involving direct sealing of DSB ends by DNA ligase IV (Lig4). During the last two decades a third player most commonly named alternative end-joining (A-EJ) has emerged, which is defined as any Ku- or Lig4-independent end-joining process. A-EJ increasingly appears as a highly error-prone bricolage on DSBs and despite expanding exploration, it still escapes full characterization. In the present review, we discuss the mechanism and regulation of A-EJ as well as its biological relevance under physiological and pathological situations, with a particular emphasis on chromosomal instability and cancer. Whether or not it is a genuine DSB repair pathway, A-EJ is emerging as an important cellular process and understanding A-EJ will certainly be a major challenge for the coming years.
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Affiliation(s)
- Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Dennis Gomez
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, 31077 Toulouse, Cedex4, France; Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France; Equipe labellisée Ligue Nationale Contre le Cancer, France.
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22
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Bindra RS, Goglia AG, Jasin M, Powell SN. Development of an assay to measure mutagenic non-homologous end-joining repair activity in mammalian cells. Nucleic Acids Res 2013; 41:e115. [PMID: 23585275 PMCID: PMC3675474 DOI: 10.1093/nar/gkt255] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Double-strand break (DSB) repair pathways are critical for the maintenance of genomic integrity and the prevention of tumorigenesis in mammalian cells. Here, we present the development and validation of a novel assay to measure mutagenic non-homologous end-joining (NHEJ) repair in living cells, which is inversely related to canonical NHEJ and is based on the sequence-altering repair of a single site-specific DSB at an intrachromosomal locus. We have combined this mutagenic NHEJ assay with an established homologous recombination (HR) assay such that both pathways can be monitored simultaneously. In addition, we report the development of a ligand-responsive I-SceI protein, in which the timing and kinetics of DSB induction can be precisely controlled by regulating protein stability and cellular localization in cells. Using this system, we report that mutagenic NHEJ repair is suppressed in growth-arrested and serum-deprived cells, suggesting that end-joining activity in proliferating cells is more likely to be mutagenic. Collectively, the novel DSB repair assay and inducible I-SceI will be useful tools to further elucidate the complexities of NHEJ and HR repair.
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Affiliation(s)
- Ranjit S Bindra
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Charles C, Ouedraogo M, Belayew A, Duez P. On-chip microelectrophoresis for the study of in vitro nonhomologous end-joining DNA double-strand break repair. Anal Biochem 2012; 425:76-9. [DOI: 10.1016/j.ab.2012.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 03/03/2012] [Accepted: 03/05/2012] [Indexed: 02/04/2023]
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Chiruvella KK, Sebastian R, Sharma S, Karande AA, Choudhary B, Raghavan SC. Time-Dependent Predominance of Nonhomologous DNA End-Joining Pathways during Embryonic Development in Mice. J Mol Biol 2012; 417:197-211. [DOI: 10.1016/j.jmb.2012.01.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 01/18/2012] [Accepted: 01/20/2012] [Indexed: 12/26/2022]
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The NF90/NF45 complex participates in DNA break repair via nonhomologous end joining. Mol Cell Biol 2011; 31:4832-43. [PMID: 21969602 DOI: 10.1128/mcb.05849-11] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nuclear factor 90 (NF90), an RNA-binding protein implicated in the regulation of gene expression, exists as a heterodimeric complex with NF45. We previously reported that depletion of the NF90/NF45 complex results in a multinucleated phenotype. Time-lapse microscopy revealed that binucleated cells arise by incomplete abscission of progeny cells followed by fusion. Multinucleate cells arose through aberrant division of binucleated cells and displayed abnormal metaphase plates and anaphase chromatin bridges suggestive of DNA repair defects. NF90 and NF45 are known to interact with the DNA-dependent protein kinase (DNA-PK), which is involved in telomere maintenance and DNA repair by nonhomologous end joining (NHEJ). We hypothesized that NF90 modulates the activity of DNA-PK. In an in vitro NHEJ assay system, DNA end joining was reduced by NF90/NF45 immunodepletion or by RNA digestion to an extent similar to that for catalytic subunit DNA-PKcs immunodepletion. In vivo, NF90/NF45-depleted cells displayed increased γ-histone 2A.X foci, indicative of an accumulation of double-strand DNA breaks (DSBs), and increased sensitivity to ionizing radiation consistent with decreased DSB repair. Further, NF90/NF45 knockdown reduced end-joining activity in vivo. These results identify the NF90/NF45 complex as a regulator of DNA damage repair mediated by DNA-PK and suggest that structured RNA may modulate this process.
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Datta K, Purkayastha S, Neumann RD, Pastwa E, Winters TA. Base damage immediately upstream from double-strand break ends is a more severe impediment to nonhomologous end joining than blocked 3'-termini. Radiat Res 2011; 175:97-112. [PMID: 21175352 PMCID: PMC3518376 DOI: 10.1667/rr2332.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Radiation-induced DNA double-strand breaks (DSBs) are critical cytotoxic lesions that are typically repaired by nonhomologous end joining (NHEJ) in human cells. Our previous work indicated that the highly cytotoxic DSBs formed by (125)I decay possess base damage clustered within 8 to 10 bases of the break and 3'-phosphate (P) and 3'-OH ends. This study examined the effect of such structures on NHEJ in in vitro assays employing either (125)I decay-induced DSB linearized plasmid DNA or structurally defined duplex oligonucleotides. Duplex oligonucleotides that possess either a 3'-P or 3'-phosphoglycolate (PG) or a ligatable 3'-OH end with either an AP site or an 8-oxo-dG 1 nucleotide upstream (-1n) from the 3'-terminus have been examined for reparability. Moderate to severe end-joining inhibition was observed for modified DSB ends or 8-oxo-dG upstream from a 3'-OH end. In contrast, abolition of end joining was observed with duplexes possessing an AP site upstream from a ligatable 3'-OH end or for a lesion combination involving 3'-P plus an upstream 8-oxo-dG. In addition, base mismatches at the -1n position were also strong inhibitors of NHEJ in this system, suggesting that destabilization of the DSB terminus as a result of base loss or improper base pairing may play a role in the inhibitory effects of these structures. Furthermore, we provide data indicating that DSB end joining is likely to occur prior to removal or repair of base lesions proximal to the DSB terminus. Our results show that base damage or base loss near a DSB end may be a severe block to NHEJ and that complex combinations of lesions presented in the context of a DSB may be more inhibitory than the individual lesions alone. In contrast, blocked DSB 3'-ends alone are only modestly inhibitory to NHEJ. Finally, DNA ligase activity is implicated as being responsible for these effects.
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Affiliation(s)
- Kamal Datta
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
| | - Shubhadeep Purkayastha
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
| | - Ronald D. Neumann
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
| | - Elzbieta Pastwa
- Department of Medicinal Chemistry, Medical University of Lodz, Lodz, Poland 92-215
| | - Thomas A. Winters
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
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Velma V, Carrero ZI, Cosman AM, Hebert MD. Coilin interacts with Ku proteins and inhibits in vitro non-homologous DNA end joining. FEBS Lett 2010; 584:4735-9. [PMID: 21070772 DOI: 10.1016/j.febslet.2010.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/15/2010] [Accepted: 11/01/2010] [Indexed: 01/18/2023]
Abstract
Coilin is a nuclear protein that plays a role in Cajal body formation. The function of nucleoplasmic coilin is unknown. Here we report that coilin interacts with Ku70 and Ku80, which are major players in the DNA repair process. Ku proteins compete with SMN and SmB' proteins for coilin interaction sites. The binding domain on coilin for Ku proteins cannot be localized to one discrete region, and only full-length coilin is capable of inhibiting in vitro non-homologous DNA end joining (NHEJ). Since Ku proteins do not accumulate in CBs, these findings suggest that nucleoplasmic coilin participates in the regulation of DNA repair.
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Affiliation(s)
- Venkatramreddy Velma
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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Baumstark-Khan C, Hellweg CE, Reitz G. Cytotoxicity and genotoxicity reporter systems based on the use of mammalian cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 118:113-51. [PMID: 20140660 DOI: 10.1007/10_2009_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
With the dramatic increase in the number of new agents arising from the chemical, pharmaceutical, and agricultural industries, there is an urgent need to develop assays for rapid evaluation of potential risks to man and environment. The panel of conventional tests used for cytotoxicity and genotoxicity and the strategies to progress from small scale assays to high content screening in toxicology are discussed. The properties of components necessary as sensors and reporters for new reporter assays, and the application of genetic strategies to design assays are reviewed. The concept of cellular reporters is based on the use of promoters of chemical stress-regulated genes ligated to a suitable luminescent or fluorescent reporter gene. Current reporter assays designed from constructs transferred into suitable cell lines are presented.
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Affiliation(s)
- Christa Baumstark-Khan
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Centre (DLR), Linder Hoehe, 51147, Cologne, Germany,
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