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Galanos P, Pappas G, Polyzos A, Kotsinas A, Svolaki I, Giakoumakis NN, Glytsou C, Pateras IS, Swain U, Souliotis VL, Georgakilas AG, Geacintov N, Scorrano L, Lukas C, Lukas J, Livneh Z, Lygerou Z, Chowdhury D, Sørensen CS, Bartek J, Gorgoulis VG. Author Correction: Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability. Genome Biol 2022; 23:107. [PMID: 35484586 PMCID: PMC9052693 DOI: 10.1186/s13059-022-02678-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Affiliation(s)
- Panagiotis Galanos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece.,Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark
| | - George Pappas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece.,Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark
| | - Alexander Polyzos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str, GR-11527, Athens, Greece
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | - Ioanna Svolaki
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | | | | | - Ioannis S Pateras
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | - Umakanta Swain
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Vassilis L Souliotis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, GR-11635, Athens, Greece
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780, Zografou, Athens, Greece
| | | | - Luca Scorrano
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, 26505, Patras, Rio, Greece
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark
| | - Jiri Bartek
- Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark. .,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77, Stockholm, Sweden.
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece. .,Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str, GR-11527, Athens, Greece. .,Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4QL, UK.
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2
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Somyajit K, Spies J, Coscia F, Kirik U, Rask MB, Lee JH, Neelsen KJ, Mund A, Jensen LJ, Paull TT, Mann M, Lukas J. Homology-directed repair protects the replicating genome from metabolic assaults. Dev Cell 2021; 56:461-477.e7. [PMID: 33621493 DOI: 10.1016/j.devcel.2021.01.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 05/19/2020] [Revised: 10/14/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Homology-directed repair (HDR) safeguards DNA integrity under various forms of stress, but how HDR protects replicating genomes under extensive metabolic alterations remains unclear. Here, we report that besides stalling replication forks, inhibition of ribonucleotide reductase (RNR) triggers metabolic imbalance manifested by the accumulation of increased reactive oxygen species (ROS) in cell nuclei. This leads to a redox-sensitive activation of the ATM kinase followed by phosphorylation of the MRE11 nuclease, which in HDR-deficient settings degrades stalled replication forks. Intriguingly, nascent DNA degradation by the ROS-ATM-MRE11 cascade is also triggered by hypoxia, which elevates signaling-competent ROS and attenuates functional HDR without arresting replication forks. Under these conditions, MRE11 degrades daughter-strand DNA gaps, which accumulate behind active replisomes and attract error-prone DNA polymerases to escalate mutation rates. Thus, HDR safeguards replicating genomes against metabolic assaults by restraining mutagenic repair at aberrantly processed nascent DNA. These findings have implications for cancer evolution and tumor therapy.
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Affiliation(s)
- Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
| | - Julian Spies
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Fabian Coscia
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ufuk Kirik
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein, Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ji-Hoon Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kai John Neelsen
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein, Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Tanya T Paull
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Matthias Mann
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
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Ercilla A, Benada J, Amitash S, Zonderland G, Baldi G, Somyajit K, Ochs F, Costanzo V, Lukas J, Toledo L. Physiological Tolerance to ssDNA Enables Strand Uncoupling during DNA Replication. Cell Rep 2021; 30:2416-2429.e7. [PMID: 32075739 DOI: 10.1016/j.celrep.2020.01.067] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 05/14/2019] [Revised: 12/17/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022] Open
Abstract
It has been long assumed that normally leading strand synthesis must proceed coordinated with the lagging strand to prevent strand uncoupling and the pathological accumulation of single-stranded DNA (ssDNA) in the cell, a dogma recently challenged by in vitro studies in prokaryotes. Here, we report that human DNA polymerases can function independently at each strand in vivo and that the resulting strand uncoupling is supported physiologically by a cellular tolerance to ssDNA. Active forks rapidly accumulate ssDNA at the lagging strand when POLA1 is inhibited without triggering a stress response, despite ssDNA formation being considered a hallmark of replication stress. Acute POLA1 inhibition causes a lethal RPA exhaustion, but cells can duplicate their DNA with limited POLA1 activity and exacerbated strand uncoupling as long as RPA molecules suffice to protect the elevated ssDNA. Although robust, this uncoupled mode of DNA replication is also an in-built weakness that can be targeted for cancer treatment.
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Affiliation(s)
- Amaia Ercilla
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jan Benada
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sampath Amitash
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Gijs Zonderland
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Giorgio Baldi
- DNA Metabolism Laboratory, FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy
| | - Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Fena Ochs
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Luis Toledo
- Center for Chromosome Stability, Institute for Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
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4
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Sedlackova H, Rask MB, Gupta R, Choudhary C, Somyajit K, Lukas J. Equilibrium between nascent and parental MCM proteins protects replicating genomes. Nature 2020; 587:297-302. [PMID: 33087936 DOI: 10.1038/s41586-020-2842-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Minichromosome maintenance proteins (MCMs) are DNA-dependent ATPases that bind to replication origins and license them to support a single round of DNA replication. A large excess of MCM2-7 assembles on chromatin in G1 phase as pre-replication complexes (pre-RCs), of which only a fraction become the productive CDC45-MCM-GINS (CMG) helicases that are required for genome duplication1-4. It remains unclear why cells generate this surplus of MCMs, how they manage to sustain it across multiple generations, and why even a mild reduction in the MCM pool compromises the integrity of replicating genomes5,6. Here we show that, for daughter cells to sustain error-free DNA replication, their mother cells build up a nuclear pool of MCMs both by recycling chromatin-bound (parental) MCMs and by synthesizing new (nascent) MCMs. Although all MCMs can form pre-RCs, it is the parental pool that is inherently stable and preferentially matures into CMGs. By contrast, nascent MCM3-7 (but not MCM2) undergo rapid proteolysis in the cytoplasm, and their stabilization and nuclear translocation require interaction with minichromosome-maintenance complex-binding protein (MCMBP), a distant MCM paralogue7,8. By chaperoning nascent MCMs, MCMBP safeguards replicating genomes by increasing chromatin coverage with pre-RCs that do not participate on replication origins but adjust the pace of replisome movement to minimize errors during DNA replication. Consequently, although the paucity of pre-RCs in MCMBP-deficient cells does not alter DNA synthesis overall, it increases the speed and asymmetry of individual replisomes, which leads to DNA damage. The surplus of MCMs therefore increases the robustness of genome duplication by restraining the speed at which eukaryotic cells replicate their DNA. Alterations in physiological fork speed might thus explain why even a minor reduction in MCM levels destabilizes the genome and predisposes to increased incidence of tumour formation.
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Affiliation(s)
- Hana Sedlackova
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajat Gupta
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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5
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Ochs F, Karemore G, Miron E, Brown J, Sedlackova H, Rask MB, Lampe M, Buckle V, Schermelleh L, Lukas J, Lukas C. Stabilization of chromatin topology safeguards genome integrity. Nature 2019; 574:571-574. [DOI: 10.1038/s41586-019-1659-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 09/10/2019] [Indexed: 11/10/2022]
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Kiesewetter B, Lamm W, Dolak W, Lukas J, Mayerhoefer M, Weber M, Kornauth C, Schiefer A, Bayer G, Simonitsch-Klupp I, Raderer M. TRANSFORMED MUCOSA-ASSOCIATED LYMPHOID TISSUE LYMPHOMAS: A SINGLE INSTITUTION RETROSPECTIVE STUDY INCLUDING PCR-BASED CLONALITY ANALYSIS. Hematol Oncol 2019. [DOI: 10.1002/hon.73_2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- B. Kiesewetter
- Department of Medicine I; Clinical Division of Oncology, Medical University of Vienna; Vienna Austria
| | - W. Lamm
- Department of Medicine I; Clinical Division of Oncology, Medical University of Vienna; Vienna Austria
| | - W. Dolak
- Department of Medicine III; Clinical Division of Gastroenterology and Hepatology, Medical University of Vienna; Vienna Austria
| | - J. Lukas
- Department of Ophthalmology and Optometry; Medical University of Vienna; Vienna Austria
| | - M.E. Mayerhoefer
- Department of Biomedical Imaging and Image-guided Therapy; Division of Nuclear Medicine, Medical University of Vienna; Vienna Austria
| | - M. Weber
- Department of Biomedical Imaging and Image-guided Therapy; Division of Nuclear Medicine, Medical University of Vienna; Vienna Austria
| | - C. Kornauth
- Department of Pathology; Medical University of Vienna; Vienna Austria
| | - A.I. Schiefer
- Department of Pathology; Medical University of Vienna; Vienna Austria
| | - G. Bayer
- Department of Pathology; Medical University of Vienna; Vienna Austria
| | | | - M. Raderer
- Department of Medicine I; Clinical Division of Oncology, Medical University of Vienna; Vienna Austria
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Kiesewetter B, Lamm W, Mayerhoefer M, Dolak W, Lukas J, Simonitsch-Klupp I, Raderer M. FIRST LINE SYSTEMIC TREATMENT IN MUCOSA-ASSOCIATED LYMPHOID TISSUE (MALT) LYMPHOMA NOT ELIGIBLE FOR H. PYLORI ERADICATION - DO WE NEED CHEMOTHERAPY? Hematol Oncol 2019. [DOI: 10.1002/hon.125_2631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- B. Kiesewetter
- Department of Medicine I; Clinical Division of Oncology, Medical University of Vienna; Vienna Austria
| | - W. Lamm
- Department of Medicine I; Clinical Division of Oncology, Medical University of Vienna; Vienna Austria
| | - M.E. Mayerhoefer
- Department of Biomedical Imaging and Image-guided Therapy; Division of Nuclear Medicine, Medical University of Vienna; Vienna Austria
| | - W. Dolak
- Department of Medicine III; Clinical Division of Gastroenterology and Hepatology, Medical University of Vienna; Vienna Austria
| | - J. Lukas
- Department of Ophthalmology and Optometry; Medical University of Vienna; Vienna Austria
| | | | - M. Raderer
- Department of Medicine I; Clinical Division of Oncology, Medical University of Vienna; Vienna Austria
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Spies J, Lukas C, Somyajit K, Rask MB, Lukas J, Neelsen KJ. 53BP1 nuclear bodies enforce replication timing at under-replicated DNA to limit heritable DNA damage. Nat Cell Biol 2019; 21:487-497. [PMID: 30804506 DOI: 10.1038/s41556-019-0293-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/21/2019] [Indexed: 01/13/2023]
Abstract
Failure to complete DNA replication is a stochastic by-product of genome doubling in almost every cell cycle. During mitosis, under-replicated DNA (UR-DNA) is converted into DNA lesions, which are inherited by daughter cells and sequestered in 53BP1 nuclear bodies (53BP1-NBs). The fate of such cells remains unknown. Here, we show that the formation of 53BP1-NBs interrupts the chain of iterative damage intrinsically embedded in UR-DNA. Unlike clastogen-induced 53BP1 foci that are repaired throughout interphase, 53BP1-NBs restrain replication of the embedded genomic loci until late S phase, thus enabling the dedicated RAD52-mediated repair of UR-DNA lesions. The absence or malfunction of 53BP1-NBs causes premature replication of the affected loci, accompanied by genotoxic RAD51-mediated recombination. Thus, through adjusting replication timing and repair pathway choice at under-replicated loci, 53BP1-NBs enable the completion of genome duplication of inherited UR-DNA and prevent the conversion of stochastic under-replications into genome instability.
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Affiliation(s)
- Julian Spies
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kumar Somyajit
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maj-Britt Rask
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Kai John Neelsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Bhattacharya S, Holmes JP, Calfa C, Lukas J, Tan-Chiu E, Clifton GT, Peoples GE, Lacher M, Wiseman CL, Williams WV. Abstract P2-09-09: Initial safety and efficacy of a phase I/IIa trial of a modified whole tumor cell targeted immunotherapy in patients with advanced breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p2-09-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: SV-BR-1-GM is a GM-CSF transfected breast cancer cell line which expresses HLA class I & II antigens. In a previous clinical trial, a partial response of widely metastatic breast cancer was seen in a patient who matched SV-BR-1-GM at HLA-DRB3*02:02. Here we report the safety and efficacy analysis with immunologic correlates of response in the initial patients in a phase I/IIa trial of SV-BR-1-GM in patients with advanced breast cancer
Methods: This phase I/IIa trial enrolled patients with recurrent and/or metastatic breast cancer refractory to standard chemotherapy/targeted-therapy. Patients received low-dose cyclophosphamide 2-3d prior to intradermal injection of SV-BR-1-GM (20x106 cells divided into 4 sites) and interferon-α into the inoculation sites (10,000 IU/site) ˜2 & 4 days subsequently. Cycles were 2 weeks x3 then q mo x 3. Adverse events (AE) were evaluated after each inoculation and graded via CTCAE v4.03. Immunologic response was measured by delayed type hypersensitivity (DTH) after each inoculation. Disease response was evaluated radiographically q3 mo and as clinically indicated (clinical trial NCT03066947).
Results: To date, twenty-two patients have been enrolled and 17 have been inoculated for a total of 39 SV-BR-1-GM inoculations given. Per inoculation, the maximum related AE was grade 1 in 64%, grade 2 in 7.7%, and grade 3 in 7.7%. There were no related grade >3 or unexpected AE. Efficacy data is available on the first six (Table). Tumor regression was seen in 2 patients. 01-002 presented with liver, bone and 20 classic miliary lung metastases (up to 9mm). This subject previously received 7 chemotherapy regimens. She matched SV-BR-1-GM at Class I & II HLA loci. Imaging at 3 mo showed virtually complete regression of all 20 identifiable lesions in the lungs. This response was maintained at 6 mo but the subject was taken off protocol because of disease progression (liver and bone). 01-005, matching HLA-A*24:02, had notable regression of cutaneous lesions, but progressed in pleural and pericardial effusions, had irreversible cardiac arrest (unlikely related). DTH increased in 01-002 from 4mm (first dose) to 47mm (8th dose). Three of 3 patients evaluated developed antibodies responses (as measured by flow cytometry with SV-BR-1) including 01-002. Interleukin 8 also increased in 01-002.
Conclusions: SV-BR-1-GM in this regimen appears to be safe and well-tolerated. In this initial exploratory analysis, SV-BR-1-GM can produce regression of pre-treated metastatic breast cancer correlating with an immunologic response. HLA matching is being evaluated as a predictor of response.
PatientAgeMetastatic Sites# Prior RegimensHLA Matches# of CyclesTumor Regression?01-00146Pleura, Lymph Nodes7 chemo/bio, 5 hormonalDRB3*02:021No01-00273Lung, Liver, Bone6 chemo, 1 hormonalA*24:02, DRB3*02:028Lungs01-00554Lymph nodes, Pleura, Skin3 chemo/bioA*24:022Skin02-00170Lymph nodes1 chemo/bioNone1No02-00361Bone, Brain3 chemoNone6No02-00474Lymph nodes, Cutaneous3 chemo/bio, 1 hormonalDRB3*02:022Lost to Follow-up
Citation Format: Bhattacharya S, Holmes JP, Calfa C, Lukas J, Tan-Chiu E, Clifton GT, Peoples GE, Lacher M, Wiseman CL, Williams WV. Initial safety and efficacy of a phase I/IIa trial of a modified whole tumor cell targeted immunotherapy in patients with advanced breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-09-09.
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Affiliation(s)
- S Bhattacharya
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - JP Holmes
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - C Calfa
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - J Lukas
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - E Tan-Chiu
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - GT Clifton
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - GE Peoples
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - M Lacher
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - CL Wiseman
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
| | - WV Williams
- Thomas Jefferson University, Philadelphia, PA; Redwood Reg Medcl Grp, Santa Rosa, CA; University of Miami, Miami, FL; The Everett Clinic, Everett, WA; Florida Cancer Specialists and Research Institute, Parkland, FL; Cancer Insight, San Antonio, TX; BriaCell Therapeutics Corporation, Berkeley, CA
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Bennetzen MV, Kosar M, Bunkenborg J, Payne MR, Bartkova J, Lindström MS, Lukas J, Andersen JS, Bartek J, Larsen DH. DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy. Cell Cycle 2018; 17:2146-2163. [PMID: 30196736 DOI: 10.1080/15384101.2018.1515552] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 10/28/2022] Open
Abstract
Ionizing radiation (IR) causes DNA double-strand breaks (DSBs) and activates a versatile cellular response regulating DNA repair, cell-cycle progression, transcription, DNA replication and other processes. In recent years proteomics has emerged as a powerful tool deepening our understanding of this multifaceted response. In this study we use SILAC-based proteomics to specifically investigate dynamic changes in cytoplasmic protein abundance after ionizing radiation; we present in-depth bioinformatics analysis and show that levels of proteins involved in autophagy (cathepsins and other lysosomal proteins), proteasomal degradation (Ubiquitin-related proteins), energy metabolism (mitochondrial proteins) and particularly translation (ribosomal proteins and translation factors) are regulated after cellular exposure to ionizing radiation. Downregulation of no less than 68 ribosomal proteins shows rapid changes in the translation pattern after IR. Additionally, we provide evidence of compartmental cytosol-nuclear translocation of numerous DNA damage related proteins using protein correlation profiling. In conclusion, these results highlight unexpected cytoplasmic processes actively orchestrated after genotoxic insults and protein translocation from the cytoplasm to the nucleus as a fundamental regulatory mechanism employed to aid cell survival and preservation of genome integrity.
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Affiliation(s)
- Martin V Bennetzen
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Martin Kosar
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark
| | - Jakob Bunkenborg
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Mark Ronald Payne
- c National Institute of Aquatic Resources , Technical University of Denmark , Lyngby , Denmark
| | - Jirina Bartkova
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Mikael S Lindström
- d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Jiri Lukas
- e Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research , Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen , Denmark
| | - Jens S Andersen
- a Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , Odense M , Denmark
| | - Jiri Bartek
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,d Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology , Karolinska Institutet , Solna , Sweden
| | - Dorthe Helena Larsen
- b Genome Integrity Unit, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark.,f Nucleolar Stress and Disease Group, Danish Cancer Society Research Center , Danish Cancer Society , Copenhagen , Denmark
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11
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Gupta R, Somyajit K, Narita T, Maskey E, Stanlie A, Kremer M, Typas D, Lammers M, Mailand N, Nussenzweig A, Lukas J, Choudhary C. DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. Cell 2018; 173:972-988.e23. [PMID: 29656893 PMCID: PMC8108093 DOI: 10.1016/j.cell.2018.03.050] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/27/2018] [Accepted: 03/21/2018] [Indexed: 01/13/2023]
Abstract
Repair of damaged DNA is essential for maintaining genome integrity and for preventing genome-instability-associated diseases, such as cancer. By combining proximity labeling with quantitative mass spectrometry, we generated high-resolution interaction neighborhood maps of the endogenously expressed DNA repair factors 53BP1, BRCA1, and MDC1. Our spatially resolved interaction maps reveal rich network intricacies, identify shared and bait-specific interaction modules, and implicate previously concealed regulators in this process. We identified a novel vertebrate-specific protein complex, shieldin, comprising REV7 plus three previously uncharacterized proteins, RINN1 (CTC-534A2.2), RINN2 (FAM35A), and RINN3 (C20ORF196). Recruitment of shieldin to DSBs, via the ATM-RNF8-RNF168-53BP1-RIF1 axis, promotes NHEJ-dependent repair of intrachromosomal breaks, immunoglobulin class-switch recombination (CSR), and fusion of unprotected telomeres. Shieldin functions as a downstream effector of 53BP1-RIF1 in restraining DNA end resection and in sensitizing BRCA1-deficient cells to PARP inhibitors. These findings have implications for understanding cancer-associated PARPi resistance and the evolution of antibody CSR in higher vertebrates.
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Affiliation(s)
- Rajat Gupta
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Kumar Somyajit
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Takeo Narita
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Elina Maskey
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Andre Stanlie
- Laboratory of Genome Integrity, NIH, Bethesda, MD 20892, USA
| | - Magdalena Kremer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, University of Cologne, 50931 Cologne, Germany
| | - Dimitris Typas
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Michael Lammers
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, University of Cologne, 50931 Cologne, Germany; Institute for Biochemistry, Synthetic and Structural Biochemistry, Felix-Hausdorff-Str. 4, University of Greifswald, 17487 Greifswald, Germany
| | - Niels Mailand
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | | | - Jiri Lukas
- Protein Signaling Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics Program, the Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark; Center for Chromosome Stability (CCS), Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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12
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Somyajit K, Gupta R, Sedlackova H, Neelsen KJ, Ochs F, Rask MB, Choudhary C, Lukas J. Redox-sensitive alteration of replisome architecture safeguards genome integrity. Science 2018; 358:797-802. [PMID: 29123070 DOI: 10.1126/science.aao3172] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/26/2017] [Indexed: 01/02/2023]
Abstract
DNA replication requires coordination between replication fork progression and deoxynucleotide triphosphate (dNTP)-generating metabolic pathways. We find that perturbation of ribonucleotide reductase (RNR) in humans elevates reactive oxygen species (ROS) that are detected by peroxiredoxin 2 (PRDX2). In the oligomeric state, PRDX2 forms a replisome-associated ROS sensor, which binds the fork accelerator TIMELESS when exposed to low levels of ROS. Elevated ROS levels generated by RNR attenuation disrupt oligomerized PRDX2 to smaller subunits, whose dissociation from chromatin enforces the displacement of TIMELESS from the replisome. This process instantly slows replication fork progression, which mitigates pathological consequences of replication stress. Thus, redox signaling couples fluctuations of dNTP biogenesis with replisome activity to reduce stress during genome duplication. We propose that cancer cells exploit this pathway to increase their adaptability to adverse metabolic conditions.
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Affiliation(s)
- Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Rajat Gupta
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Hana Sedlackova
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Kai John Neelsen
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Fena Ochs
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark.
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13
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Galanos P, Pappas G, Polyzos A, Kotsinas A, Svolaki I, Giakoumakis NN, Glytsou C, Pateras IS, Swain U, Souliotis VL, Georgakilas AG, Geacintov N, Scorrano L, Lukas C, Lukas J, Livneh Z, Lygerou Z, Chowdhury D, Sørensen CS, Bartek J, Gorgoulis VG. Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability. Genome Biol 2018; 19:37. [PMID: 29548335 PMCID: PMC5857109 DOI: 10.1186/s13059-018-1401-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/30/2018] [Indexed: 02/07/2023] Open
Abstract
Background Genomic instability promotes evolution and heterogeneity of tumors. Unraveling its mechanistic basis is essential for the design of appropriate therapeutic strategies. In a previous study, we reported an unexpected oncogenic property of p21WAF1/Cip1, showing that its chronic expression in a p53-deficient environment causes genomic instability by deregulation of the replication licensing machinery. Results We now demonstrate that p21WAF1/Cip1 can further fuel genomic instability by suppressing the repair capacity of low- and high-fidelity pathways that deal with nucleotide abnormalities. Consequently, fewer single nucleotide substitutions (SNSs) occur, while formation of highly deleterious DNA double-strand breaks (DSBs) is enhanced, crafting a characteristic mutational signature landscape. Guided by the mutational signatures formed, we find that the DSBs are repaired by Rad52-dependent break-induced replication (BIR) and single-strand annealing (SSA) repair pathways. Conversely, the error-free synthesis-dependent strand annealing (SDSA) repair route is deficient. Surprisingly, Rad52 is activated transcriptionally in an E2F1-dependent manner, rather than post-translationally as is common for DNA repair factor activation. Conclusions Our results signify the importance of mutational signatures as guides to disclose the repair history leading to genomic instability. We unveil how chronic p21WAF1/Cip1 expression rewires the repair process and identifies Rad52 as a source of genomic instability and a candidate therapeutic target. Electronic supplementary material The online version of this article (10.1186/s13059-018-1401-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Panagiotis Galanos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece.,Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark
| | - George Pappas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece.,Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark
| | - Alexander Polyzos
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str, GR-11527, Athens, Greece
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | - Ioanna Svolaki
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | | | | | - Ioannis S Pateras
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece
| | - Umakanta Swain
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Vassilis L Souliotis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, GR-11635, Athens, Greece
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780, Zografou, Athens, Greece
| | | | - Luca Scorrano
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Zoi Lygerou
- Laboratory of Biology, School of Medicine, University of Patras, 26505, Patras, Rio, Greece
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.,Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen, Denmark
| | - Jiri Bartek
- Danish Cancer Society Research Centre, Strandboulevarden 49, DK-2100, Copenhagen, Denmark. .,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77, Stockholm, Sweden.
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str, GR-11527, Athens, Greece. .,Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Str, GR-11527, Athens, Greece. .,Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Wilmslow Road, Manchester, M20 4QL, UK.
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14
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Abstract
Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA breakage, and, ultimately, cell death. Despite many years of intensive research into the molecular underpinnings of the eukaryotic replication checkpoint, the mechanisms underlying the dismal consequences of its failure remain enigmatic. A recent development offers a unifying model in which the replication checkpoint guards against global exhaustion of rate-limiting replication regulators. Here we discuss how such a mechanism can prevent catastrophic genome disruption and suggest how to harness this knowledge to advance therapeutic strategies to eliminate cancer cells that inherently proliferate under increased DNA replication stress.
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Affiliation(s)
- Luis Toledo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
| | - Kai John Neelsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
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15
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Sotiriou SK, Kamileri I, Lugli N, Evangelou K, Da-Ré C, Huber F, Padayachy L, Tardy S, Nicati NL, Barriot S, Ochs F, Lukas C, Lukas J, Gorgoulis VG, Scapozza L, Halazonetis TD. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks. Mol Cell 2017; 64:1127-1134. [PMID: 27984746 PMCID: PMC5179496 DOI: 10.1016/j.molcel.2016.10.038] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/08/2016] [Accepted: 10/28/2016] [Indexed: 02/01/2023]
Abstract
Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose depletion inhibited G1 to S phase progression when oncogenic cyclin E was overexpressed. RAD52, a gene dispensable for normal development in mice, was among the top hits. In cells in which fork collapse was induced by oncogenes or chemicals, the Rad52 protein localized to DRS foci. Depletion of Rad52 by siRNA or knockout of the gene by CRISPR/Cas9 compromised restart of collapsed forks and led to DNA damage in cells experiencing DRS. Furthermore, in cancer-prone, heterozygous APC mutant mice, homozygous deletion of the Rad52 gene suppressed tumor growth and prolonged lifespan. We therefore propose that mammalian RAD52 facilitates repair of collapsed DNA replication forks in cancer cells. Mammalian RAD52 is involved in the oncogene-induced DNA replication stress response Mammalian RAD52 functions in the repair of collapsed DNA replication forks Rad52 deficiency prolongs the lifespan of Apcmin/+ mice
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Affiliation(s)
- Sotirios K Sotiriou
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Irene Kamileri
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Natalia Lugli
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Konstantinos Evangelou
- Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Caterina Da-Ré
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Florian Huber
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Sebastien Tardy
- School of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, CMU, University of Geneva and University of Lausanne, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Noemie L Nicati
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland; School of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, CMU, University of Geneva and University of Lausanne, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Samia Barriot
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Fena Ochs
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Vassilis G Gorgoulis
- Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece; Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PL, UK; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, Department of Pharmaceutical Biochemistry, CMU, University of Geneva and University of Lausanne, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva, Switzerland.
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16
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Kiesewetter B, Mayerhoefer M, Dolak W, Lukas J, Simonitsch-Klupp I, Raderer M. PROGRESSION-FREE SURVIVAL FOLLOWING LENALIDOMIDE-BASED TREATMENT IS SIGNIFICANTLY LONGER IN EXTRAGASTRIC THAN IN GASTRIC MARGINAL ZONE B-CELL LYMPHOMA OF THE MUCOSA-ASSOCIATED LYMPHOID TISSUE LYMPHOMA (MALT LYMPHOMA). Hematol Oncol 2017. [DOI: 10.1002/hon.2438_77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- B. Kiesewetter
- Medicine I, Clin. Div. of Oncology; Medical University Vienna; Vienna Austria
| | | | - W. Dolak
- Medicine III, Clin. Division of Gastroenterology and Hepatology; Medical University Vienna; Vienna Austria
| | - J. Lukas
- Ophthalmology; Medical University Vienna; Vienna Austria
| | | | - M. Raderer
- Medicine I, Clin. Div. of Oncology; Medical University Vienna; Vienna Austria
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17
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Ochs F, Somyajit K, Altmeyer M, Rask MB, Lukas J, Lukas C. 53BP1 fosters fidelity of homology-directed DNA repair. Nat Struct Mol Biol 2016; 23:714-21. [PMID: 27348077 DOI: 10.1038/nsmb.3251] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/06/2016] [Indexed: 12/26/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) in mammals is coordinated by the ubiquitin-dependent accumulation of 53BP1 at DSB-flanking chromatin. Owing to its ability to limit DNA-end processing, 53BP1 is thought to promote nonhomologous end-joining (NHEJ) and to suppress homology-directed repair (HDR). Here, we show that silencing 53BP1 or exhausting its capacity to bind damaged chromatin changes limited DSB resection to hyper-resection and results in a switch from error-free gene conversion by RAD51 to mutagenic single-strand annealing by RAD52. Thus, rather than suppressing HDR, 53BP1 fosters its fidelity. These findings illuminate causes and consequences of synthetic viability acquired through 53BP1 silencing in cells lacking the BRCA1 tumor suppressor. We show that such cells survive DSB assaults at the cost of increasing reliance on RAD52-mediated HDR, which may fuel genome instability. However, our findings suggest that when challenged by DSBs, BRCA1- and 53BP1-deficient cells may become hypersensitive to, and be eliminated by, RAD52 inhibition.
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Affiliation(s)
- Fena Ochs
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kumar Somyajit
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Altmeyer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maj-Britt Rask
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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18
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Kratky J, Vitkova H, Bartakova J, Lukas J, Jiskra J. Neck Muscles and Content of Carotid Artery as Reference Tissue for Strain Ratio – a Novel Approach to Improve the Diagnostic Performance of Thyroid Elastography? Exp Clin Endocrinol Diabetes 2016; 124:192-7. [DOI: 10.1055/s-0035-1569359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- J. Kratky
- Third Department of Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague
| | - H. Vitkova
- Third Department of Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague
| | - J. Bartakova
- Third Department of Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague
| | - J. Lukas
- Department of Otolaryngology – Head and Neck Surgery, Na Homolce Hospital, Prague, and Department of Otolaryngology, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - J. Jiskra
- Third Department of Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague
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19
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Lukas J, Hitnausova B, Jiskra J, Syrucek M. Tumor aggressiveness risk factors in the differentiated thyroid carcinoma. ACTA ACUST UNITED AC 2016; 117:91-3. [PMID: 26830039 DOI: 10.4149/bll_2016_018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The differentiated thyroid carcinoma (DTC) is the most frequent malignancy in endocrinology (95%). Our aim was to retrospectively compare risk factors of tumor aggressiveness and history of thyroid disease in patients with conventional DTC and differentiated thyroid microcarcinoma (DTMC). METHODS Retrospective analysis of 167 patients after total thyroidectomy with a histologically confirmed DTC, of which 83 patients with conventional DTC (> 1 cm) and 84 with DTMC (≤ 1 cm). The analyzed factors were tumor size, its aggressiveness (i.e. multifocal or bilateral occurrence, angioinvasion, extracapsular growth, presence of cervical lymph node metastases, distant metastases, and early local relapse) and medical history of thyroid diseases. RESULTS In the DTMC group, there were 80/84 (95.2%) papillary carcinomas compared with 58/83 (69.9%) in the conventional DTC group (p=0.001). Patients with DTMC were significantly older than those with conventional DTC (p=0.006). In the conventional DTC group, there was a significantly higher occurrence of angioinvasion and extracapsular growth (p=0.001), cervical lymph node metastases (p=0.013), relapse (p=0.018), and distant metastases (p=0.007), compared with the DTMC group. CONCLUSION In patients with DTMC, there was a significantly lower presence of risk factors of tumor aggressiveness, compared with the conventional DTC group (Tab. 2, Ref. 17).
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Moudry P, Watanabe K, Wolanin KM, Bartkova J, Wassing IE, Watanabe S, Strauss R, Troelsgaard Pedersen R, Oestergaard VH, Lisby M, Andújar-Sánchez M, Maya-Mendoza A, Esashi F, Lukas J, Bartek J. TOPBP1 regulates RAD51 phosphorylation and chromatin loading and determines PARP inhibitor sensitivity. J Cell Biol 2016; 212:281-8. [PMID: 26811421 PMCID: PMC4748576 DOI: 10.1083/jcb.201507042] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 07/10/2015] [Accepted: 01/03/2016] [Indexed: 01/01/2023] Open
Abstract
Topoisomerase IIβ-binding protein 1 (TOPBP1) participates in DNA replication and DNA damage response; however, its role in DNA repair and relevance for human cancer remain unclear. Here, through an unbiased small interfering RNA screen, we identified and validated TOPBP1 as a novel determinant whose loss sensitized human cells to olaparib, an inhibitor of poly(ADP-ribose) polymerase. We show that TOPBP1 acts in homologous recombination (HR) repair, impacts olaparib response, and exhibits aberrant patterns in subsets of human ovarian carcinomas. TOPBP1 depletion abrogated RAD51 loading to chromatin and formation of RAD51 foci, but without affecting the upstream HR steps of DNA end resection and RPA loading. Furthermore, TOPBP1 BRCT domains 7/8 are essential for RAD51 foci formation. Mechanistically, TOPBP1 physically binds PLK1 and promotes PLK1 kinase-mediated phosphorylation of RAD51 at serine 14, a modification required for RAD51 recruitment to chromatin. Overall, our results provide mechanistic insights into TOPBP1's role in HR, with potential clinical implications for cancer treatment.
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Affiliation(s)
- Pavel Moudry
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Kenji Watanabe
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Kamila M Wolanin
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Jirina Bartkova
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark Department of Medical Biochemistry and Biophysics, Science For Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institute, 17121 Solna, Sweden
| | - Isabel E Wassing
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK
| | - Sugiko Watanabe
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Robert Strauss
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | | | - Vibe H Oestergaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Miguel Andújar-Sánchez
- Department of Pathology, Familial and Hereditary Cancer Unit, University Hospital, 35010 Las Palmas de Gran Canaria, Spain
| | | | - Fumiko Esashi
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, England, UK
| | - Jiri Lukas
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jiri Bartek
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic Department of Medical Biochemistry and Biophysics, Science For Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institute, 17121 Solna, Sweden
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Abstract
Long non-coding RNAs (lncRNAs) have emerged as regulators of various biological processes, but to which extent lncRNAs play a role in genome integrity maintenance is not well understood. In this issue of EMBO Reports, Sharma et al [1] identify the DNA damage-induced lncRNA DDSR1 as an integral player of the DNA damage response (DDR). DDSR1 has both an early role by modulating repair pathway choices, and a later function when it regulates gene expression. Sharma et al [1] thus uncover a dual role for a hitherto uncharacterized lncRNA during the cellular response to DNA damage.
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Affiliation(s)
- Jiri Lukas
- NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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Kiesewetter B, Mayerhoefer M, Dolak W, Simonitsch-Klupp I, Lukas J, Raderer M. 3227 A phase II trial of ofatumumab for mucosa-associated lymphoid tissue lymphoma (MALT lymphoma) - An interim analysis. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31804-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Altmeyer M, Neelsen KJ, Teloni F, Pozdnyakova I, Pellegrino S, Grøfte M, Rask MBD, Streicher W, Jungmichel S, Nielsen ML, Lukas J. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose). Nat Commun 2015; 6:8088. [PMID: 26286827 PMCID: PMC4560800 DOI: 10.1038/ncomms9088] [Citation(s) in RCA: 390] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 07/16/2015] [Indexed: 01/01/2023] Open
Abstract
Intrinsically disordered proteins can phase separate from the soluble intracellular space, and tend to aggregate under pathological conditions. The physiological functions and molecular triggers of liquid demixing by phase separation are not well understood. Here we show in vitro and in vivo that the nucleic acid-mimicking biopolymer poly(ADP-ribose) (PAR) nucleates intracellular liquid demixing. PAR levels are markedly induced at sites of DNA damage, and we provide evidence that PAR-seeded liquid demixing results in rapid, yet transient and fully reversible assembly of various intrinsically disordered proteins at DNA break sites. Demixing, which relies on electrostatic interactions between positively charged RGG repeats and negatively charged PAR, is amplified by aggregation-prone prion-like domains, and orchestrates the earliest cellular responses to DNA breakage. We propose that PAR-seeded liquid demixing is a general mechanism to dynamically reorganize the soluble nuclear space with implications for pathological protein aggregation caused by derailed phase separation.
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Affiliation(s)
- Matthias Altmeyer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark.,Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Kai J Neelsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Federico Teloni
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Irina Pozdnyakova
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Stefania Pellegrino
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Merete Grøfte
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Maj-Britt Druedahl Rask
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Werner Streicher
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Stephanie Jungmichel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Michael Lund Nielsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
| | - Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, Copenhagen DK-2200, Denmark
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24
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Zong D, Callén E, Pegoraro G, Lukas C, Lukas J, Nussenzweig A. Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining. Nucleic Acids Res 2015; 43:4950-61. [PMID: 25916843 PMCID: PMC4446425 DOI: 10.1093/nar/gkv336] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/01/2015] [Indexed: 11/13/2022] Open
Abstract
DNA double strand breaks (DSBs) formed during S phase are preferentially repaired by homologous recombination (HR), whereas G1 DSBs, such as those occurring during immunoglobulin class switch recombination (CSR), are repaired by non-homologous end joining (NHEJ). The DNA damage response proteins 53BP1 and BRCA1 regulate the balance between NHEJ and HR. 53BP1 promotes CSR in part by mediating synapsis of distal DNA ends, and in addition, inhibits 5’ end resection. BRCA1 antagonizes 53BP1 dependent DNA end-blocking activity during S phase, which would otherwise promote mutagenic NHEJ and genome instability. Recently, it was shown that supra-physiological levels of the E3 ubiquitin ligase RNF168 results in the hyper-accumulation of 53BP1/BRCA1 which accelerates DSB repair. Here, we ask whether increased expression of RNF168 or 53BP1 impacts physiological versus mutagenic NHEJ. We find that the anti-resection activities of 53BP1 are rate-limiting for mutagenic NHEJ but not for physiological CSR. As heterogeneity in the expression of RNF168 and 53BP1 is found in human tumors, our results suggest that deregulation of the RNF168/53BP1 pathway could alter the chemosensitivity of BRCA1 deficient tumors.
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Affiliation(s)
- Dali Zong
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
| | - Elsa Callén
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Center for Cancer Research, National Cancer Institute; National Institute of Health, Bethesda, MD 20892, USA
| | - Claudia Lukas
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Jiri Lukas
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - André Nussenzweig
- Laboratory of Genome Integrity; National Cancer Institute; National Institutes of Health; Bethesda, MD 20892, USA
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Gudjonsson T, Altmeyer M, Savic V, Toledo L, Dinant C, Grøfte M, Bartkova J, Poulsen M, Oka Y, Bekker-Jensen S, Mailand N, Neumann B, Heriche JK, Shearer R, Saunders D, Bartek J, Lukas J, Lukas C. TRIP12 and UBR5 Suppress Spreading of Chromatin Ubiquitylation at Damaged Chromosomes. Cell 2014. [DOI: 10.1016/j.cell.2014.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Kosar M, Bartkova J, Hubackova S, Hodny Z, Lukas J, Bartek J. Senescence-associated heterochromatin foci are dispensable for cellular senescence, occur in a cell type- and insult-dependent manner and follow expression of p16ink4a. Cell Cycle 2014; 10:457-68. [DOI: 10.4161/cc.10.3.14707] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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27
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Sørensen CS, Syljuåsen RG, Lukas J, Bartek J. ATR, Claspin and the Rad9-Rad1-Hus1 Complex Regulate Chk1 and Cdc25A in the Absence of DNA Damage. Cell Cycle 2014. [DOI: 10.4161/cc.3.7.972] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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28
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Lukas J, Drabek J, Dudesek B, Vazan P, Stranska J, Jancik S, Mackova M, Syrucek M, Lukas D, Duskova J, Dundr P, Hintnausova B, Jiskra J. Correlation among the BRAF gene mutation status, clinicopathological features of primary tumour, and lymph node metastasizing of papillary thyroid carcinoma. Exp Clin Endocrinol Diabetes 2014; 122:268-72. [PMID: 24839220 DOI: 10.1055/s-0034-1372624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is the most common malignant thyroid tumour. A common mutation of papillary thyroid carcinoma (PTC) is the somatic mutation of the BRAF (V600E) gene. AIM The aim was to 1) determine the association of lymph node metastases of PTC with the BRAF gene mutation of primary tumour; 2) evaluate association of the BRAF mutation in the -primary tumour with clinicopathological para-meters; 3) examine the extent of genetic heterogeneity by monitoring the BRAF mutation in multicentric tumours. SUBJECTS AND METHODS Retrospective analysis of the BRAF (V600E) mutation in PTC and PTC neck lymph node metastases in 156 patients operated from 2003 to 2012 in Prague and Zlín, the Czech Republic, using a qPCR assay. The results were correlated with clinicopathological factors. RESULTS DNA was successfully extracted from 137 samples. The BRAF (V600E) mutation was detected in 78 cases (56.9%). The patients with BRAF p.Val600Glu mutation of primary tumour had only non-significantly higher risk of cervical lymph node metastases [OR=2.39 (95%) CI 1.00-5.75, p=0.052]. In the classic papillary variant, the BRAF (V600E) mutation was found significantly more often than in other PTC subtypes (p=0.022). We did not confirm any significant association between the BRAF (V600E) mutation and other clinicopathological findings. CONCLUSION Except for the higher prevalence in papillary variant of PTC, BRAF p.Val600Glu mutation was not associated with other prognostic clinicopathological factors of PTC. BRAF mutation cannot be regarded as a reliable marker of node metastases in patients with PTC.
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Affiliation(s)
- J Lukas
- Department of Otolaryngology - Head and Neck Surgery, Na Homolce Hospital, Prague, Czech Republic
| | - J Drabek
- Laboratory of Experimental Medicine, the Institute of Molecular and -Translational Medicine of the Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - B Dudesek
- Department of Surgery, Atlas Hospital, Zlín, Czech Republic
| | - P Vazan
- Biopsy and Cytology Laboratory of J.A.Baťa, Zlín, Czech Republic
| | - J Stranska
- Laboratory of Experimental Medicine, the Institute of Molecular and -Translational Medicine of the Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - S Jancik
- Laboratory of Experimental Medicine, the Institute of Molecular and -Translational Medicine of the Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - M Mackova
- Department of Nuclear Medicine and Endocrinology, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - M Syrucek
- Department of Pathology, Na Homolce Hospital, Prague, Czech Republic
| | - D Lukas
- Surgery Clinics, 3rd Medical Faculty, Charles University and Faculty Hospital Královské Vinohrady, Prague, Czech Republic
| | - J Duskova
- Institute of Pathology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - P Dundr
- Institute of Pathology, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - B Hintnausova
- Department of Endocrinology, Na Homolce Hospital, Prague, Czech -Republic
| | - J Jiskra
- The 3rd Department of Medicine - Department of Endocrinology and -Metabolism 1st Faculty of Medicine, Charles University in Prague and -General University Hospital in Prague, Czech Republic
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29
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Lukas J, Bojtarova E, Mistrik M, Bujdak J, Sopko L, Hatalova A, Martisova M. Treatment difficulty with acute GVHD - frequent cause of mortality after allogeneic hematopoietic stem cell transplantation. ACTA ACUST UNITED AC 2014; 115:80-2. [PMID: 24601700 DOI: 10.4149/bll_2014_017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Acute graft-versus-host disease (aGvHD) remains a significant cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). METHODS In this study, we have retrospectively evaluated the major risk factors for the development of aGvHD in 100 patients who underwent allogeneic transplantation at the University Hospital in Bratislava between January 2007 and December 2011. RESULTS 29 patients acquired acute GvHD (Grade I - 12 patients, G II - 5 , G III - 3, G IV - 9). We proved a higher incidence of developing aGvHD in patients with unrelated donor type, TBI conditioning and cyclosporine (CsA) replacement with mycophenolate mofetil due to CsA nephrotoxicity, while other risk factors such as older patient age, the use of peripheral blood progenitor cells and donor/recipient sex mismatch were without statistical significance. The average time of onset of aGvHD has been 57 days (range 13-260) after HSCT. Corticosteroids were used as standard initial therapy with 52 % complete response (CR) rate, although the likelihood of response rapidly decreased with increasing severity of disease (G IV - 100 % refracterness). The response to primary therapy also correlated with overall survival. Patients with steroid-refractory aGvHD received a different second-line therapies (antithymocyte globulin, anti-TNFα antibody, anti CD52 antibody) with response rate 45 % (CR - 18 %, PR - 27 %). CONCLUSION Outcome for the patients with steroid-refractory aGvHD was poor, disease very often returned or progressed with one year mortality rate 81 % , that represents an important therapeutic problem (Tab. 2, Ref. 10).
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30
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Toledo LI, Altmeyer M, Rask MB, Lukas C, Larsen DH, Povlsen LK, Bekker-Jensen S, Mailand N, Bartek J, Lukas J. ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 2014; 155:1088-103. [PMID: 24267891 DOI: 10.1016/j.cell.2013.10.043] [Citation(s) in RCA: 593] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/19/2013] [Accepted: 10/18/2013] [Indexed: 11/26/2022]
Abstract
ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors.
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Affiliation(s)
- Luis Ignacio Toledo
- Chromosome Stability and Dynamics Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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31
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Yamada M, Watanabe K, Mistrik M, Vesela E, Protivankova I, Mailand N, Lee M, Masai H, Lukas J, Bartek J. ATR-Chk1-APC/CCdh1-dependent stabilization of Cdc7-ASK (Dbf4) kinase is required for DNA lesion bypass under replication stress. Genes Dev 2014; 27:2459-72. [PMID: 24240236 PMCID: PMC3841735 DOI: 10.1101/gad.224568.113] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [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] [Indexed: 12/17/2022]
Abstract
Cdc7 kinase regulates DNA replication. However, its role in DNA repair and recombination is poorly understood. Here we describe a pathway that stabilizes the human Cdc7-ASK (activator of S-phase kinase; also called Dbf4), its regulation, and its function in cellular responses to compromised DNA replication. Stalled DNA replication evoked stabilization of the Cdc7-ASK (Dbf4) complex in a manner dependent on ATR-Chk1-mediated checkpoint signaling and its interplay with the anaphase-promoting complex/cyclosome(Cdh1) (APC/C(Cdh1)) ubiquitin ligase. Mechanistically, Chk1 kinase inactivates APC/C(Cdh1) through degradation of Cdh1 upon replication block, thereby stabilizing APC/C(Cdh1) substrates, including Cdc7-ASK (Dbf4). Furthermore, motif C of ASK (Dbf4) interacts with the N-terminal region of RAD18 ubiquitin ligase, and this interaction is required for chromatin binding of RAD18. Impaired interaction of ASK (Dbf4) with RAD18 disables foci formation by RAD18 and hinders chromatin loading of translesion DNA polymerase η. These findings define a novel mechanism that orchestrates replication checkpoint signaling and ubiquitin-proteasome machinery with the DNA damage bypass pathway to guard against replication collapse under conditions of replication stress.
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Affiliation(s)
- Masayuki Yamada
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-775 15 Olomouc, Czech Republic
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32
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Toledo L, Altmeyer M, Rask MB, Lukas C, Larsen D, Povlsen L, Bekker-Jensen S, Mailand N, Bartek J, Lukas J. ATR Prohibits Replication Catastrophe by Preventing Global Exhaustion of RPA. Cell 2014. [DOI: 10.1016/j.cell.2014.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Watanabe S, Watanabe K, Akimov V, Bartkova J, Blagoev B, Lukas J, Bartek J. JMJD1C demethylates MDC1 to regulate the RNF8 and BRCA1-mediated chromatin response to DNA breaks. Nat Struct Mol Biol 2013; 20:1425-33. [PMID: 24240613 DOI: 10.1038/nsmb.2702] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/30/2013] [Indexed: 12/29/2022]
Abstract
Chromatin ubiquitylation flanking DNA double-strand breaks (DSBs), mediated by RNF8 and RNF168 ubiquitin ligases, orchestrates a two-branch pathway, recruiting repair factors 53BP1 or the RAP80-BRCA1 complex. We report that human demethylase JMJD1C regulates the RAP80-BRCA1 branch of this DNA-damage response (DDR) pathway. JMJD1C was stabilized by interaction with RNF8, was recruited to DSBs, and was required for local ubiquitylations and recruitment of RAP80-BRCA1 but not 53BP1. JMJD1C bound to RNF8 and MDC1, and demethylated MDC1 at Lys45, thereby promoting MDC1-RNF8 interaction, RNF8-dependent MDC1 ubiquitylation and recruitment of RAP80-BRCA1 to polyubiquitylated MDC1. Furthermore, JMJD1C restricted formation of RAD51 repair foci, and JMJD1C depletion caused resistance to ionizing radiation and PARP inhibitors, phenotypes relevant to aberrant loss of JMJD1C in subsets of breast carcinomas. These findings identify JMJD1C as a DDR component, with implications for genome-integrity maintenance, tumorigenesis and cancer treatment.
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Affiliation(s)
- Sugiko Watanabe
- 1] Danish Cancer Society Research Center, Copenhagen, Denmark. [2] [3]
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34
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Altmeyer M, Toledo L, Gudjonsson T, Grøfte M, Rask MB, Lukas C, Akimov V, Blagoev B, Bartek J, Lukas J. The chromatin scaffold protein SAFB1 renders chromatin permissive for DNA damage signaling. Mol Cell 2013; 52:206-20. [PMID: 24055346 DOI: 10.1016/j.molcel.2013.08.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/08/2013] [Accepted: 08/14/2013] [Indexed: 01/25/2023]
Abstract
Although the general relevance of chromatin modifications for genotoxic stress signaling, cell-cycle checkpoint activation, and DNA repair is well established, how these modifications reach initial thresholds in order to trigger robust responses remains largely unexplored. Here, we identify the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly(ADP-ribose)-polymerase 1- and poly(ADP-ribose)-dependent manner and is required for unperturbed cell-cycle checkpoint activation and guarding cells against replicative stress. Altogether, our data reveal that transient recruitment of an architectural chromatin component is required in order to overcome physiological barriers by making chromatin permissive for DNA damage signaling, whereas the ensuing exclusion of SAFB1 may help prevent excessive signaling.
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Affiliation(s)
- Matthias Altmeyer
- Chromosome Stability and Dynamics Group, Department of Disease Biology, the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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Abstract
Signal amplifications are vital for chromatin function, yet they also bear the risk of transforming into unrestrained, self-escalating, and potentially harmful responses. Examples of inbuilt limitations are emerging, revealing how chromatin transactions are confined within physiological boundaries.
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Affiliation(s)
- Matthias Altmeyer
- Chromosome Stability and Dynamics Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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36
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Hovakimyan M, Maass F, Petersen J, Holzmann C, Witt M, Lukas J, Frech MJ, Hübner R, Rolfs A, Wree A. Combined therapy with cyclodextrin/allopregnanolone and miglustat improves motor but not cognitive functions in Niemann-Pick Type C1 mice. Neuroscience 2013; 252:201-11. [PMID: 23948640 DOI: 10.1016/j.neuroscience.2013.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [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: 05/22/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 12/21/2022]
Abstract
Niemann-Pick Type C1 (NPC1) is an autosomal recessive disorder characterized by the accumulation of cholesterol and glycosphingolipids. Combination-treatment utilizing cyclodextrin, allopregnanolone and miglustat (CYCLO/ALLO/miglustat) can ameliorate NPC1 disease in a mutant mouse model. The present study was designed to add behavioral analysis in NPC1 mutant mice upon CYCLO/ALLO/miglustat therapy. NPC1 mutant (BALB/cJ NPC1NIH) and control mice were used. For the combination treatment mice were injected with CYCLO/ALLO weekly, starting at P7. The miglustat injection was performed daily from P10 till P23. Starting at P23, miglustat was added to the powdered chow. For the sham treatment of control and mutant mice the same schedule was used with 0.9% NaCl injection. Locomotor activity was assessed in open field, elevated plus maze and accelerod tests. For assessment of spatial learning and memory the Morris water maze test was conducted. Electron microscopy has been performed to support the behavioral data. The sham-treated mutant mice exhibited motor impairments in all performed tests. In the water maze the sham-treated mutants exhibited impairment in remembering the location of the hidden platform. CYCLO/ALLO/miglustat treatment positively influenced motor dysfunction: total distance and number of visits significantly increased, and accelerod performance improved. The spatial learning, however, did not benefit from therapy. At the morphological level, an excessive accumulation of electron-dense material was seen in the cerebellar Purkinje cells of mutant mice. A regression of these autophagosomal inclusions was seen upon therapy. CYCLO/ALLO/miglustat therapy ameliorates motor but not cognitive deficits in NPC1 mutant mice, suggesting unequal vulnerability of different brain areas to the treatment.
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Affiliation(s)
- M Hovakimyan
- Institute of Anatomy, University of Rostock, Gertrudenstrasse 9, D-18057 Rostock, Germany.
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Oplustilova L, Wolanin K, Mistrik M, Korinkova G, Simkova D, Bouchal J, Lenobel R, Bartkova J, Lau A, O’Connor MJ, Lukas J, Bartek J. Correction to Oplustilova L, et al. Cell Cycle Volume 11, Issue 20; pp. 3837–50. Cell Cycle 2013. [PMCID: PMC3735712 DOI: 10.4161/cc.25393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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38
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Bennetzen MV, Larsen DH, Dinant C, Watanabe S, Bartek J, Lukas J, Andersen JS. Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response. Cell Cycle 2013; 12:1688-95. [PMID: 23656789 DOI: 10.4161/cc.24758] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [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: 01/07/2023] Open
Abstract
Genotoxic insults, such as ionizing radiation (IR), cause DNA damage that evokes a multifaceted cellular DNA damage response (DDR). DNA damage signaling events that control protein activity, subcellular localization, DNA binding, protein-protein interactions, etc. rely heavily on time-dependent posttranslational modifications (PTMs). To complement our previous analysis of IR-induced temporal dynamics of nuclear phosphoproteome, we now identify a range of human nuclear proteins that are dynamically regulated by acetylation, and predominantly deacetylation, during IR-induced DDR by using mass spectrometry-based proteomic approaches. Apart from cataloging acetylation sites through SILAC proteomic analyses before IR and at 5 and 60 min after IR exposure of U2OS cells, we report that: (1) key components of the transcriptional machinery, such as EP300 and CREBBP, are dynamically acetylated; (2) that nuclear acetyltransferases themselves are regulated, not on the protein abundance level, but by (de)acetylation; and (3) that the recently reported p53 co-activator and methyltransferase MLL3 is acetylated on five lysines during the DDR. For selected examples, protein immunoprecipitation and immunoblotting were used to assess lysine acetylation status and thereby validate the mass spectrometry data. We thus present evidence that nuclear proteins, including those known to regulate cellular functions via epigenetic modifications of histones, are regulated by (de)acetylation in a timely manner upon cell's exposure to genotoxic insults. Overall, these results present a resource of temporal profiles of a spectrum of protein acetylation sites during DDR and provide further insights into the highly dynamic nature of regulatory PTMs that help orchestrate the maintenance of genome integrity.
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Affiliation(s)
- Martin V Bennetzen
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Affiliation(s)
- Jiri Lukas
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark.
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Altmeyer M, Lukas J. To spread or not to spread--chromatin modifications in response to DNA damage. Curr Opin Genet Dev 2013; 23:156-65. [PMID: 23312207 DOI: 10.1016/j.gde.2012.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/31/2012] [Accepted: 11/05/2012] [Indexed: 10/27/2022]
Abstract
Chromatin modifications in response to DNA damage are vital for genome integrity. Multiple proteins and pathways required to generate specialized chromatin domains around DNA lesions have been identified and the increasing amount of information calls for unifying concepts that would allow us to grasp the ever-increasing complexity. This review aims at contributing to this trend by focusing on feed-forward and feedback mechanisms, which in mammalian cells determine the extent of chromatin modifications after DNA damage. We highlight the emerging notion that the nodal points of these highly dynamic pathways operate in a rate-limiting mode, whose deregulation can disrupt physiological boundaries between damaged and undamaged chromatin, dictate repair pathway choice, and determine the fate of cells exposed to genotoxic stress.
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Affiliation(s)
- Matthias Altmeyer
- Chromosome Stability and Dynamics Unit, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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Oplustilova L, Wolanin K, Mistrik M, Korinkova G, Simkova D, Bouchal J, Lenobel R, Bartkova J, Lau A, O’Connor MJ, Lukas J, Bartek J. Evaluation of candidate biomarkers to predict cancer cell sensitivity or resistance to PARP-1 inhibitor treatment. Cell Cycle 2012; 11:3837-50. [PMID: 22983061 PMCID: PMC3495826 DOI: 10.4161/cc.22026] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Impaired DNA damage response pathways may create vulnerabilities of cancer cells that can be exploited therapeutically. One such selective vulnerability is the sensitivity of BRCA1- or BRCA2-defective tumors (hence defective in DNA repair by homologous recombination, HR) to inhibitors of the poly(ADP-ribose) polymerase-1 (PARP-1), an enzyme critical for repair pathways alternative to HR. While promising, treatment with PARP-1 inhibitors (PARP-1i) faces some hurdles, including (1) acquired resistance, (2) search for other sensitizing, non-BRCA1/2 cancer defects and (3) lack of biomarkers to predict response to PARP-1i. Here we addressed these issues using PARP-1i on 20 human cell lines from carcinomas of the breast, prostate, colon, pancreas and ovary. Aberrations of the Mre11-Rad50-Nbs1 (MRN) complex sensitized cancer cells to PARP-1i, while p53 status was less predictive, even in response to PARP-1i combinations with camptothecin or ionizing radiation. Furthermore, monitoring PARsylation and Rad51 foci formation as surrogate markers for PARP activity and HR, respectively, supported their candidacy for biomarkers of PARP-1i responses. As to resistance mechanisms, we confirmed the role of the multidrug resistance efflux transporters and its reversibility. More importantly, we demonstrated that shRNA lentivirus-mediated depletion of 53BP1 in human BRCA1-mutant breast cancer cells increased their resistance to PARP-1i. Given the preferential loss of 53BP1 in BRCA-defective and triple-negative breast carcinomas, our findings warrant assessment of 53BP1 among candidate predictive biomarkers of response to PARPi. Overall, this study helps characterize genetic and functional determinants of cellular responses to PARP-1i and contributes to the search for biomarkers to exploit PARP inhibitors in cancer therapy.
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Affiliation(s)
- Lenka Oplustilova
- Danish Cancer Society Research Center; Copenhagen, Denmark
- AstraZeneca; iMed Oncology; Macclesfield, Cheshire, UK
| | - Kamila Wolanin
- Danish Cancer Society Research Center; Copenhagen, Denmark
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Gabriela Korinkova
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Dana Simkova
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Jan Bouchal
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
| | - Rene Lenobel
- Laboratory of Growth Regulators; Palacky University Olomouc; Olomouc, Czech Republic
| | | | - Alan Lau
- AstraZeneca; iMed Oncology; Macclesfield, Cheshire, UK
| | | | - Jiri Lukas
- Danish Cancer Society Research Center; Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen, Denmark
| | - Jiri Bartek
- Danish Cancer Society Research Center; Copenhagen, Denmark
- Institute of Molecular and Translational Medicine; Faculty of Medicine and Dentistry; Palacky University; Olomouc, Czech Republic
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Gudjonsson T, Altmeyer M, Savic V, Toledo L, Dinant C, Grøfte M, Bartkova J, Poulsen M, Oka Y, Bekker-Jensen S, Mailand N, Neumann B, Heriche JK, Shearer R, Saunders D, Bartek J, Lukas J, Lukas C. TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes. Cell 2012; 150:697-709. [PMID: 22884692 DOI: 10.1016/j.cell.2012.06.039] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/26/2012] [Accepted: 06/10/2012] [Indexed: 12/29/2022]
Abstract
Histone ubiquitylation is a prominent response to DNA double-strand breaks (DSBs), but how these modifications are confined to DNA lesions is not understood. Here, we show that TRIP12 and UBR5, two HECT domain ubiquitin E3 ligases, control accumulation of RNF168, a rate-limiting component of a pathway that ubiquitylates histones after DNA breakage. We find that RNF168 can be saturated by increasing amounts of DSBs. Depletion of TRIP12 and UBR5 allows accumulation of RNF168 to supraphysiological levels, followed by massive spreading of ubiquitin conjugates and hyperaccumulation of ubiquitin-regulated genome caretakers such as 53BP1 and BRCA1. Thus, regulatory and proteolytic ubiquitylations are wired in a self-limiting circuit that promotes histone ubiquitylation near the DNA lesions but at the same time counteracts its excessive spreading to undamaged chromosomes. We provide evidence that this mechanism is vital for the homeostasis of ubiquitin-controlled events after DNA breakage and can be subverted during tumorigenesis.
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Affiliation(s)
- Thorkell Gudjonsson
- Chromosome Biology Unit, Danish Cancer Society Research Center and Center for Genotoxic Stress Research, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
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Lukas J. Jiri Lukas: Visualizing genome integrity maintenance. Interview by Caitlin Sedwick. J Cell Biol 2012; 198:4-5. [PMID: 22778274 PMCID: PMC3392934 DOI: 10.1083/jcb.1981pi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Lukas studies how cells detect and deal with DNA damage throughout the cell cycle.
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Falck J, Forment JV, Coates J, Mistrik M, Lukas J, Bartek J, Jackson SP. CDK targeting of NBS1 promotes DNA-end resection, replication restart and homologous recombination. EMBO Rep 2012; 13:561-8. [PMID: 22565321 PMCID: PMC3367243 DOI: 10.1038/embor.2012.58] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/28/2012] [Accepted: 04/13/2012] [Indexed: 12/14/2022] Open
Abstract
The conserved MRE11–RAD50–NBS1 (MRN) complex is an important sensor of DNA double-strand breaks (DSBs) and facilitates DNA repair by homologous recombination (HR) and end joining. Here, we identify NBS1 as a target of cyclin-dependent kinase (CDK) phosphorylation. We show that NBS1 serine 432 phosphorylation occurs in the S, G2 and M phases of the cell cycle and requires CDK activity. This modification stimulates MRN-dependent conversion of DSBs into structures that are substrates for repair by HR. Impairment of NBS1 phosphorylation not only negatively affects DSB repair by HR, but also prevents resumption of DNA replication after replication-fork stalling. Thus, CDK-mediated NBS1 phosphorylation defines a molecular switch that controls the choice of repair mode for DSBs.
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Affiliation(s)
- Jacob Falck
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
| | - Josep V Forment
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Julia Coates
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Martin Mistrik
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
- Institute of Molecular and Translational Medicine, Palacky University, Olomouc CZ-77515, Czech Republic
| | - Jiri Lukas
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
| | - Jiri Bartek
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
- Institute of Molecular and Translational Medicine, Palacky University, Olomouc CZ-77515, Czech Republic
| | - Stephen P Jackson
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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Moudry P, Lukas C, Macurek L, Hanzlikova H, Hodny Z, Lukas J, Bartek J. Ubiquitin-activating enzyme UBA1 is required for cellular response to DNA damage. Cell Cycle 2012; 11:1573-82. [PMID: 22456334 DOI: 10.4161/cc.19978] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The cellular DNA damage response (DDR) machinery that maintains genomic integrity and prevents severe pathologies, including cancer, is orchestrated by signaling through protein modifications. Protein ubiquitylation regulates repair of DNA double-strand breaks (DSBs), toxic lesions caused by various metabolic as well as environmental insults such as ionizing radiation (IR). Whereas several components of the DSB-evoked ubiquitylation cascade have been identified, including RNF168 and BRCA1 ubiquitin ligases, whose genetic defects predispose to a syndrome mimicking ataxia-telangiectasia and cancer, respectively, the identity of the apical E1 enzyme involved in DDR has not been established. Here, we identify ubiquitin-activating enzyme UBA1 as the E1 enzyme required for responses to IR and replication stress in human cells. We show that siRNA-mediated knockdown of UBA1, but not of another UBA family member UBA6, impaired formation of both ubiquitin conjugates at the sites of DNA damage and IR-induced foci (IRIF) by the downstream components of the DSB response pathway, 53BP1 and BRCA1. Furthermore, chemical inhibition of UBA1 prevented IRIF formation and severely impaired DSB repair and formation of 53BP1 bodies in G 1, a marker of response to replication stress. In contrast, the upstream steps of DSB response, such as phosphorylation of histone H2AX and recruitment of MDC1, remained unaffected by UBA1 depletion. Overall, our data establish UBA1 as the apical enzyme critical for ubiquitylation-dependent signaling of both DSBs and replication stress in human cells, with implications for maintenance of genomic integrity, disease pathogenesis and cancer treatment.
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Affiliation(s)
- Pavel Moudry
- Department of Genome Integrity, Institute of Molecular Genetics of the ASCR, v.v.i., Prague, Czech Republic
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Poulsen M, Lukas C, Lukas J, Bekker-Jensen S, Mailand N. Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks. ACTA ACUST UNITED AC 2012; 197:189-99. [PMID: 22492721 PMCID: PMC3328375 DOI: 10.1083/jcb.201109100] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNF169 competes with repair factors to bind to ubiquitylated chromatin at sites of DNA damage, influencing repair pathway utilization. Nonproteolytic ubiquitylation of chromatin surrounding deoxyribonucleic acid double-strand breaks (DSBs), mediated by the RNF8/RNF168 ubiquitin ligases, plays a key role in recruiting repair factors, including 53BP1 and BRCA1, to reestablish genome integrity. In this paper, we show that human RNF169, an uncharacterized E3 ubiquitin ligase paralogous to RNF168, accumulated in DSB repair foci through recognition of RNF168-catalyzed ubiquitylation products by its motif interacting with ubiquitin domain. Unexpectedly, RNF169 was dispensable for chromatin ubiquitylation and ubiquitin-dependent accumulation of repair factors at DSB sites. Instead, RNF169 functionally competed with 53BP1 and RAP80–BRCA1 for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of their recruitment to DSB sites. By delaying accumulation of 53BP1 and RAP80 at damaged chromatin, RNF169 stimulated homologous recombination and restrained nonhomologous end joining, affecting cell survival after DSB infliction. Our results show that RNF169 functions in a noncanonical fashion to harness RNF168-mediated protein recruitment to DSB-containing chromatin, thereby contributing to regulation of DSB repair pathway utilization.
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Affiliation(s)
- Maria Poulsen
- Ubiquitin Signaling Group, Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Hamerlik P, Lathia JD, Rasmussen R, Wu Q, Bartkova J, Lee M, Moudry P, Bartek J, Fischer W, Lukas J, Rich JN, Bartek J. Autocrine VEGF-VEGFR2—Neuropilin-1 signaling promotes glioma stem-like cell viability and tumor growth. J Biophys Biochem Cytol 2012. [DOI: 10.1083/jcb1966oia9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Hamerlik P, Lathia JD, Rasmussen R, Wu Q, Bartkova J, Lee M, Moudry P, Bartek J, Fischer W, Lukas J, Rich JN, Bartek J. Autocrine VEGF-VEGFR2-Neuropilin-1 signaling promotes glioma stem-like cell viability and tumor growth. ACTA ACUST UNITED AC 2012; 209:507-20. [PMID: 22393126 PMCID: PMC3302235 DOI: 10.1084/jem.20111424] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autocrine VEGFR2 signaling in glioma stem-like cells evades VEGF neutralization. Although vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) is traditionally regarded as an endothelial cell protein, evidence suggests that VEGFRs may be expressed by cancer cells. Glioblastoma multiforme (GBM) is a lethal cancer characterized by florid vascularization and aberrantly elevated VEGF. Antiangiogenic therapy with the humanized VEGF antibody bevacizumab reduces GBM tumor growth; however, the clinical benefits are transient and invariably followed by tumor recurrence. In this study, we show that VEGFR2 is preferentially expressed on the cell surface of the CD133+ human glioma stem-like cells (GSCs), whose viability, self-renewal, and tumorigenicity rely, at least in part, on signaling through the VEGF-VEGFR2–Neuropilin-1 (NRP1) axis. We find that the limited impact of bevacizumab-mediated VEGF blockage may reflect ongoing autocrine signaling through VEGF–VEGFR2–NRP1, which is associated with VEGFR2–NRP1 recycling and a pool of active VEGFR2 within a cytosolic compartment of a subset of human GBM cells. Whereas bevacizumab failed to inhibit prosurvival effects of VEGFR2-mediated signaling, GSC viability under unperturbed or radiation-evoked stress conditions was attenuated by direct inhibition of VEGFR2 tyrosine kinase activity and/or shRNA-mediated knockdown of VEGFR2 or NRP1. We propose that direct inhibition of VEGFR2 kinase may block the highly dynamic VEGF–VEGFR2–NRP1 pathway and inspire a GBM treatment strategy to complement the currently prevalent ligand neutralization approach.
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Affiliation(s)
- Petra Hamerlik
- Danish Cancer Society Research Center and Centre for Genotoxic Stress Research, DK-2100 Copenhagen, Denmark
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Jungmichel S, Clapperton JA, Lloyd J, Hari FJ, Spycher C, Pavic L, Li J, Haire LF, Bonalli M, Larsen DH, Lukas C, Lukas J, MacMillan D, Nielsen ML, Stucki M, Smerdon SJ. The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator. Nucleic Acids Res 2012; 40:3913-28. [PMID: 22234878 PMCID: PMC3351161 DOI: 10.1093/nar/gkr1300] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mdc1 is a large modular phosphoprotein scaffold that maintains signaling and repair complexes at double-stranded DNA break sites. Mdc1 is anchored to damaged chromatin through interaction of its C-terminal BRCT-repeat domain with the tail of γH2AX following DNA damage, but the role of the N-terminal forkhead-associated (FHA) domain remains unclear. We show that a major binding target of the Mdc1 FHA domain is a previously unidentified DNA damage and ATM-dependent phosphorylation site near the N-terminus of Mdc1 itself. Binding to this motif stabilizes a weak self-association of the FHA domain to form a tight dimer. X-ray structures of free and complexed Mdc1 FHA domain reveal a 'head-to-tail' dimerization mechanism that is closely related to that seen in pre-activated forms of the Chk2 DNA damage kinase, and which both positively and negatively influences Mdc1 FHA domain-mediated interactions in human cells prior to and following DNA damage.
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Affiliation(s)
- Stephanie Jungmichel
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich - Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Moudry P, Lukas C, Macurek L, Neumann B, Heriche JK, Pepperkok R, Ellenberg J, Hodny Z, Lukas J, Bartek J. Nucleoporin NUP153 guards genome integrity by promoting nuclear import of 53BP1. Cell Death Differ 2011; 19:798-807. [PMID: 22075984 DOI: 10.1038/cdd.2011.150] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
53BP1 is a mediator of DNA damage response (DDR) and a tumor suppressor whose accumulation on damaged chromatin promotes DNA repair and enhances DDR signaling. Using foci formation of 53BP1 as a readout in two human cell lines, we performed an siRNA-based functional high-content microscopy screen for modulators of cellular response to ionizing radiation (IR). Here, we provide the complete results of this screen as an information resource, and validate and functionally characterize one of the identified 'hits': a nuclear pore component NUP153 as a novel factor specifically required for 53BP1 nuclear import. Using a range of cell and molecular biology approaches including live-cell imaging, we show that knockdown of NUP153 prevents 53BP1, but not several other DDR factors, from entering the nuclei in the newly forming daughter cells. This translates into decreased IR-induced 53BP1 focus formation, delayed DNA repair and impaired cell survival after IR. In addition, NUP153 depletion exacerbates DNA damage caused by replication stress. Finally, we show that the C-terminal part of NUP153 is required for effective 53BP1 nuclear import, and that 53BP1 is imported to the nucleus through the NUP153-importin-β interplay. Our data define the structure-function relationships within this emerging 53BP1-NUP153/importin-β pathway and implicate this mechanism in the maintenance of genome integrity.
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Affiliation(s)
- P Moudry
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, Prague CZ-142 20, Czech Republic
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