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Gaudreau-Lapierre A, Klonisch T, Nicolas H, Thanasupawat T, Trinkle-Mulcahy L, Hombach-Klonisch S. Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. Int J Mol Sci 2023; 24:ijms24044246. [PMID: 36835656 PMCID: PMC9966875 DOI: 10.3390/ijms24044246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
The non-histone chromatin binding protein High Mobility Group AT-hook protein 2 (HMGA2) has important functions in chromatin remodeling, and genome maintenance and protection. Expression of HMGA2 is highest in embryonic stem cells, declines during cell differentiation and cell aging, but it is re-expressed in some cancers, where high HMGA2 expression frequently coincides with a poor prognosis. The nuclear functions of HMGA2 cannot be explained by binding to chromatin alone but involve complex interactions with other proteins that are incompletely understood. The present study used biotin proximity labeling, followed by proteomic analysis, to identify the nuclear interaction partners of HMGA2. We tested two different biotin ligase HMGA2 constructs (BioID2 and miniTurbo) with similar results, and identified known and new HMGA2 interaction partners, with functionalities mainly in chromatin biology. These HMGA2 biotin ligase fusion constructs offer exciting new possibilities for interactome discovery research, enabling the monitoring of nuclear HMGA2 interactomes during drug treatments.
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Affiliation(s)
- Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Research Institute in Oncology and Hematology (RIOH), CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hannah Nicolas
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thatchawan Thanasupawat
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Correspondence: ; Tel.: +1-204-789-3982; Fax: +1-204-789-3920
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2
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Marchante M, Buigues A, Ramirez-Martin N, Martinez J, Pellicer N, Pellicer A, Herraiz S. Single intraovarian dose of stem cell- and platelet-secreted factors mitigates age-related ovarian infertility in a murine model. Am J Obstet Gynecol 2023; 228:561.e1-561.e17. [PMID: 36706857 DOI: 10.1016/j.ajog.2023.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/26/2023]
Abstract
BACKGROUND Systemic administration of soluble factors from bone marrow-derived stem cells combined with activated platelet-rich plasma (SC-PRP) restored ovarian function, mediated through paracrine signaling, in murine models of chemotherapy-induced ovarian damage and human tissue from poor responder patients. However, the effects against age-related infertility and the efficacy of local administration have not been evaluated yet. OBJECTIVE This study aimed to assess whether a single intraovarian dose of stem cells combined with activated platelet-rich plasma can recover ovarian function, oocyte quality, and developmental competence in older mice. STUDY DESIGN The effects of stem cells combined with activated platelet-rich plasma against age-related infertility were assessed following controlled ovarian stimulation in an aging murine model reproducing 3 physiological stages of women's reproductive life, namely young, advanced maternal age, and menopausal (n=12 animals per group). Female mice were randomized to receive a single intraovarian injection (10 μL/ovary) of either saline, activated platelet-rich plasma, or stem cells combined with activated platelet-rich plasma. Seven days later, the mice were stimulated, naturally mated, and sacrificed to harvest their ovaries for histologic assessment and molecular analysis and their oviducts to evaluate oocyte maturation and to assess early embryo development. RESULTS A single intraovarian injection of stem cells combined with activated platelet-rich plasma promoted follicle activation and development in young, advanced maternal age, and old mice. Furthermore, stem cells combined with activated platelet-rich plasma rescued fertility in older mice by enhancing the quantity and quality of ovulated mature oocytes and supporting early embryo development to the blastocyst stage in all the evaluated ages. These fertility outcomes were positively associated with mitochondrial quality, treatment-increased mitochondrial DNA copy numbers, and reduced oxidative damage and apoptosis. Finally, the effects observed by histologic analysis were supported at the proteomic level. Functional proteomic analyses revealed molecular mechanisms involved in oocyte maturation and quality, mitochondrial function, and recovery of the ovarian stroma. CONCLUSION Bone marrow-derived stem cells combined with activated platelet-rich plasma is a promising treatment with the potential to improve the reproductive outcomes of women with age-related infertility, exceeding the restorative effects of platelet-rich plasma alone. Although further research in human ovarian samples is still required, the autologous nature of stem cell factors collected by noninvasive mobilization, their combination with platelet-rich plasma, and the local administration route suggest that stem cells combined with activated platelet-rich plasma treatment could be a potentially effective and safe application for future clinical practice.
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Affiliation(s)
- María Marchante
- IVI Foundation, Valencia, Spain; Department of Pediatrics, Obstetrics and Gynecology, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Anna Buigues
- IVI Foundation, Valencia, Spain; Reproductive Medicine Research Group, Instituto Investigación Sanitaria La Fe (IIS la Fe), Valencia, Spain
| | - Noelia Ramirez-Martin
- IVI Foundation, Valencia, Spain; Reproductive Medicine Research Group, Instituto Investigación Sanitaria La Fe (IIS la Fe), Valencia, Spain
| | - Jessica Martinez
- IVI Foundation, Valencia, Spain; Reproductive Medicine Research Group, Instituto Investigación Sanitaria La Fe (IIS la Fe), Valencia, Spain
| | - Nuria Pellicer
- Reproductive Medicine Research Group, Instituto Investigación Sanitaria La Fe (IIS la Fe), Valencia, Spain
| | - Antonio Pellicer
- Reproductive Medicine Research Group, Instituto Investigación Sanitaria La Fe (IIS la Fe), Valencia, Spain; IVI-RMA Valencia, Valencia, Spain; IVI-RMA Rome, Rome, Italy
| | - Sonia Herraiz
- IVI Foundation, Valencia, Spain; Reproductive Medicine Research Group, Instituto Investigación Sanitaria La Fe (IIS la Fe), Valencia, Spain.
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3
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Sigismondo G, Arseni L, Palacio-Escat N, Hofmann TG, Seiffert M, Krijgsveld J. Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair. Nucleic Acids Res 2023; 51:687-711. [PMID: 36629267 PMCID: PMC9881138 DOI: 10.1093/nar/gkac1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
The DNA damage response (DDR) is essential to maintain genome stability, and its deregulation predisposes to carcinogenesis while encompassing attractive targets for cancer therapy. Chromatin governs the DDR via the concerted interplay among different layers, including DNA, histone post-translational modifications (hPTMs) and chromatin-associated proteins. Here, we employ multi-layered proteomics to characterize chromatin-mediated functional interactions of repair proteins, signatures of hPTMs and the DNA-bound proteome during DNA double-strand break (DSB) repair at high temporal resolution. Our data illuminate the dynamics of known and novel DDR-associated factors both at chromatin and at DSBs. We functionally attribute novel chromatin-associated proteins to repair by non-homologous end-joining (NHEJ), homologous recombination (HR) and DSB repair pathway choice. We reveal histone reader ATAD2, microtubule organizer TPX2 and histone methyltransferase G9A as regulators of HR and involved in poly-ADP-ribose polymerase-inhibitor sensitivity. Furthermore, we distinguish hPTMs that are globally induced by DNA damage from those specifically acquired at sites flanking DSBs (γH2AX foci-specific) and profiled their dynamics during the DDR. Integration of complementary chromatin layers implicates G9A-mediated monomethylation of H3K56 in DSBs repair via HR. Our data provide a dynamic chromatin-centered view of the DDR that can be further mined to identify novel mechanistic links and cell vulnerabilities in DSB repair.
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Affiliation(s)
- Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nicolàs Palacio-Escat
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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4
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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5
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Bader AS, Luessing J, Hawley BR, Skalka GL, Lu WT, Lowndes N, Bushell M. DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci. Nucleic Acids Res 2022; 50:10487-10502. [PMID: 36200807 PMCID: PMC9561282 DOI: 10.1093/nar/gkac843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
Proteins with RNA-binding activity are increasingly being implicated in DNA damage responses (DDR). Additionally, DNA:RNA-hybrids are rapidly generated around DNA double-strand breaks (DSBs), and are essential for effective repair. Here, using a meta-analysis of proteomic data, we identify novel DNA repair proteins and characterise a novel role for DDX17 in DNA repair. We found DDX17 to be required for both cell survival and DNA repair in response to numerous agents that induce DSBs. Analysis of DSB repair factor recruitment to damage sites suggested a role for DDX17 early in the DSB ubiquitin cascade. Genome-wide mapping of R-loops revealed that while DDX17 promotes the formation of DNA:RNA-hybrids around DSB sites, this role is specific to loci that have low levels of pre-existing hybrids. We propose that DDX17 facilitates DSB repair at loci that are inefficient at forming DNA:RNA-hybrids by catalysing the formation of DSB-induced hybrids, thereby allowing propagation of the damage response.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - Janna Luessing
- Centre for Chromosome Biology, Biomedical Sciences Biulding (BSB), School of Biological & Checmical Sciences, University of Galway, Galway, H91W2TY, Ireland
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | | | - Wei-Ting Lu
- The Francis Crick Institute, London NW1 1AT, UK
| | - Noel F Lowndes
- Centre for Chromosome Biology, Biomedical Sciences Biulding (BSB), School of Biological & Checmical Sciences, University of Galway, Galway, H91W2TY, Ireland
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
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6
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Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I, El-Khamisy SF. A mechanism for oxidative damage repair at gene regulatory elements. Nature 2022; 609:1038-1047. [PMID: 36171374 DOI: 10.1038/s41586-022-05217-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
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Affiliation(s)
- Swagat Ray
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK.,School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Arwa A Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Jacob Parker
- School of Biosciences, University of Sheffield, Sheffield, UK.,Center for Advanced Parkinson Research, Harvard Medical School, Boston, MA, USA
| | | | - Nelma M Palminha
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, UK
| | - Cleide D S Souza
- School of Biosciences, University of Sheffield, Sheffield, UK.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mateusz Jurga
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, University of Sheffield, Sheffield, UK. .,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK. .,Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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7
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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8
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Zhang M, Seitz C, Chang G, Iqbal F, Lin H, Liu J. A guide for single-particle chromatin tracking in live cell nuclei. Cell Biol Int 2022; 46:683-700. [PMID: 35032142 PMCID: PMC9035067 DOI: 10.1002/cbin.11762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a sys-tematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation pur-poses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengdi Zhang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hua Lin
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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9
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Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. The emerging role of ISWI chromatin remodeling complexes in cancer. J Exp Clin Cancer Res 2021; 40:346. [PMID: 34736517 PMCID: PMC8567610 DOI: 10.1186/s13046-021-02151-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Disordered chromatin remodeling regulation has emerged as an essential driving factor for cancers. Imitation switch (ISWI) family are evolutionarily conserved ATP-dependent chromatin remodeling complexes, which are essential for cellular survival and function through multiple genetic and epigenetic mechanisms. Omics sequencing and a growing number of basic and clinical studies found that ISWI family members displayed widespread gene expression and genetic status abnormalities in human cancer. Their aberrant expression is closely linked to patient outcome and drug response. Functional or componential alteration in ISWI-containing complexes is critical for tumor initiation and development. Furthermore, ISWI-non-coding RNA regulatory networks and some non-coding RNAs derived from exons of ISWI member genes play important roles in tumor progression. Therefore, unveiling the transcriptional regulation mechanism underlying ISWI family sparked a booming interest in finding ISWI-based therapies in cancer. This review aims at describing the current state-of-the-art in the role of ISWI subunits and complexes in tumorigenesis, tumor progression, immunity and drug response, and presenting deep insight into the physiological and pathological implications of the ISWI transcription machinery in cancers.
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Affiliation(s)
- Yanan Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Han Gong
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Pan Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yajuan Cui
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Heng Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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10
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Monitoring Dark-State Dynamics of a Single Nitrogen-Vacancy Center in Nanodiamond by Auto-Correlation Spectroscopy: Photonionization and Recharging. NANOMATERIALS 2021; 11:nano11040979. [PMID: 33920225 PMCID: PMC8070252 DOI: 10.3390/nano11040979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022]
Abstract
In this letter, the photon-induced charge conversion dynamics of a single Nitrogen-Vacancy (NV) center in nanodiamond between two charge states, negative (NV−) and neutral (NV0), is studied by the auto-correlation function. It is observed that the ionization of NV− converts to NV0, which is regarded as the dark state of the NV−, leading to fluorescence intermittency in single NV centers. A new method, based on the auto-correlation calculation of the time-course fluorescence intensity from NV centers, was developed to quantify the transition kinetics and yielded the calculation of transition rates from NV− to NV0 (ionization) and from NV0 to NV− (recharging). Based on our experimental investigation, we found that the NV−-NV0 transition is wavelength-dependent, and more frequent transitions were observed when short-wavelength illumination was used. From the analysis of the auto-correlation curve, it is found that the transition time of NV− to NV0 (ionization) is around 0.1 μs, but the transition time of NV0 to NV− (recharging) is around 20 ms. Power-dependent measurements reveal that the ionization rate increases linearly with the laser power, while the recharging rate has a quadratic increase with the laser power. This difference suggests that the ionization in the NV center is a one-photon process, while the recharging of NV0 to NV− is a two-photon process. This work, which offers theoretical and experimental explanations of the emission property of a single NV center, is expected to help the utilization of the NV center for quantum information science, quantum communication, and quantum bioimaging.
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11
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Kiyomitsu T, Boerner S. The Nuclear Mitotic Apparatus (NuMA) Protein: A Key Player for Nuclear Formation, Spindle Assembly, and Spindle Positioning. Front Cell Dev Biol 2021; 9:653801. [PMID: 33869212 PMCID: PMC8047419 DOI: 10.3389/fcell.2021.653801] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 01/10/2023] Open
Abstract
The nuclear mitotic apparatus (NuMA) protein is well conserved in vertebrates, and dynamically changes its subcellular localization from the interphase nucleus to the mitotic/meiotic spindle poles and the mitotic cell cortex. At these locations, NuMA acts as a key structural hub in nuclear formation, spindle assembly, and mitotic spindle positioning, respectively. To achieve its variable functions, NuMA interacts with multiple factors, including DNA, microtubules, the plasma membrane, importins, and cytoplasmic dynein. The binding of NuMA to dynein via its N-terminal domain drives spindle pole focusing and spindle positioning, while multiple interactions through its C-terminal region define its subcellular localizations and functions. In addition, NuMA can self-assemble into high-ordered structures which likely contribute to spindle positioning and nuclear formation. In this review, we summarize recent advances in NuMA’s domains, functions and regulations, with a focus on human NuMA, to understand how and why vertebrate NuMA participates in these functions in comparison with invertebrate NuMA-related proteins.
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Affiliation(s)
- Tomomi Kiyomitsu
- Cell Division Dynamics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Japan
| | - Susan Boerner
- Cell Division Dynamics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Japan
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12
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Serra-Marques A, Houtekamer R, Hintzen D, Canty JT, Yildiz A, Dumont S. The mitotic protein NuMA plays a spindle-independent role in nuclear formation and mechanics. J Cell Biol 2020; 219:e202004202. [PMID: 33044554 PMCID: PMC7555356 DOI: 10.1083/jcb.202004202] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/15/2020] [Accepted: 09/11/2020] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic cells typically form a single, round nucleus after mitosis, and failures to do so can compromise genomic integrity. How mammalian cells form such a nucleus remains incompletely understood. NuMA is a spindle protein whose disruption results in nuclear fragmentation. What role NuMA plays in nuclear integrity, and whether its perceived role stems from its spindle function, are unclear. Here, we use live imaging to demonstrate that NuMA plays a spindle-independent role in forming a single, round nucleus. NuMA keeps the decondensing chromosome mass compact at mitotic exit and promotes a mechanically robust nucleus. NuMA's C terminus binds DNA in vitro and chromosomes in interphase, while its coiled-coil acts as a central regulatory and structural element: it prevents NuMA from binding chromosomes at mitosis, regulates its nuclear mobility, and is essential for nuclear formation. Thus, NuMA plays a structural role over the cell cycle, building and maintaining the spindle and nucleus, two of the cell's largest structures.
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Affiliation(s)
- Andrea Serra-Marques
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
| | - Ronja Houtekamer
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Dorine Hintzen
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - John T. Canty
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA
- Department of Physics, University of California, Berkeley, Berkeley, CA
| | - Sophie Dumont
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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13
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Schlam-Babayov S, Bensimon A, Harel M, Geiger T, Aebersold R, Ziv Y, Shiloh Y. Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. EMBO J 2020; 40:e104400. [PMID: 33215756 DOI: 10.15252/embj.2020104400] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
The DNA damage response (DDR) is a complex signaling network that relies on cascades of protein phosphorylation, which are initiated by three protein kinases of the family of PI3-kinase-related protein kinases (PIKKs): ATM, ATR, and DNA-PK. ATM is missing or inactivated in the genome instability syndrome, ataxia-telangiectasia (A-T). The relative shares of these PIKKs in the response to genotoxic stress and the functional relationships among them are central questions in the genome stability field. We conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells treated with the double-strand break-inducing chemical, neocarzinostatin, and validated the results with the targeted proteomic technique, selected reaction monitoring. We also matched our results with 34 published screens for DDR factors, creating a valuable resource for identifying strong candidates for novel DDR players. We uncovered fine-tuned dynamics between the PIKKs following genotoxic stress, such as DNA-PK-dependent attenuation of ATM. In A-T cells, partial compensation for ATM absence was provided by ATR and DNA-PK, with distinct roles and kinetics. The results highlight intricate relationships between these PIKKs in the DDR.
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Affiliation(s)
- Sapir Schlam-Babayov
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michal Harel
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Yael Ziv
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Yosef Shiloh
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
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14
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Rajeevan A, Keshri R, Kapoor S, Kotak S. NuMA interaction with chromatin is vital for proper chromosome decondensation at the mitotic exit. Mol Biol Cell 2020; 31:2437-2451. [PMID: 32845810 PMCID: PMC7851854 DOI: 10.1091/mbc.e20-06-0415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
NuMA is an abundant long coiled-coil protein that plays a prominent role in spindle organization during mitosis. In interphase, NuMA is localized to the nucleus and hypothesized to control gene expression and chromatin organization. However, because of the prominent mitotic phenotype upon NuMA loss, its precise function in the interphase nucleus remains elusive. Here, we report that NuMA is associated with chromatin in interphase and prophase but released upon nuclear envelope breakdown (NEBD) by the action of Cdk1. We uncover that NuMA directly interacts with DNA via evolutionarily conserved sequences in its C-terminus. Notably, the expression of the DNA-binding-deficient mutant of NuMA affects chromatin decondensation at the mitotic exit, and nuclear shape in interphase. We show that the nuclear shape defects observed upon mutant NuMA expression are due to its potential to polymerize into higher-order fibrillar structures. Overall, this work establishes the spindle-independent function of NuMA in choreographing proper chromatin decompaction and nuclear shape by directly associating with the DNA.
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Affiliation(s)
- Ashwathi Rajeevan
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bangalore, India
| | - Riya Keshri
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bangalore, India
| | - Sukriti Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bangalore, India
| | - Sachin Kotak
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bangalore, India
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15
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Mohamadalizadeh-Hanjani Z, Shahbazi S, Geranpayeh L. Investigation of the SPAG5 gene expression and amplification related to the NuMA mRNA levels in breast ductal carcinoma. World J Surg Oncol 2020; 18:225. [PMID: 32838814 PMCID: PMC7445913 DOI: 10.1186/s12957-020-02001-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/12/2020] [Indexed: 12/26/2022] Open
Abstract
Background The cell proliferative markers are very important in breast cancer. Since SPAG5 and NuMA proteins play a significant role in the mitosis regulatory network and cell division, we aimed to study their mRNA levels as well as SPAG5 gene amplification correlated to clinicopathological status in ductal carcinoma of the breast. Methods SPAG5 and NuMA gene expressions were investigated in 40 breast cancer tissues and normal adjacent tissues via real-time PCR. PUM1 was selected as the reference gene. QMF PCR method was applied to study SPAG5 gene amplification and AGBL2, BOD1L, and POR were designated as internal control genes. Gene amplification was determined by calculating a dosage quotient for each DNA fragment. Results Increased SPAG5 mRNA expression was detected in breast cancer tissues (p = 0.005) and related to tumor size. No significant difference was observed between NuMA gene expression level in tumor tissue and the normal adjacent tissue (p = 0.56). However, we observed that NuMA expression was significantly increased in ER-positive tumor tissues. There was no clear correlation pattern between SPAG5 and NuMA mRNA levels (r = 0.33). Seventeen percent of tissues showed complete amplification in SPAG5 gene fragments. Conclusion Our results were consistent with the previous publications regarding SPAG5 gene expression and amplification in breast cancer with an emphasis on the prominent role of this protein in tumor pathogenesis. Our results failed to yield any correlation between SPAG5 and NuMA mRNA levels which implies independence of these genes in breast cancer pathogenesis.
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Affiliation(s)
| | - Shirin Shahbazi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Loabat Geranpayeh
- Department of Surgery, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
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16
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Mass Spectrometric Comparison of HPV-Positive and HPV-Negative Oropharyngeal Cancer. Cancers (Basel) 2020; 12:cancers12061531. [PMID: 32545200 PMCID: PMC7352546 DOI: 10.3390/cancers12061531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) consist of two distinct biological entities. While the numbers of classical, tobacco-induced HNSCC are declining, tumors caused by human papillomavirus (HPV) infection are increasing in many countries. HPV-positive HNSCC mostly arise in the oropharynx and are characterized by an enhanced sensitivity towards radiotherapy and a favorable prognosis. To identify molecular differences between both entities on the protein level, we conducted a mass spectrometric comparison of eight HPV-positive and nine HPV-negative oropharyngeal tumors (OPSCC). Overall, we identified 2051 proteins, of which 31 were found to be differentially expressed. Seventeen of these can be assorted to three functional groups, namely DNA replication, nuclear architecture and cytoskeleton regulation, with the differences in the last group potentially reflecting an enhanced migratory and invasive capacity. Furthermore, a number of identified proteins have been described to directly impact on DNA double-strand break repair or radiation sensitivity (e.g., SLC3A2, cortactin, RBBP4, Numa1), offering explanations for the differential prognosis. The unequal expression of three proteins (SLC3A2, MCM2 and lamin B1) was confirmed by immunohistochemical staining using a tissue microarray containing 205 OPSCC samples. The expression levels of SLC3A2 and lamin B1 were found be of prognostic relevance in patients with HPV-positive and HPV-negative OPSCC, respectively.
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17
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Bensimon A, Koch JP, Francica P, Roth SM, Riedo R, Glück AA, Orlando E, Blaukat A, Aebersold DM, Zimmer Y, Aebersold R, Medová M. Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. Mol Oncol 2020; 14:1185-1206. [PMID: 32336009 PMCID: PMC7266272 DOI: 10.1002/1878-0261.12696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that interference with growth factor receptor tyrosine kinase (RTK) signaling can affect DNA damage response (DDR) networks, with a consequent impact on cellular responses to DNA‐damaging agents widely used in cancer treatment. In that respect, the MET RTK is deregulated in abundance and/or activity in a variety of human tumors. Using two proteomic techniques, we explored how disrupting MET signaling modulates global cellular phosphorylation response to ionizing radiation (IR). Following an immunoaffinity‐based phosphoproteomic discovery survey, we selected candidate phosphorylation sites for extensive characterization by targeted proteomics focusing on phosphorylation sites in both signaling networks. Several substrates of the DDR were confirmed to be modulated by sequential MET inhibition and IR, or MET inhibition alone. Upon combined treatment, for two substrates, NUMA1 S395 and CHEK1 S345, the gain and loss of phosphorylation, respectively, were recapitulated using invivo tumor models by immunohistochemistry, with possible utility in future translational research. Overall, we have corroborated phosphorylation sites at the intersection between MET and the DDR signaling networks, and suggest that these represent a class of proteins at the interface between oncogene‐driven proliferation and genomic stability.
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Affiliation(s)
- Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland
| | - Jonas P Koch
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Paola Francica
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Selina M Roth
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Rahel Riedo
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Astrid A Glück
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Eleonora Orlando
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Andree Blaukat
- Global Research & Development, Merck KGaA, Darmstadt, Germany
| | - Daniel M Aebersold
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland.,Faculty of Science, University of Zürich, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
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18
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Locatelli M, Vidi PA. Special issue: Nuclear architecture and chromatin motions in the DNA damage response. Mutat Res 2020; 821:111721. [PMID: 32846362 PMCID: PMC9581968 DOI: 10.1016/j.mrfmmm.2020.111721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Maëlle Locatelli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
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19
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Gisler S, Maia ARR, Chandrasekaran G, Kopparam J, van Lohuizen M. A genome-wide enrichment screen identifies NUMA1-loss as a resistance mechanism against mitotic cell-death induced by BMI1 inhibition. PLoS One 2020; 15:e0227592. [PMID: 32343689 PMCID: PMC7188281 DOI: 10.1371/journal.pone.0227592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/24/2020] [Indexed: 02/02/2023] Open
Abstract
BMI1 is a core protein of the polycomb repressive complex 1 (PRC1) that is overexpressed in several cancer types, making it a promising target for cancer therapies. However, the underlying mechanisms and interactions associated with BMI1-induced tumorigenesis are often context-dependent and complex. Here, we performed a drug resistance screen on mutagenized human haploid HAP1 cells treated with BMI1 inhibitor PTC-318 to find new genetic and mechanistic features associated with BMI1-dependent cancer cell proliferation. Our screen identified NUMA1-mutations as the most significant inducer of PTC-318 cell death resistance. Independent validations on NUMA1-proficient HAP1 and non-small cell lung cancer cell lines exposed to BMI1 inhibition by PTC-318 or BMI1 knockdown resulted in cell death following mitotic arrest. Interestingly, cells with CRISPR-Cas9 derived NUMA1 knockout also showed a mitotic arrest phenotype following BMI1 inhibition but, contrary to cells with wildtype NUMA1, these cells were resistant to BMI1-dependent cell death. The current study brings new insights to BMI1 inhibition-induced mitotic lethality in cancer cells and presents a previously unknown role of NUMA1 in this process.
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Affiliation(s)
- Santiago Gisler
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ana Rita R. Maia
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gayathri Chandrasekaran
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jawahar Kopparam
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Amsterdam, The Netherlands
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20
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Cutiongco MFA, Jensen BS, Reynolds PM, Gadegaard N. Predicting gene expression using morphological cell responses to nanotopography. Nat Commun 2020; 11:1384. [PMID: 32170111 PMCID: PMC7070086 DOI: 10.1038/s41467-020-15114-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
Cells respond in complex ways to their environment, making it challenging to predict a direct relationship between the two. A key problem is the lack of informative representations of parameters that translate directly into biological function. Here we present a platform to relate the effects of cell morphology to gene expression induced by nanotopography. This platform utilizes the ‘morphome’, a multivariate dataset of cell morphology parameters. We create a Bayesian linear regression model that uses the morphome to robustly predict changes in bone, cartilage, muscle and fibrous gene expression induced by nanotopography. Furthermore, through this model we effectively predict nanotopography-induced gene expression from a complex co-culture microenvironment. The information from the morphome uncovers previously unknown effects of nanotopography on altering cell–cell interaction and osteogenic gene expression at the single cell level. The predictive relationship between morphology and gene expression arising from cell-material interaction shows promise for exploration of new topographies. The surface nanotopography of biomaterials direct cell behavior, but screening for desired effects is inefficient. Here, the authors introduce a platform that enables prediction of nanotopography-induced gene expression changes from changes in cell morphology, including in co-culture environments.
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Affiliation(s)
- Marie F A Cutiongco
- Divison of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | | | - Paul M Reynolds
- Divison of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK
| | - Nikolaj Gadegaard
- Divison of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, UK.
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21
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Tong S. Circular RNA SMARCA5 may serve as a tumor suppressor in non-small cell lung cancer. J Clin Lab Anal 2020; 34:e23195. [PMID: 31944395 PMCID: PMC7246390 DOI: 10.1002/jcla.23195] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/12/2019] [Accepted: 12/18/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND This study aimed to investigate the correlation of circular RNA SMARCA5 (circ-SMARCA5) expression with clinicopathological characteristics and survival profiles, furthermore, to explore the function of circ-SMARCA5 on regulating cell proliferation and chemotherapy sensitivity in non-small cell lung cancer (NSCLC). METHODS A total of 460 NSCLC patients were retrospectively reviewed, and circ-SMARCA5 expressions in tumor tissue and adjacent tissue were detected by RT-qPCR. Clinical characteristics were collected. Disease-free survival (DFS) and overall survival (OS) were calculated. In vitro, circ-SMARCA5 overexpression and control overexpression plasmids were transfected into NCI-H1437 as well as NCI-H1299 cells, which were further treated with different concentrations of cisplatin and gemcitabine. RESULTS Circ-SMARCA5 expression was decreased in tumor tissues compared to adjacent tissues. Moreover, circ-SMARCA5 expression negatively correlated with tumor size, lymph node metastasis, and TNM stage, but positively correlated with DFS and OS. Subsequent analysis displayed that circ-SMARCA5 high expression independently predicted prolonged DFS and OS. In vitro, circ-SMARCA5 expression was reduced in NSCLC cell lines (NCI-H650, NCI-H1299, NCI-H1437, and A549) compared to human normal lung bronchus epithelial cell line (BEAS-2B). In NCI-H1437 and NCI-H1299 cells, cell proliferation was decreased by circ-SMARCA5 overexpression, furthermore, chemosensitivity to cisplatin and gemcitabine were enhanced in circ-SMARCA5 overexpression treated cells compared to the control cells. CONCLUSION Circ-SMARCA5 may serve as a tumor suppressor in NSCLC, which provides insight to the exploration of novel strategies in NSCLC management.
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Affiliation(s)
- Suiju Tong
- Department of Pharmacy, People's Hospital of Dongxihu District Wuhan City, Wuhan, China
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22
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Salvador Moreno N, Liu J, Haas KM, Parker LL, Chakraborty C, Kron SJ, Hodges K, Miller LD, Langefeld C, Robinson PJ, Lelièvre SA, Vidi PA. The nuclear structural protein NuMA is a negative regulator of 53BP1 in DNA double-strand break repair. Nucleic Acids Res 2019; 47:2703-2715. [PMID: 30812030 PMCID: PMC6451129 DOI: 10.1093/nar/gkz138] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 01/13/2023] Open
Abstract
P53-binding protein 1 (53BP1) mediates DNA repair pathway choice and promotes checkpoint activation. Chromatin marks induced by DNA double-strand breaks and recognized by 53BP1 enable focal accumulation of this multifunctional repair factor at damaged chromatin. Here, we unveil an additional level of regulation of 53BP1 outside repair foci. 53BP1 movements are constrained throughout the nucleoplasm and increase in response to DNA damage. 53BP1 interacts with the structural protein NuMA, which controls 53BP1 diffusion. This interaction, and colocalization between the two proteins in vitro and in breast tissues, is reduced after DNA damage. In cell lines and breast carcinoma NuMA prevents 53BP1 accumulation at DNA breaks, and high NuMA expression predicts better patient outcomes. Manipulating NuMA expression alters PARP inhibitor sensitivity of BRCA1-null cells, end-joining activity, and immunoglobulin class switching that rely on 53BP1. We propose a mechanism involving the sequestration of 53BP1 by NuMA in the absence of DNA damage. Such a mechanism may have evolved to disable repair functions and may be a decisive factor for tumor responses to genotoxic treatments.
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Affiliation(s)
- Naike Salvador Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Jing Liu
- Department of Physics, Indiana university-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Karen M Haas
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Chaitali Chakraborty
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kurt Hodges
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Comprehensive Cancer Center of Wake Forest University
| | - Carl Langefeld
- Comprehensive Cancer Center of Wake Forest University.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Paul J Robinson
- Department of Basic Medical Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.,Comprehensive Cancer Center of Wake Forest University
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23
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Alvarez-Saavedra M, Yan K, De Repentigny Y, Hashem LE, Chaudary N, Sarwar S, Yang D, Ioshikhes I, Kothary R, Hirayama T, Yagi T, Picketts DJ. Snf2h Drives Chromatin Remodeling to Prime Upper Layer Cortical Neuron Development. Front Mol Neurosci 2019; 12:243. [PMID: 31680852 PMCID: PMC6811508 DOI: 10.3389/fnmol.2019.00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 01/23/2023] Open
Abstract
Alterations in the homeostasis of either cortical progenitor pool, namely the apically located radial glial (RG) cells or the basal intermediate progenitors (IPCs) can severely impair cortical neuron production. Such changes are reflected by microcephaly and are often associated with cognitive defects. Genes encoding epigenetic regulators are a frequent cause of intellectual disability and many have been shown to regulate progenitor cell growth, including our inactivation of the Smarca1 gene encoding Snf2l, which is one of two ISWI mammalian orthologs. Loss of the Snf2l protein resulted in dysregulation of Foxg1 and IPC proliferation leading to macrocephaly. Here we show that inactivation of the closely related Smarca5 gene encoding the Snf2h chromatin remodeler is necessary for embryonic IPC expansion and subsequent specification of callosal projection neurons. Telencephalon-specific Smarca5 cKO embryos have impaired cell cycle kinetics and increased cell death, resulting in fewer Tbr2+ and FoxG1+ IPCs by mid-neurogenesis. These deficits give rise to adult mice with a dramatic reduction in Satb2+ upper layer neurons, and partial agenesis of the corpus callosum. Mice survive into adulthood but molecularly display reduced expression of the clustered protocadherin genes that may further contribute to altered dendritic arborization and a hyperactive behavioral phenotype. Our studies provide novel insight into the developmental function of Snf2h-dependent chromatin remodeling processes during brain development.
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Affiliation(s)
- Matías Alvarez-Saavedra
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Yves De Repentigny
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lukas E Hashem
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Nidhi Chaudary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Shihab Sarwar
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Doo Yang
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Ilya Ioshikhes
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rashmi Kothary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, Tokushima, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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24
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Densham RM, Morris JR. Moving Mountains-The BRCA1 Promotion of DNA Resection. Front Mol Biosci 2019; 6:79. [PMID: 31552267 PMCID: PMC6733915 DOI: 10.3389/fmolb.2019.00079] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) occur in our cells in the context of chromatin. This type of lesion is toxic, entirely preventing genome continuity and causing cell death or terminal arrest. Several repair mechanisms can act on DNA surrounding a DSB, only some of which carry a low risk of mutation, so that which repair process is utilized is critical to the stability of genetic material of cells. A key component of repair outcome is the degree of DNA resection directed to either side of the break site. This in turn determines the subsequent forms of repair in which DNA homology plays a part. Here we will focus on chromatin and chromatin-bound complexes which constitute the "mountains" that block resection, with a particular focus on how the breast and ovarian cancer predisposition protein-1 (BRCA1) contributes to repair outcomes through overcoming these blocks.
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Affiliation(s)
| | - Joanna R. Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham, United Kingdom
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25
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Abstract
This study utilized a Förster resonance energy transfer (FRET)-based molecular tension sensor and live cell imaging to evaluate the effect of osteocytes, a mechanosensitive bone cell, on the migratory behavior of tumor cells. Two cell lines derived from MDA-MB-231 breast cancer cells were transfected with the vinculin tension sensor to quantitatively evaluate the force in focal adhesions of the tumor cell. Tumor cells treated with MLO-A5 osteocyte-conditioned media (CM) decreased the tensile forces in their focal adhesions and decreased their migratory potential. Tumor cells treated with media derived from MLO-A5 cells exposed to fluid flow-driven shear stress (FFCM) increased the tensile forces and increased migratory potential. Focal adhesion tension in tumor cells was also affected by distance from MLO-A5 cells when the two cells were co-cultured, where tumor cells close to MLO-A5 cells exhibited lower tension and decreased cell motility. Overall, this study demonstrates that focal adhesion tension is involved in altered migratory potential of tumor cells, and tumor-osteocyte interactions decrease the tension and motility of tumor cells.
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26
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Jimeno S, Mejías-Navarro F, Prados-Carvajal R, Huertas P. Controlling the balance between chromosome break repair pathways. DNA Repair (Amst) 2019; 115:95-134. [DOI: 10.1016/bs.apcsb.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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27
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Drissi R, Chauvin A, McKenna A, Lévesque D, Blais-Brochu S, Jean D, Boisvert FM. Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks. Cell Cycle 2018; 17:2593-2609. [PMID: 30516086 PMCID: PMC6300108 DOI: 10.1080/15384101.2018.1553336] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA replication during S phase involves thousands of replication forks that must be coordinated to ensure that every DNA section is replicated only once. The minichromosome maintenance proteins, MCM2 to MCM7, form a heteromeric DNA helicase required for both the initiation and elongation of DNA replication. Although only two DNA helicase activities are necessary to establish a bidirectional replication fork from each replication origin, a large excess of MCM complexes is amassed and distributed along the chromatin. The function of the additional MCM complexes is not well understood, as most are displaced from the DNA during the S-phase, apparently without playing an active role in DNA replication. DNA damage response (DDR) kinases activated by stalled forks prevent the replication machinery from being activated, indicating a tight relationship between DDR and DNA replication. To investigate the role of MCM proteins in the cellular response to DNA damage, we used shRNA targeting MCM2 or MCM3 to determine the impact of a reduction in MCM complex. The alteration of MCM proteins induced a change in the activation of key factors of the DDR in response to Etoposide treatment. Etoposide-induced DNA damage affected the phosphorylation of γ-H2AX, CHK1 and CHK2 without affecting cell viability. Using assays measuring homologous recombination (HR) and non-homologous end-joining (NHEJ), we identified a decrease in both HR and NHEJ associated with a decrease in MCM complex.
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Affiliation(s)
- Romain Drissi
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Anaïs Chauvin
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Alyson McKenna
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Lévesque
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Simon Blais-Brochu
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Jean
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - François-Michel Boisvert
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
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28
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Torrecilla I, Oehler J, Ramadan K. The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0282. [PMID: 28847819 PMCID: PMC5577460 DOI: 10.1098/rstb.2016.0282] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
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29
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Fu X, Zhang C, Meng H, Zhang K, Shi L, Cao C, Wang Y, Su C, Xin L, Ren Y, Zhang W, Sun X, Ge L, Silvennoinen O, Yao Z, Yang X, Yang J. Oncoprotein Tudor-SN is a key determinant providing survival advantage under DNA damaging stress. Cell Death Differ 2018; 25:1625-1637. [PMID: 29459768 DOI: 10.1038/s41418-018-0068-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/12/2023] Open
Abstract
Herein, Tudor-SN was identified as a DNA damage response (DDR)-related protein that plays important roles in the early stage of DDR. X-ray or laser irradiation could evoke the accumulation of Tudor-SN to DNA damage sites in a poly(ADP-ribosyl)ation-dependent manner via interaction with PARP-1. Additionally, we illustrated that the SN domain of Tudor-SN mediated the association of these two proteins. The accumulated Tudor-SN further recruited SMARCA5 (ATP-dependent chromatin remodeller) and GCN5 (histone acetyltransferase) to DNA damage sites, resulting in chromatin relaxation, and consequently activating the ATM kinase and downstream DNA repair signalling pathways to promote cell survival. Consistently, the loss-of-function of Tudor-SN attenuated the enrichment of SMARCA5, GCN5 and acetylation of histone H3 (acH3) at DNA break sites and abolished chromatin relaxation; as a result, the cells exhibited DNA repair and cell survival deficiency. As Tudor-SN protein is highly expressed in different tumours, it is likely to be involved in the radioresistance of cancer treatment.
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Affiliation(s)
- Xiao Fu
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Chunyan Zhang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Hao Meng
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Kai Zhang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Lei Shi
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Cheng Cao
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Ye Wang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Chao Su
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Lingbiao Xin
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Yuanyuan Ren
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Wei Zhang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xiaoming Sun
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Lin Ge
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Olli Silvennoinen
- Institute of Medical Technology, University of Tampere, Tampere University Hospital, Biokatu 8, 33014, Tampere, Finland
| | - Zhi Yao
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xi Yang
- Department of Immunology, University of Manitoba, 471 Apotex Centre, 750 McDermot Avenue, Winnipeg, MB, R3E 0T5, Canada.
| | - Jie Yang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Key Laboratory of Cellular and Molecular Immunology in Tianjin, Department of Biochemistry and Molecular Biology, Excellent Talent Project, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China.
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30
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Jayaraman S, Chittiboyina S, Bai Y, Abad PC, Vidi PA, Stauffacher CV, Lelièvre SA. The nuclear mitotic apparatus protein NuMA controls rDNA transcription and mediates the nucleolar stress response in a p53-independent manner. Nucleic Acids Res 2017; 45:11725-11742. [PMID: 28981686 PMCID: PMC5714241 DOI: 10.1093/nar/gkx782] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
The nuclear mitotic apparatus protein, NuMA, is involved in major cellular events such as DNA damage response, apoptosis and p53-mediated growth-arrest, all of which are under the control of the nucleolus upon stress. Proteomic investigation has identified NuMA among hundreds of nucleolar proteins. Yet, the precise link between NuMA and nucleolar function remains undetermined. We confirm that NuMA is present in the nucleolus and reveal redistribution of NuMA upon actinomycin D or doxorubicin-induced nucleolar stress. NuMA coimmunoprecipitates with RNA polymerase I, with ribosomal proteins RPL26 and RPL24, and with components of B-WICH, an ATP-dependent chromatin remodeling complex associated with rDNA transcription. NuMA also binds to 18S and 28S rRNAs and localizes to rDNA promoter regions. Downregulation of NuMA expression triggers nucleolar stress, as shown by decreased nascent pre-rRNA synthesis, fibrillarin perinucleolar cap formation and upregulation of p27kip1, but not p53. Physiologically relevant nucleolar stress induction with reactive oxygen species reaffirms a p53-independent p27kip1 response pathway and leads to nascent pre-rRNA reduction. It also promotes the decrease in the amount of NuMA. This previously uncharacterized function of NuMA in rDNA transcription and p53-independent nucleolar stress response supports a central role for this nuclear structural protein in cellular homeostasis.
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Affiliation(s)
- Swaathi Jayaraman
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907-2026, USA.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2026, USA
| | - Shirisha Chittiboyina
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907-2026, USA
| | - Yunfeng Bai
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907-2026, USA
| | - Patricia C Abad
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907-2026, USA
| | - Pierre-Alexandre Vidi
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907-2026, USA
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2026, USA.,Center for Cancer Research, Purdue University, West Lafayette, IN 47907-2026, USA
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907-2026, USA.,Center for Cancer Research, Purdue University, West Lafayette, IN 47907-2026, USA
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31
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Non-canonical reader modules of BAZ1A promote recovery from DNA damage. Nat Commun 2017; 8:862. [PMID: 29021563 PMCID: PMC5636791 DOI: 10.1038/s41467-017-00866-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 07/27/2017] [Indexed: 01/08/2023] Open
Abstract
Members of the ISWI family of chromatin remodelers mobilize nucleosomes to control DNA accessibility and, in some cases, are required for recovery from DNA damage. However, it remains poorly understood how the non-catalytic ISWI subunits BAZ1A and BAZ1B might contact chromatin to direct the ATPase SMARCA5. Here, we find that the plant homeodomain of BAZ1A, but not that of BAZ1B, has the unusual function of binding DNA. Furthermore, the BAZ1A bromodomain has a non-canonical gatekeeper residue and binds relatively weakly to acetylated histone peptides. Using CRISPR-Cas9-mediated genome editing we find that BAZ1A and BAZ1B each recruit SMARCA5 to sites of damaged chromatin and promote survival. Genetic engineering of structure-designed bromodomain and plant homeodomain mutants reveals that reader modules of BAZ1A and BAZ1B, even when non-standard, are critical for DNA damage recovery in part by regulating ISWI factors loading at DNA lesions and supporting transcriptional programs required for survival. ISWI chromatin remodelers regulate DNA accessibility and have been implicated in DNA damage repair. Here, the authors uncover functions, in response to DNA damage, for the bromodomain of the ISWI subunit BAZ1B and for the non-canonical PHD and bromodomain modules of the paralog BAZ1A.
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32
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Vidi PA, Anderson KA, Chen H, Anderson R, Salvador-Moreno N, Mora DC, Poutasse C, Laurienti PJ, Daniel SS, Arcury TA. Personal samplers of bioavailable pesticides integrated with a hair follicle assay of DNA damage to assess environmental exposures and their associated risks in children. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2017; 822:27-33. [PMID: 28844239 PMCID: PMC5607735 DOI: 10.1016/j.mrgentox.2017.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/21/2017] [Accepted: 07/10/2017] [Indexed: 11/19/2022]
Abstract
Agriculture in the United States employs youth ages ten and older in work environments with high pesticide levels. Younger children in rural areas may also be affected by indirect pesticide exposures. The long-term effects of pesticides on health and development are difficult to assess and poorly understood. Yet, epidemiologic studies suggest associations with cancer as well as cognitive deficits. We report a practical and cost-effective approach to assess environmental pesticide exposures and their biological consequences in children. Our approach combines silicone wristband personal samplers and DNA damage quantification from hair follicles, and was tested as part of a community-based participatory research (CBPR) project involving ten Latino children from farmworker households in North Carolina. Our study documents high acceptance among Latino children and their caregivers of these noninvasive sampling methods. The personal samplers detected organophosphates, organochlorines, and pyrethroids in the majority of the participants (70%, 90%, 80%, respectively). Pesticides were detected in all participant samplers, with an average of 6.2±2.4 detections/participant sampler. DNA damage in epithelial cells from the sheath and bulb of plucked hairs follicles was quantified by immunostaining 53BP1-labled DNA repair foci. This method is sensitive, as shown by dose response analyses to γ radiations where the lowest dose tested (0.1Gy) led to significant increased 53BP1 foci density. Immunolabeling of DNA repair foci has significant advantages over the comet assay in that specific regions of the follicles can be analyzed. In this cohort of child participants, significant association was found between the number of pesticide detections and DNA damage in the papilla region of the hairs. We anticipate that this monitoring approach of bioavailable pesticides and genotoxicity will enhance our knowledge of the biological effects of pesticides to guide education programs and safety policies.
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Affiliation(s)
- Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Comprehensive Cancer Center of Wake Forest University, Winston-Salem, NC 27157, USA.
| | - Kim A Anderson
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR 97331, USA
| | - Haiying Chen
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Rebecca Anderson
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Naike Salvador-Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Dana C Mora
- Department of Family and Community Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Carolyn Poutasse
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR 97331, USA
| | - Paul J Laurienti
- Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Stephanie S Daniel
- Department of Family and Community Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Thomas A Arcury
- Department of Family and Community Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; Center for Worker Health, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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33
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Oppikofer M, Bai T, Gan Y, Haley B, Liu P, Sandoval W, Ciferri C, Cochran AG. Expansion of the ISWI chromatin remodeler family with new active complexes. EMBO Rep 2017; 18:1697-1706. [PMID: 28801535 DOI: 10.15252/embr.201744011] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
ISWI chromatin remodelers mobilize nucleosomes to control DNA accessibility. Complexes isolated to date pair one of six regulatory subunits with one of two highly similar ATPases. However, we find that each endogenously expressed ATPase co-purifies with every regulatory subunit, substantially increasing the diversity of ISWI complexes, and we additionally identify BAZ2B as a novel, seventh regulatory subunit. Through reconstitution of catalytically active human ISWI complexes, we demonstrate that the new interactions described here are stable and direct. Finally, we profile the nucleosome remodeling functions of the now expanded family of ISWI chromatin remodelers. By revealing the combinatorial nature of ISWI complexes, we provide a basis for better understanding ISWI function in normal settings and disease.
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Affiliation(s)
- Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Tianyi Bai
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yutian Gan
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Liu
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
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34
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Vega SL, Liu E, Arvind V, Bushman J, Sung HJ, Becker ML, Lelièvre S, Kohn J, Vidi PA, Moghe PV. High-content image informatics of the structural nuclear protein NuMA parses trajectories for stem/progenitor cell lineages and oncogenic transformation. Exp Cell Res 2016; 351:11-23. [PMID: 28034673 DOI: 10.1016/j.yexcr.2016.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 12/15/2022]
Abstract
Stem and progenitor cells that exhibit significant regenerative potential and critical roles in cancer initiation and progression remain difficult to characterize. Cell fates are determined by reciprocal signaling between the cell microenvironment and the nucleus; hence parameters derived from nuclear remodeling are ideal candidates for stem/progenitor cell characterization. Here we applied high-content, single cell analysis of nuclear shape and organization to examine stem and progenitor cells destined to distinct differentiation endpoints, yet undistinguishable by conventional methods. Nuclear descriptors defined through image informatics classified mesenchymal stem cells poised to either adipogenic or osteogenic differentiation, and oligodendrocyte precursors isolated from different regions of the brain and destined to distinct astrocyte subtypes. Nuclear descriptors also revealed early changes in stem cells after chemical oncogenesis, allowing the identification of a class of cancer-mitigating biomaterials. To capture the metrology of nuclear changes, we developed a simple and quantitative "imaging-derived" parsing index, which reflects the dynamic evolution of the high-dimensional space of nuclear organizational features. A comparative analysis of parsing outcomes via either nuclear shape or textural metrics of the nuclear structural protein NuMA indicates the nuclear shape alone is a weak phenotypic predictor. In contrast, variations in the NuMA organization parsed emergent cell phenotypes and discerned emergent stages of stem cell transformation, supporting a prognosticating role for this protein in the outcomes of nuclear functions.
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Affiliation(s)
- Sebastián L Vega
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Er Liu
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Varun Arvind
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jared Bushman
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Piscataway, NJ, United States; School of Pharmacy, University of Wyoming, Laramie, WY, United States
| | - Hak-Joon Sung
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Piscataway, NJ, United States; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Matthew L Becker
- Department of Polymer Science and Engineering, University of Akron, Akron, OH, United States
| | - Sophie Lelièvre
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, United States
| | - Joachim Kohn
- Department of Chemistry and Chemical Biology, New Jersey Center for Biomaterials, Piscataway, NJ, United States
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States.
| | - Prabhas V Moghe
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States; Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States.
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35
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Zimmerlin L, Park TS, Huo JS, Verma K, Pather SR, Talbot CC, Agarwal J, Steppan D, Zhang YW, Considine M, Guo H, Zhong X, Gutierrez C, Cope L, Canto-Soler MV, Friedman AD, Baylin SB, Zambidis ET. Tankyrase inhibition promotes a stable human naïve pluripotent state with improved functionality. Development 2016; 143:4368-4380. [PMID: 27660325 DOI: 10.1242/dev.138982] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/11/2016] [Indexed: 01/04/2023]
Abstract
The derivation and maintenance of human pluripotent stem cells (hPSCs) in stable naïve pluripotent states has a wide impact in human developmental biology. However, hPSCs are unstable in classical naïve mouse embryonic stem cell (ESC) WNT and MEK/ERK signal inhibition (2i) culture. We show that a broad repertoire of conventional hESC and transgene-independent human induced pluripotent stem cell (hiPSC) lines could be reverted to stable human preimplantation inner cell mass (ICM)-like naïve states with only WNT, MEK/ERK, and tankyrase inhibition (LIF-3i). LIF-3i-reverted hPSCs retained normal karyotypes and genomic imprints, and attained defining mouse ESC-like functional features, including high clonal self-renewal, independence from MEK/ERK signaling, dependence on JAK/STAT3 and BMP4 signaling, and naïve-specific transcriptional and epigenetic configurations. Tankyrase inhibition promoted a stable acquisition of a human preimplantation ICM-like ground state via modulation of WNT signaling, and was most efficacious in efficiently reprogrammed conventional hiPSCs. Importantly, naïve reversion of a broad repertoire of conventional hiPSCs reduced lineage-primed gene expression and significantly improved their multilineage differentiation capacities. Stable naïve hPSCs with reduced genetic variability and improved functional pluripotency will have great utility in regenerative medicine and human disease modeling.
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Affiliation(s)
- Ludovic Zimmerlin
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Tea Soon Park
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Jeffrey S Huo
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Karan Verma
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Sarshan R Pather
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences at Johns Hopkins, Baltimore, MD 21205, USA
| | - Jasmin Agarwal
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Diana Steppan
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Yang W Zhang
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Michael Considine
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Hong Guo
- Division of Pediatric Oncology, Baltimore, MD 21205, USA
| | - Xiufeng Zhong
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christian Gutierrez
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Leslie Cope
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - M Valeria Canto-Soler
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Stephen B Baylin
- Division of Cancer Biology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Elias T Zambidis
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA .,Division of Pediatric Oncology, Baltimore, MD 21205, USA
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36
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Agarwal P, Miller KM. The nucleosome: orchestrating DNA damage signaling and repair within chromatin. Biochem Cell Biol 2016; 94:381-395. [PMID: 27240007 DOI: 10.1139/bcb-2016-0017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.
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Affiliation(s)
- Poonam Agarwal
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA.,Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA.,Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX 78712, USA
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37
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Epigenomic regulation of oncogenesis by chromatin remodeling. Oncogene 2016; 35:4423-36. [PMID: 26804164 DOI: 10.1038/onc.2015.513] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/27/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023]
Abstract
Disruption of the intricate gene expression program represents one of major driving factors for the development, progression and maintenance of human cancer, and is often associated with acquired therapeutic resistance. At the molecular level, cancerous phenotypes are the outcome of cellular functions of critical genes, regulatory interactions of histones and chromatin remodeling complexes in response to dynamic and persistent upstream signals. A large body of genetic and biochemical evidence suggests that the chromatin remodelers integrate the extracellular and cytoplasmic signals to control gene activity. Consequently, widespread dysregulation of chromatin remodelers and the resulting inappropriate expression of regulatory genes, together, lead to oncogenesis. We summarize the recent developments and current state of the dysregulation of the chromatin remodeling components as the driving mechanism underlying the growth and progression of human tumors. Because chromatin remodelers, modifying enzymes and protein-protein interactions participate in interpreting the epigenetic code, selective chromatin remodelers and bromodomains have emerged as new frontiers for pharmacological intervention to develop future anti-cancer strategies to be used either as single-agent or in combination therapies with chemotherapeutics or radiotherapy.
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38
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Cavazza T, Vernos I. The RanGTP Pathway: From Nucleo-Cytoplasmic Transport to Spindle Assembly and Beyond. Front Cell Dev Biol 2016; 3:82. [PMID: 26793706 PMCID: PMC4707252 DOI: 10.3389/fcell.2015.00082] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/07/2015] [Indexed: 01/03/2023] Open
Abstract
The small GTPase Ran regulates the interaction of transport receptors with a number of cellular cargo proteins. The high affinity binding of the GTP-bound form of Ran to import receptors promotes cargo release, whereas its binding to export receptors stabilizes their interaction with the cargo. This basic mechanism linked to the asymmetric distribution of the two nucleotide-bound forms of Ran between the nucleus and the cytoplasm generates a switch like mechanism controlling nucleo-cytoplasmic transport. Since 1999, we have known that after nuclear envelope breakdown (NEBD) Ran and the above transport receptors also provide a local control over the activity of factors driving spindle assembly and regulating other aspects of cell division. The identification and functional characterization of RanGTP mitotic targets is providing novel insights into mechanisms essential for cell division. Here we review our current knowledge on the RanGTP system and its regulation and we focus on the recent advances made through the characterization of its mitotic targets. We then briefly review the novel functions of the pathway that were recently described. Altogether, the RanGTP system has moonlighting functions exerting a spatial control over protein interactions that drive specific functions depending on the cellular context.
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Affiliation(s)
- Tommaso Cavazza
- Cell and Developmental Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Isabelle Vernos
- Cell and Developmental Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca I Estudis AvançatsBarcelona, Spain
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39
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Kovac M, Blattmann C, Ribi S, Smida J, Mueller NS, Engert F, Castro-Giner F, Weischenfeldt J, Kovacova M, Krieg A, Andreou D, Tunn PU, Dürr HR, Rechl H, Schaser KD, Melcher I, Burdach S, Kulozik A, Specht K, Heinimann K, Fulda S, Bielack S, Jundt G, Tomlinson I, Korbel JO, Nathrath M, Baumhoer D. Exome sequencing of osteosarcoma reveals mutation signatures reminiscent of BRCA deficiency. Nat Commun 2015; 6:8940. [PMID: 26632267 PMCID: PMC4686819 DOI: 10.1038/ncomms9940] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 10/19/2015] [Indexed: 12/27/2022] Open
Abstract
Osteosarcomas are aggressive bone tumours with a high degree of genetic heterogeneity, which has historically complicated driver gene discovery. Here we sequence exomes of 31 tumours and decipher their evolutionary landscape by inferring clonality of the individual mutation events. Exome findings are interpreted in the context of mutation and SNP array data from a replication set of 92 tumours. We identify 14 genes as the main drivers, of which some were formerly unknown in the context of osteosarcoma. None of the drivers is clearly responsible for the majority of tumours and even TP53 mutations are frequently mapped into subclones. However, >80% of osteosarcomas exhibit a specific combination of single-base substitutions, LOH, or large-scale genome instability signatures characteristic of BRCA1/2-deficient tumours. Our findings imply that multiple oncogenic pathways drive chromosomal instability during osteosarcoma evolution and result in the acquisition of BRCA-like traits, which could be therapeutically exploited.
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Affiliation(s)
- Michal Kovac
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4031 Basel, Switzerland
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Claudia Blattmann
- Pediatrics 5 (Oncology, Hematology, Immunology), Klinikum Stuttgart Olgahospital, Kriegsbergstrasse 62, 70174 Stuttgart, Germany
- Department of Pediatric Hematology, Oncology, Immunology and Pulmology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Sebastian Ribi
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4031 Basel, Switzerland
| | - Jan Smida
- Institute of Radiation Biology, Clinical Cooperation Group Osteosarcoma, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Pediatric Oncology Center, Department of Pediatrics, Technische Universität München and Comprehensive Cancer Center, Kölner Platz 1, 80804 Munich, Germany
| | - Nikola S. Mueller
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Florian Engert
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Komturstrasse 3a, 60528 Frankfurt, Germany
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Francesc Castro-Giner
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Joachim Weischenfeldt
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Monika Kovacova
- The Institute of Mathematics and Physics, Faculty of Mechanical Engineering, Slovak University of Technology, 84248 Bratislava, Slovak Republic
| | - Andreas Krieg
- Orthopaedic Department, Basel University Childrens Hospital (UKBB), Spitalstrasse 33, 4056 Basel, Switzerland
| | - Dimosthenis Andreou
- Department of Orthopedic Oncology, Sarcoma Center Berlin-Brandenburg, HELIOS Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125 Berlin, Germany
| | - Per-Ulf Tunn
- Department of Orthopedic Oncology, Sarcoma Center Berlin-Brandenburg, HELIOS Klinikum Berlin-Buch, Schwanebecker Chaussee 50, 13125 Berlin, Germany
| | - Hans Roland Dürr
- Department of Orthopedic Surgery, Ludwig-Maximilians-University Munich, Campus Grosshadern, Marchionistrasse 15, 81377 Munich, Germany
| | - Hans Rechl
- Clinic and Policlinic of Orthopedics and Sports Orthopedics, Technische Universität München, Ismaninger Strasse 22, 81675 Munich, Germany
| | - Klaus-Dieter Schaser
- Department of Orthopaedics and Trauma Surgery, University Hospital Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Ingo Melcher
- Center for Musculoskeletal Surgery, Charité—University Medicine Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Burdach
- Pediatric Oncology Center, Department of Pediatrics, Technische Universität München and Comprehensive Cancer Center, Kölner Platz 1, 80804 Munich, Germany
| | - Andreas Kulozik
- Department of Pediatric Hematology, Oncology, Immunology and Pulmology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Katja Specht
- Institute of Pathology, Technische Universität München, Trogerstrasse 18, 81675 Munich, Germany
| | - Karl Heinimann
- Medical Genetics, University Hospital Basel, Burgfelderstrasse 101, 4055 Basel, Switzerland
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Komturstrasse 3a, 60528 Frankfurt, Germany
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan Bielack
- Pediatrics 5 (Oncology, Hematology, Immunology), Klinikum Stuttgart Olgahospital, Kriegsbergstrasse 62, 70174 Stuttgart, Germany
| | - Gernot Jundt
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4031 Basel, Switzerland
| | - Ian Tomlinson
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jan O. Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michaela Nathrath
- Institute of Radiation Biology, Clinical Cooperation Group Osteosarcoma, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Pediatric Oncology Center, Department of Pediatrics, Technische Universität München and Comprehensive Cancer Center, Kölner Platz 1, 80804 Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Mönchebergstrasse 41-43, 34125 Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4031 Basel, Switzerland
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40
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Chen JWC, Barker AR, Wakefield JG. The Ran Pathway in Drosophila melanogaster Mitosis. Front Cell Dev Biol 2015; 3:74. [PMID: 26636083 PMCID: PMC4659922 DOI: 10.3389/fcell.2015.00074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/09/2015] [Indexed: 11/29/2022] Open
Abstract
Over the last two decades, the small GTPase Ran has emerged as a central regulator of both mitosis and meiosis, particularly in the generation, maintenance, and regulation of the microtubule (MT)-based bipolar spindle. Ran-regulated pathways in mitosis bear many similarities to the well-characterized functions of Ran in nuclear transport and, as with transport, the majority of these mitotic effects are mediated through affecting the physical interaction between karyopherins and Spindle Assembly Factors (SAFs)—a loose term describing proteins or protein complexes involved in spindle assembly through promoting nucleation, stabilization, and/or depolymerization of MTs, through anchoring MTs to specific structures such as centrosomes, chromatin or kinetochores, or through sliding MTs along each other to generate the force required to achieve bipolarity. As such, the Ran-mediated pathway represents a crucial functional module within the wider spindle assembly landscape. Research into mitosis using the model organism Drosophila melanogaster has contributed substantially to our understanding of centrosome and spindle function. However, in comparison to mammalian systems, very little is known about the contribution of Ran-mediated pathways in Drosophila mitosis. This article sets out to summarize our understanding of the roles of the Ran pathway components in Drosophila mitosis, focusing on the syncytial blastoderm embryo, arguing that it can provide important insights into the conserved functions on Ran during spindle formation.
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Affiliation(s)
- Jack W C Chen
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - Amy R Barker
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK ; Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London London, UK
| | - James G Wakefield
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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41
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Xu Z, Wang F, Fan F, Gu Y, Shan N, Meng X, Cheng S, Liu Y, Wang C, Song Y, Xu R. Quantitative Proteomics Reveals That the Inhibition of Na+/K+-ATPase Activity Affects S-Phase Progression Leading to a Chromosome Segregation Disorder by Attenuating the Aurora A Function in Hepatocellular Carcinoma Cells. J Proteome Res 2015; 14:4594-602. [PMID: 26491887 DOI: 10.1021/acs.jproteome.5b00724] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhongwei Xu
- Central
Laboratory, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Fengmei Wang
- Department
of Gastroenterology and Hepatology, The Third Central Hospital of Tianjin, Tianjin 300170, China
| | - Fengxu Fan
- Central
Laboratory, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Yanjun Gu
- Affiliated Hospital of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Nana Shan
- Central
Laboratory, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Xiangyan Meng
- Department
of Physiology and Pathophysiology, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Shixiang Cheng
- Affiliated Hospital of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Yingfu Liu
- Central
Laboratory, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Chengyan Wang
- Central
Laboratory, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Yueying Song
- Central
Laboratory, Logistics University of Chinese People’s Armed Police Force, Tianjin 300162, China
| | - Ruicheng Xu
- Tianjin Key Laboratory for Biomarkers of Occupational and Environmental Hazard, No. 1 Huizhi Huan Road, DongLi District, Tianjin 300309, China
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42
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Abstract
Regulation of chromatin structure is an essential component of the DNA damage response (DDR), which effectively preserves the integrity of DNA by a network of multiple DNA repair and associated signaling pathways. Within the DDR, chromatin is modified and remodeled to facilitate efficient DNA access, to control the activity of repair proteins and to mediate signaling. The mammalian ISWI family has recently emerged as one of the major ATP-dependent chromatin remodeling complex families that function in the DDR, as it is implicated in at least 3 major DNA repair pathways: homologous recombination, non-homologous end-joining and nucleotide excision repair. In this review, we discuss the various manners through which different ISWI complexes regulate DNA repair and how they are targeted to chromatin containing damaged DNA.
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Key Words
- ACF1
- ACF1, ATP-utilizing Chromatin assembly and remodeling Factor 1
- ATP-dependent chromatin remodeling
- BER, Base Excision Repair
- DDR, DNA Damage Response
- DNA damage response
- DSB, Double Strand Break
- GG-NER, Global Genome Nucleotide Excision Repair
- HR, Homologous Recombination
- Homologous Recombination
- ISWI
- ISWI, Imitation SWItch
- MRN, MRE11/Rad50/NBS1
- NER, Nucleotide Excision Repair
- NHEJ, Non-Homologous End Joining
- Non-Homologous End-Joining
- Nucleotide Excision Repair
- PAR, Poly(ADP-Ribose)
- RNApolII, RNA Polymerase II
- RSF1, Remodeling and Spacing Factor 1
- SMARCA, SWI-SNF-related Matrix-associated Actin-dependent Regulator of Chromatin A
- SMARCA5/SNF2H
- TC-NER, Transcription-Coupled Nucleotide Excision Repair
- WSTF
- WSTF, Williams Syndrome Transcription Factor
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Affiliation(s)
- Özge Z Aydin
- a Department of Genetics ; Cancer Genomics Netherlands; Erasmus MC ; Rotterdam , The Netherlands
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43
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Chromatin Remodelers: From Function to Dysfunction. Genes (Basel) 2015; 6:299-324. [PMID: 26075616 PMCID: PMC4488666 DOI: 10.3390/genes6020299] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 12/20/2022] Open
Abstract
Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.
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44
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Saito Y, Zhou H, Kobayashi J. Chromatin modification and NBS1: their relationship in DNA double-strand break repair. Genes Genet Syst 2015; 90:195-208. [DOI: 10.1266/ggs.15-00010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yuichiro Saito
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University
| | - Hui Zhou
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University
| | - Junya Kobayashi
- Department of Genome Repair Dynamics, Radiation Biology Center, Kyoto University
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45
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Cui Y, Irudayaraj J. Inside single cells: quantitative analysis with advanced optics and nanomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:387-407. [PMID: 25430077 DOI: 10.1002/wnan.1321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
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46
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Identification and characterization of novel NuMA isoforms. Biochem Biophys Res Commun 2014; 454:387-92. [DOI: 10.1016/j.bbrc.2014.10.104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 01/22/2023]
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