1
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Pierzynska-Mach A, Czada C, Vogel C, Gwosch E, Osswald X, Bartoschek D, Diaspro A, Kappes F, Ferrando-May E. DEK oncoprotein participates in heterochromatin replication via SUMO-dependent nuclear bodies. J Cell Sci 2023; 136:jcs261329. [PMID: 37997922 PMCID: PMC10753498 DOI: 10.1242/jcs.261329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The correct inheritance of chromatin structure is key for maintaining genome function and cell identity and preventing cellular transformation. DEK, a conserved non-histone chromatin protein, has recognized tumor-promoting properties, its overexpression being associated with poor prognosis in various cancer types. At the cellular level, DEK displays pleiotropic functions, influencing differentiation, apoptosis and stemness, but a characteristic oncogenic mechanism has remained elusive. Here, we report the identification of DEK bodies, focal assemblies of DEK that regularly occur at specific, yet unidentified, sites of heterochromatin replication exclusively in late S-phase. In these bodies, DEK localizes in direct proximity to active replisomes in agreement with a function in the early maturation of heterochromatin. A high-throughput siRNA screen, supported by mutational and biochemical analyses, identifies SUMO as one regulator of DEK body formation, linking DEK to the complex SUMO protein network that controls chromatin states and cell fate. This work combines and refines our previous data on DEK as a factor essential for heterochromatin integrity and facilitating replication under stress, and delineates an avenue of further study for unraveling the contribution of DEK to cancer development.
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Affiliation(s)
| | - Christina Czada
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Christopher Vogel
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Eva Gwosch
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Xenia Osswald
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Denis Bartoschek
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
| | - Alberto Diaspro
- Nanoscopy & NIC@IIT, Istituto Italiano di Tecnologia, Genoa 16152, Italy
- DIFILAB, Department of Physics, University of Genoa, Genoa 16146, Italy
| | - Ferdinand Kappes
- Duke Kunshan University, Division of Natural and Applied Sciences, Kunshan 215316, People's Republic of China
| | - Elisa Ferrando-May
- Department of Biology, Bioimaging Center, University of Konstanz, Konstanz 78464, Germany
- German Cancer Research Center, Heidelberg 69120, Germany
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2
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Wilcher KE, Page ERH, Privette Vinnedge LM. The impact of the chromatin binding DEK protein in hematopoiesis and acute myeloid leukemia. Exp Hematol 2023; 123:18-27. [PMID: 37172756 PMCID: PMC10330528 DOI: 10.1016/j.exphem.2023.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Hematopoiesis is an exquisitely regulated process of cellular differentiation to create diverse cell types of the blood. Genetic mutations, or aberrant regulation of gene transcription, can interrupt normal hematopoiesis. This can have dire pathological consequences, including acute myeloid leukemia (AML), in which generation of the myeloid lineage of differentiated cells is interrupted. In this literature review, we discuss how the chromatin remodeling DEK protein can control hematopoietic stem cell quiescence, hematopoietic progenitor cell proliferation, and myelopoiesis. We further discuss the oncogenic consequences of the t(6;9) chromosomal translocation, which creates the DEK-NUP214 (aka: DEK-CAN) fusion gene, during the pathogenesis of AML. Combined, the literature indicates that DEK is crucial for maintaining homeostasis of hematopoietic stem and progenitor cells, including myeloid progenitors.
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Affiliation(s)
- Katherine E Wilcher
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Current: Wright State University Boonshoft School of Medicine, Fairborn, OH
| | - Evan R H Page
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Lisa M Privette Vinnedge
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.
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3
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Guo H, Prell M, Königs H, Xu N, Waldmann T, Hermans-Sachweh B, Ferrando-May E, Lüscher B, Kappes F. Bacterial Growth Inhibition Screen (BGIS) identifies a loss-of-function mutant of the DEK oncogene, indicating DNA modulating activities of DEK in chromatin. FEBS Lett 2021; 595:1438-1453. [PMID: 33686684 DOI: 10.1002/1873-3468.14070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
The DEK oncoprotein regulates cellular chromatin function via a number of protein-protein interactions. However, the biological relevance of its unique pseudo-SAP/SAP-box domain, which transmits DNA modulating activities in vitro, remains largely speculative. As hypothesis-driven mutations failed to yield DNA-binding null (DBN) mutants, we combined random mutagenesis with the Bacterial Growth Inhibition Screen (BGIS) to overcome this bottleneck. Re-expression of a DEK-DBN mutant in newly established human DEK knockout cells failed to reduce the increase in nuclear size as compared to wild type, indicating roles for DEK-DNA interactions in cellular chromatin organization. Our results extend the functional roles of DEK in metazoan chromatin and highlight the predictive ability of recombinant protein toxicity in E. coli for unbiased studies of eukaryotic DNA modulating protein domains.
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Affiliation(s)
- Haihong Guo
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Malte Prell
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Hiltrud Königs
- Institute of Pathology, Medical School, RWTH Aachen University, Germany
| | - Nengwei Xu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Dushu Lake Higher Education Town, Suzhou Industrial Park, China
| | - Tanja Waldmann
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Germany
| | | | - Elisa Ferrando-May
- Bioimaging Center, Department of Biology, University of Konstanz, Germany
| | - Bernhard Lüscher
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
| | - Ferdinand Kappes
- Institute for Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Germany
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Dushu Lake Higher Education Town, Suzhou Industrial Park, China
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4
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Smith EA, Krumpelbeck EF, Jegga AG, Greis KD, Ali AM, Meetei AR, Wells SI. The nuclear DEK interactome supports multi-functionality. Proteins 2018; 86:88-97. [PMID: 29082557 PMCID: PMC5730476 DOI: 10.1002/prot.25411] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/20/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023]
Abstract
DEK is an oncoprotein that is overexpressed in many forms of cancer and participates in numerous cellular pathways. Of these different pathways, relevant interacting partners and functions of DEK are well described in regard to the regulation of chromatin structure, epigenetic marks, and transcription. Most of this understanding was derived by investigating DNA-binding and chromatin processing capabilities of the oncoprotein. To facilitate the generation of mechanism-driven hypotheses regarding DEK activities in underexplored areas, we have developed the first DEK interactome model using tandem-affinity purification and mass spectrometry. With this approach, we identify IMPDH2, DDX21, and RPL7a as novel DEK binding partners, hinting at new roles for the oncogene in de novo nucleotide biosynthesis and ribosome formation. Additionally, a hydroxyurea-specific interaction with replication protein A (RPA) was observed, suggesting that a DEK-RPA complex may form in response to DNA replication fork stalling. Taken together, these findings highlight diverse activities for DEK across cellular pathways and support a model wherein this molecule performs a plethora of functions.
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Affiliation(s)
- Eric A. Smith
- Department of Oncology; Cincinnati Children’s Hospital Medical Center; Cincinnati, OH, 45219; USA
| | - Eric F. Krumpelbeck
- Department of Oncology; Cincinnati Children’s Hospital Medical Center; Cincinnati, OH, 45219; USA
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45219, USA
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine; Cincinnati, OH 45219, USA
| | - Abdullah M. Ali
- Department of Oncology; Cincinnati Children’s Hospital Medical Center; Cincinnati, OH, 45219; USA
| | - Amom R. Meetei
- Department of Oncology; Cincinnati Children’s Hospital Medical Center; Cincinnati, OH, 45219; USA
| | - Susanne I. Wells
- Department of Oncology; Cincinnati Children’s Hospital Medical Center; Cincinnati, OH, 45219; USA
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5
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Neuroanatomical Distribution of DEK Protein in Corticolimbic Circuits Associated with Learning and Memory in Adult Male and Female Mice. Neuroscience 2017; 371:254-267. [PMID: 29175155 DOI: 10.1016/j.neuroscience.2017.11.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 02/08/2023]
Abstract
DEK, a chromatin-remodeling gene expressed in most human tissues, is known for its role in cancer biology and autoimmune diseases. DEK depletion in vitro reduces cellular proliferation, induces DNA damage subsequently leading to apoptosis, and down-regulates canonical Wnt/β-catenin signaling, a molecular pathway essential for learning and memory. Despite a recognized role in cancer (non-neuronal) cells, DEK expression and function is not well characterized in the central nervous system. We conducted a gene ontology analysis (ToppGene), using a cancer database to identify genes associated with DEK deficiency, which pinpointed several genes associated with cognitive-related diseases (i.e., Alzheimer's disease, presenile dementia). Based on this information, we examined DEK expression in corticolimbic structures associated with learning and memory in adult male and female mice using immunohistochemistry. DEK was expressed throughout the brain in both sexes, including the medial prefrontal cortex (prelimbic, infralimbic and dorsal peduncular). DEK was also abundant in all amygdalar subdivisions (basolateral, central and medial) and in the hippocampus including the CA1, CA2, CA3, dentate gyrus (DG), ventral subiculum and entorhinal cortex. Of note, compared to males, females had significantly higher DEK immunoreactivity in the CA1, indicating a sex difference in this region. DEK was co-expressed with neuronal and microglial markers in the CA1 and DG, whereas only a small percentage of DEK cells were in apposition to astrocytes in these areas. Given the reported inverse cellular and molecular profiles (e.g., cell survival, Wnt pathway) between cancer and Alzheimer's disease, these findings suggest a potentially important role of DEK in cognition.
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6
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Nakashima T, Tomita H, Hirata A, Ishida K, Hisamatsu K, Hatano Y, Kanayama T, Niwa A, Noguchi K, Kato K, Miyazaki T, Tanaka T, Shibata T, Hara A. Promotion of cell proliferation by the proto-oncogene DEK enhances oral squamous cell carcinogenesis through field cancerization. Cancer Med 2017; 6:2424-2439. [PMID: 28834425 PMCID: PMC5633549 DOI: 10.1002/cam4.1157] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 12/11/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) develops through a multistep carcinogenic process involving field cancerization. The DEK gene is a proto-oncogene with functions in genetic and epigenetic modifications, and has oncogenic functions, including cellular proliferation, differentiation, and senescence. DEK overexpression is associated with malignancies; however, the functional roles of DEK overexpression are unclear. We demonstrated that DEK-expressing cells were significantly increased in human dysplasia/carcinoma in situ and OSCC. Furthermore, we generated ubiquitous and squamous cell-specific doxycycline (DOX)-inducible Dek mice (iDek and iDek-e mice respectively). Both DOX+ iDek and iDek-e mice did not show differences in the oral mucosa compared with DOX- mice. In the environment exposed to carcinogen, DOX-treated (DOX+) iDek mice showed field cancerization and OSCC development. Microarray analysis revealed that DEK overexpression was mediated by the upregulation of DNA replication- and cell cycle-related genes, particularly those related to the G1 /S transition. Tongue tumors overexpressing DEK showed increased proliferating cell nuclear antigen and elongator complex protein 3 expression. Our data suggest that DEK overexpression enhanced carcinogenesis, including field cancerization, in OSCC by stimulating the G1 /S phase transition and promoting DNA replication, providing important insights into the potential applications of DEK as a target in the treatment and prevention of OSCC.
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Affiliation(s)
- Takayuki Nakashima
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
- Department of Oral Maxillofacial SurgeryGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Hiroyuki Tomita
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Akihiro Hirata
- Division of Animal ExperimentLife Science Research CenterGifu University1‐1 YanagidoGifu501‐1194Japan
| | - Kazuhisa Ishida
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
- Department of Oral Maxillofacial SurgeryGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Kenji Hisamatsu
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Yuichiro Hatano
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Tomohiro Kanayama
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Ayumi Niwa
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Kei Noguchi
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Keizo Kato
- Department of Oral Maxillofacial SurgeryGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Tatsuhiko Miyazaki
- Division of PathologyGifu University Hospital1‐1 YanagidoGifu501‐1194Japan
| | - Takuji Tanaka
- Department of Diagnostic Pathology (DDP) and Research Center of Diagnostic Pathology (RC‐DiP)Gifu Municipal Hospital7‐1 Kashima‐choGifu500‐8513Japan
| | - Toshiyuki Shibata
- Department of Oral Maxillofacial SurgeryGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
| | - Akira Hara
- Department of Tumor PathologyGifu University Graduate School of Medicine1‐1 YanagidoGifu501‐1194Japan
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7
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Liu Y, Hawkins OE, Vilgelm AE, Pawlikowski JS, Ecsedy JA, Sosman JA, Kelley MC, Richmond A. Combining an Aurora Kinase Inhibitor and a Death Receptor Ligand/Agonist Antibody Triggers Apoptosis in Melanoma Cells and Prevents Tumor Growth in Preclinical Mouse Models. Clin Cancer Res 2015; 21:5338-48. [PMID: 26152738 DOI: 10.1158/1078-0432.ccr-15-0293] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/30/2015] [Indexed: 01/07/2023]
Abstract
PURPOSE Preclinical studies show that inhibition of aurora kinases in melanoma tumors induces senescence and reduces tumor growth, but does not cause tumor regression. Additional preclinical models are needed to identify agents that will synergize with aurora kinase inhibitors to induce tumor regression. EXPERIMENTAL DESIGN We combined treatment with an aurora kinase A inhibitor, MLN8237, with agents that activate death receptors (Apo2L/TRAIL or death receptor 5 agonists) and monitored the ability of this treatment to induce tumor apoptosis and melanoma tumor regression using human cell lines and patient-derived xenograft (PDX) mouse models. RESULTS We found that this combined treatment led to apoptosis and markedly reduced cell viability. Mechanistic analysis showed that the induction of tumor cell senescence in response to the AURKA inhibitor resulted in a decreased display of Apo2L/TRAIL decoy receptors and increased display of one Apo2L/TRAIL receptor (death receptor 5), resulting in enhanced response to death receptor ligand/agonists. When death receptors were activated in senescent tumor cells, both intrinsic and extrinsic apoptotic pathways were induced independent of BRAF, NRAS, or p53 mutation status. Senescent tumor cells exhibited BID-mediated mitochondrial depolarization in response to Apo2L/TRAIL treatment. In addition, senescent tumor cells had a lower apoptotic threshold due to decreased XIAP and survivin expression. Melanoma tumor xenografts of one human cell line and one PDX displayed total blockage of tumor growth when treated with MLN8237 combined with DR5 agonist antibody. CONCLUSIONS These findings provide a strong rationale for combining senescence-inducing therapeutics with death receptor agonists for improved cancer treatment.
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Affiliation(s)
- Yan Liu
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee. Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Oriana E Hawkins
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anna E Vilgelm
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey S Pawlikowski
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeffrey A Ecsedy
- Translational Medicine, Takeda Pharmaceuticals International C, Cambridge, Massachusetts
| | - Jeffrey A Sosman
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mark C Kelley
- Division of Surgical Oncology, Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ann Richmond
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee.
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8
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Logan GE, Mor-Vaknin N, Braunschweig T, Jost E, Schmidt PV, Markovitz DM, Mills KI, Kappes F, Percy MJ. DEK oncogene expression during normal hematopoiesis and in Acute Myeloid Leukemia (AML). Blood Cells Mol Dis 2015; 54:123-31. [PMID: 25128083 DOI: 10.1016/j.bcmd.2014.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/24/2022]
Abstract
DEK is important in regulating cellular processes including proliferation, differentiation and maintenance of stem cell phenotype. The translocation t(6;9) in Acute Myeloid Leukemia (AML), which fuses DEK with NUP214, confers a poor prognosis and a higher risk of relapse. The over-expression of DEK in AML has been reported, but different studies have shown diminished levels in pediatric and promyelocytic leukemias. This study has characterized DEK expression, in silico, using a large multi-center cohort of leukemic and normal control cases. Overall, DEK was under-expressed in AML compared to normal bone marrow (NBM). Studying specific subtypes of AML confirmed either no significant change or a significant reduction in DEK expression compared to NBM. Importantly, the similarity of DEK expression between AML and NBM was confirmed using immunohistochemistry analysis of tissue mircorarrays. In addition, stratification of AML patients based on median DEK expression levels indicated that DEK showed no effect on the overall survival of patients. DEK expression during normal hematopoiesis did reveal a relationship with specific cell types implicating a distinct function during myeloid differentiation. Whilst DEK may play a potential role in hematopoiesis, it remains to be established whether it is important for leukemagenesis, except when involved in the t(6;9) translocation.
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MESH Headings
- Animals
- Chromosomal Proteins, Non-Histone/biosynthesis
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 9/genetics
- Cohort Studies
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- Databases, Genetic
- Disease-Free Survival
- Gene Expression Regulation, Leukemic
- Hematopoiesis
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Multicenter Studies as Topic
- Oncogene Proteins/biosynthesis
- Oncogene Proteins/genetics
- Poly-ADP-Ribose Binding Proteins
- Survival Rate
- Translocation, Genetic
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Affiliation(s)
- Gemma E Logan
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom.
| | - Nirit Mor-Vaknin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA.
| | - Till Braunschweig
- Institute of Pathology, Medical School, RWTH Aachen University, Aachen, Germany.
| | - Edgar Jost
- Clinic for Oncology, Hematology and Stem Cell Transplantation, Medical School, RWTH Aachen University, Aachen, Germany.
| | - Pia Verena Schmidt
- Clinic for Oncology, Hematology and Stem Cell Transplantation, Medical School, RWTH Aachen University, Aachen, Germany.
| | - David M Markovitz
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA.
| | - Ken I Mills
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom.
| | - Ferdinand Kappes
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.
| | - Melanie J Percy
- Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, Belfast, United Kingdom; Haematology Department, Belfast City Hospital, Belfast Health and Social Care Trust, Belfast, United Kingdom.
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9
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Waidmann S, Kusenda B, Mayerhofer J, Mechtler K, Jonak C. A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis. THE PLANT CELL 2014; 26:4328-44. [PMID: 25387881 PMCID: PMC4277211 DOI: 10.1105/tpc.114.129254] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/01/2014] [Accepted: 10/22/2014] [Indexed: 05/19/2023]
Abstract
Chromatin is a major determinant in the regulation of virtually all DNA-dependent processes. Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. The evolutionarily conserved DEK domain-containing protein is implicated in important chromatin-related processes in animals, but little is known about its DNA targets and protein interaction partners. In plants, the role of DEK has remained elusive. In this work, we identified DEK3 as a chromatin-associated protein in Arabidopsis thaliana. DEK3 specifically binds histones H3 and H4. Purification of other proteins associated with nuclear DEK3 also established DNA topoisomerase 1α and proteins of the cohesion complex as in vivo interaction partners. Genome-wide mapping of DEK3 binding sites by chromatin immunoprecipitation followed by deep sequencing revealed enrichment of DEK3 at protein-coding genes throughout the genome. Using DEK3 knockout and overexpressor lines, we show that DEK3 affects nucleosome occupancy and chromatin accessibility and modulates the expression of DEK3 target genes. Furthermore, functional levels of DEK3 are crucial for stress tolerance. Overall, data indicate that DEK3 contributes to modulation of Arabidopsis chromatin structure and function.
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Affiliation(s)
- Sascha Waidmann
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Branislav Kusenda
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Juliane Mayerhofer
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Claudia Jonak
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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10
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Waldmann T, Schneider R. Targeting histone modifications—epigenetics in cancer. Curr Opin Cell Biol 2013; 25:184-9. [DOI: 10.1016/j.ceb.2013.01.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/22/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
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11
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Privette Vinnedge LM, Kappes F, Nassar N, Wells SI. Stacking the DEK: from chromatin topology to cancer stem cells. Cell Cycle 2013; 12:51-66. [PMID: 23255114 PMCID: PMC3570517 DOI: 10.4161/cc.23121] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Stem cells are essential for development and tissue maintenance and display molecular markers and functions distinct from those of differentiated cell types in a given tissue. Malignant cells that exhibit stem cell-like activities have been detected in many types of cancers and have been implicated in cancer recurrence and drug resistance. Normal stem cells and cancer stem cells have striking commonalities, including shared cell surface markers and signal transduction pathways responsible for regulating quiescence vs. proliferation, self-renewal, pluripotency and differentiation. As the search continues for markers that distinguish between stem cells, progenitor cells and cancer stem cells, growing evidence suggests that a unique chromatin-associated protein called DEK may confer stem cell-like qualities. Here, we briefly describe current knowledge regarding stem and progenitor cells. We then focus on new findings that implicate DEK as a regulator of stem and progenitor cell qualities, potentially through its unusual functions in the regulation of local or global chromatin organization.
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Affiliation(s)
- Lisa M Privette Vinnedge
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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12
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Kavanaugh GM, Wise-Draper TM, Morreale RJ, Morrison MA, Gole B, Schwemberger S, Tichy ED, Lu L, Babcock GF, Wells JM, Drissi R, Bissler JJ, Stambrook PJ, Andreassen PR, Wiesmüller L, Wells SI. The human DEK oncogene regulates DNA damage response signaling and repair. Nucleic Acids Res 2011; 39:7465-76. [PMID: 21653549 PMCID: PMC3177200 DOI: 10.1093/nar/gkr454] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 05/16/2011] [Indexed: 12/04/2022] Open
Abstract
The human DEK gene is frequently overexpressed and sometimes amplified in human cancer. Consistent with oncogenic functions, Dek knockout mice are partially resistant to chemically induced papilloma formation. Additionally, DEK knockdown in vitro sensitizes cancer cells to DNA damaging agents and induces cell death via p53-dependent and -independent mechanisms. Here we report that DEK is important for DNA double-strand break repair. DEK depletion in human cancer cell lines and xenografts was sufficient to induce a DNA damage response as assessed by detection of γH2AX and FANCD2. Phosphorylation of H2AX was accompanied by contrasting activation and suppression, respectively, of the ATM and DNA-PK pathways. Similar DNA damage responses were observed in primary Dek knockout mouse embryonic fibroblasts (MEFs), along with increased levels of DNA damage and exaggerated induction of senescence in response to genotoxic stress. Importantly, Dek knockout MEFs exhibited distinct defects in non-homologous end joining (NHEJ) when compared to their wild-type counterparts. Taken together, the data demonstrate new molecular links between DEK and DNA damage response signaling pathways, and suggest that DEK contributes to DNA repair.
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Affiliation(s)
- Gina M. Kavanaugh
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Trisha M. Wise-Draper
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Richard J. Morreale
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Monique A. Morrison
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Boris Gole
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sandy Schwemberger
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Elisia D. Tichy
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lu Lu
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - George F. Babcock
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - James M. Wells
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Rachid Drissi
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John J. Bissler
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Peter J. Stambrook
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Paul R. Andreassen
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lisa Wiesmüller
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Susanne I. Wells
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Gynecological Oncology, Department of Gynecology and Obstetrics, Ulm University, D-89075 Ulm, Germany, Research, Shriners Hospitals for Children, Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Division of Molecular and Developmental Biology, Cincinnati Children's Hospital Medical Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Magharious M, D'Onofrio PM, Hollander A, Zhu P, Chen J, Koeberle PD. Quantitative iTRAQ analysis of retinal ganglion cell degeneration after optic nerve crush. J Proteome Res 2011; 10:3344-62. [PMID: 21627321 DOI: 10.1021/pr2004055] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Retinal ganglion cells (RGCs) are central nervous system (CNS) neurons that transmit visual information from the retina to the brain. Apoptotic RGC degeneration causes visual impairment that can be modeled by optic nerve crush. Neuronal apoptosis is also a salient feature of CNS trauma, ischemia (stroke), and diseases of the CNS such as Alzheimer's, Parkinson's, multiple sclerosis, and amyotrophic lateral sclerosis. Optic nerve crush induces the apoptotic cell death of ∼ 70% of RGCs within the first 14 days after injury. This model is particularly attractive for studying adult neuron apoptosis because the time-course of RGC death is well established and axon regeneration within the myelinated optic nerve can be concurrently evaluated. Here, we performed a large scale iTRAQ proteomic study to identify and quantify proteins of the rat retina at 1, 3, 4, 7, 14, and 21 days after optic nerve crush. In total, 337 proteins were identified, and 110 were differentially regulated after injury. Of these, 58 proteins were upregulated (>1.3 ×), 46 were downregulated (<0.7 ×), and 6 showed both positive and negative regulation over 21 days, relative to normal retinas. Among the differentially expressed proteins, Thymosin-β4 showed an early upregulation at 3 days, the time-point that immediately precedes the induction of RGC apoptosis after injury. We examined the effect of exogenous Thymosin-β4 administration on RGC death after optic nerve injury. Intraocular injections of Thymosin-β4 significantly increased RGC survival by ∼ 3-fold compared to controls and enhanced axon regeneration after crush, demonstrating therapeutic potential for CNS insults. Overall, our study identified numerous proteins that are differentially regulated at key time-points after optic nerve crush, and how the temporal profiles of their expression parallel RGC death. This data will aid in the future development of novel therapeutics to promote neuronal survival and regeneration in the adult CNS.
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Affiliation(s)
- Mark Magharious
- Graduate Department of Rehabilitation Science, University of Toronto, Canada
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14
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Mor-Vaknin N, Kappes F, Dick AE, Legendre M, Damoc C, Teitz-Tennenbaum S, Kwok R, Ferrando-May E, Adams BS, Markovitz DM. DEK in the synovium of patients with juvenile idiopathic arthritis: characterization of DEK antibodies and posttranslational modification of the DEK autoantigen. ARTHRITIS AND RHEUMATISM 2011; 63:556-67. [PMID: 21280010 PMCID: PMC3117121 DOI: 10.1002/art.30138] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVE DEK is a nuclear phosphoprotein and autoantigen in a subset of children with juvenile idiopathic arthritis (JIA). Autoantibodies to DEK are also found in a broad spectrum of disorders associated with abnormal immune activation. We previously demonstrated that DEK is secreted by macrophages, is released by apoptotic T cells, and attracts leukocytes. Since DEK has been identified in the synovial fluid (SF) of patients with JIA, this study was undertaken to investigate how DEK protein and/or autoantibodies may contribute to the pathogenesis of JIA. METHODS DEK autoantibodies, immune complexes (ICs), and synovial macrophages were purified from the SF of patients with JIA. DEK autoantibodies and ICs were purified by affinity-column chromatography and analyzed by 2-dimensional gel electrophoresis, immunoblotting, and enzyme-linked immunosorbent assay. DEK in supernatants and exosomes was purified by serial centrifugation and immunoprecipitation with magnetic beads, and posttranslational modifications of DEK were identified by nano-liquid chromatography tandem mass spectrometry (nano-LC-MS/MS). RESULTS DEK autoantibodies and protein were found in the SF of patients with JIA. Secretion of DEK by synovial macrophages was observed both in a free form and via exosomes. DEK autoantibodies (IgG2) may activate the complement cascade, primarily recognize the C-terminal portion of DEK protein, and exhibit higher affinity for acetylated DEK. Consistent with these observations, DEK underwent acetylation on an unprecedented number of lysine residues, as demonstrated by nano-LC-MS/MS. CONCLUSION These results indicate that DEK can contribute directly to joint inflammation in JIA by generating ICs through high-affinity interaction between DEK and DEK autoantibodies, a process enhanced by acetylation of DEK in the inflamed joint.
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15
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Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A, Thiede B. IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT. J Proteome Res 2010; 10:913-20. [PMID: 21067241 DOI: 10.1021/pr1009977] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.
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Affiliation(s)
- Magnus Ø Arntzen
- The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
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16
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Fahrer J, Popp O, Malanga M, Beneke S, Markovitz DM, Ferrando-May E, Bürkle A, Kappes F. High-affinity interaction of poly(ADP-ribose) and the human DEK oncoprotein depends upon chain length. Biochemistry 2010; 49:7119-30. [PMID: 20669926 PMCID: PMC2929705 DOI: 10.1021/bi1004365] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a molecular DNA damage sensor that catalyzes the synthesis of the complex biopolymer poly(ADP-ribose) (PAR) under consumption of NAD(+). PAR engages in fundamental cellular processes such as DNA metabolism and transcription and interacts noncovalently with specific binding proteins involved in DNA repair and regulation of chromatin structure. A factor implicated in DNA repair and chromatin organization is the DEK oncoprotein, an abundant and conserved constituent of metazoan chromatin, and the only member of its protein class. We have recently demonstrated that DEK, under stress conditions, is covalently modified with PAR by PARP-1, leading to a partial release of DEK into the cytoplasm. Additionally, we have also observed a noncovalent interaction between DEK and PAR, which we detail here. Using sequence alignment, we identify three functional PAR-binding sites in the DEK primary sequence and confirm their functionality in PAR binding studies. Furthermore, we show that the noncovalent binding to DEK is dependent on PAR chain length as revealed by an overlay blot technique and a PAR electrophoretic mobility shift assay. Intriguingly, DEK promotes the formation of a defined complex with a 54mer PAR (K(D) = 6 x 10(-8) M), whereas no specific interaction is detected with a short PAR chain (18mer). In stark contrast to covalent poly(ADP-ribosyl)ation of DEK, the noncovalent interaction does not affect the overall ability of DEK to bind to DNA. Instead the noncovalent interaction interferes with subsequent DNA-dependent multimerization activities of DEK, as seen in South-Western, electrophoretic mobility shift, topology, and aggregation assays. In particular, noncovalent attachment of PAR to DEK promotes the formation of DEK-DEK complexes by competing with DNA binding. This was seen by the reduced affinity of PAR-bound DEK for DNA templates in solution. Taken together, our findings deepen the molecular understanding of the DEK-PAR interplay and support the existence of a cellular "PAR code" represented by PAR chain length.
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Affiliation(s)
- Jörg Fahrer
- Institute of Pharmacology and Toxicology, University of Ulm Medical Center, Ulm, Germany
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Oliver Popp
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Maria Malanga
- Department of Structural and Functional Biology, University Federico II of Naples, Naples, Italy
| | - Sascha Beneke
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - David M. Markovitz
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan, USA
- Cellular & Molecular Biology Program, University of Michigan Medical Center, Ann Arbor, Michigan, USA
- Program in Immunology, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Elisa Ferrando-May
- Bioimaging Center, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ferdinand Kappes
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical Center, Ann Arbor, Michigan, USA
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Brunner A, Keidel EM, Dosch D, Kellermann J, Lottspeich F. ICPLQuant - A software for non-isobaric isotopic labeling proteomics. Proteomics 2010; 10:315-26. [PMID: 19953540 DOI: 10.1002/pmic.200900174] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acquired during a proteomics project. A new software suite, ICPLQuant, has been developed to accurately quantify isotope-coded protein label (ICPL)-labeled peptides on the MS level during LC-MALDI and peptide mass fingerprint experiments. The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time-consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining. The accuracy of quantification, selection of peptides for MS/MS-identification and the automated output of a protein list of regulated proteins are demonstrated by the comparative analysis of four different mixtures of three proteins (Ovalbumin, Horseradish Peroxidase and Rabbit Albumin) spiked into the complex protein background of the DGPF Proteome Marker.
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Affiliation(s)
- Achim Brunner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany.
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18
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Hua Y, Hu H, Peng X. Progress in studies on the DEK protein and its involvement in cellular apoptosis. SCIENCE IN CHINA. SERIES C, LIFE SCIENCES 2009; 52:637-42. [PMID: 19641868 DOI: 10.1007/s11427-009-0088-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 03/30/2009] [Indexed: 12/12/2022]
Abstract
DEK protein is an ubiquitous phosphorylated nuclear protein. Specific binding of DEK to DNA could change the topology of DNA and then affect the gene activity of the underlying DNA sequences. It is speculated that there might be some potential relationship between the stress reaction of cells and DEK proteins. The phosphorylation status of DEK protein is altered during death-receptor-mediated cell apoptosis. Both phosphorylation and poly(ADP-ribosyl)ation could promote the release of DEK from apoptotic nuclei to extracellular environment, and in this case DEK becomes a potential autoantigen of some autoimmune diseases. The available evidence powerfully suggests that DEK protein is closely relevant to apoptosis. The overexpression of DEK protein has dual function in cell apoptosis, in terms of inhibiting or triggering cell apoptosis.
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Affiliation(s)
- Ying Hua
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
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19
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Applications of chemical tagging approaches in combination with 2DE and mass spectrometry. Methods Mol Biol 2009; 519:83-101. [PMID: 19381578 DOI: 10.1007/978-1-59745-281-6_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Chemical modification reactions play an important role in various protocols for mass-spectrometry-based proteome analysis; this applies to both gel-based and gel-free proteomics workflows. In combination with two-dimensional gel electrophoresis (2DE), the addition of "tags" by means of chemical reactions serves several purposes. Potential benefits include increased sensitivity or sequence coverage for peptide mass fingerprinting and improved peptide fragmentation for de novo sequencing studies. Tagging strategies can also be used to obtain complementary quantitative information in addition to densitometry, and they may be employed for the study of post-translational modifications. In combination with the unique advantages of 2DE as a separation technique, such approaches provide a powerful toolbox for proteomic research. In this review, relevant examples from recent literature will be given to illustrate the capabilities of chemical tagging approaches, and methodological requirements will be discussed.
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Kappes F, Fahrer J, Khodadoust MS, Tabbert A, Strasser C, Mor-Vaknin N, Moreno-Villanueva M, Bürkle A, Markovitz DM, Ferrando-May E. DEK is a poly(ADP-ribose) acceptor in apoptosis and mediates resistance to genotoxic stress. Mol Cell Biol 2008; 28:3245-57. [PMID: 18332104 PMCID: PMC2423161 DOI: 10.1128/mcb.01921-07] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/08/2008] [Accepted: 03/04/2008] [Indexed: 12/28/2022] Open
Abstract
DEK is a nuclear phosphoprotein implicated in oncogenesis and autoimmunity and a major component of metazoan chromatin. The intracellular cues that control the binding of DEK to DNA and its pleiotropic functions in DNA- and RNA-dependent processes have remained mainly elusive so far. Our recent finding that the phosphorylation status of DEK is altered during death receptor-mediated apoptosis suggested a potential involvement of DEK in stress signaling. In this study, we show that in cells committed to die, a portion of the cellular DEK pool is extensively posttranslationally modified by phosphorylation and poly(ADP-ribosyl)ation. Through interference with DEK expression, we further show that DEK promotes the repair of DNA lesions and protects cells from genotoxic agents that typically trigger poly(ADP-ribose) polymerase activation. The posttranslational modification of DEK during apoptosis is accompanied by the removal of the protein from chromatin and its release into the extracellular space. Released modified DEK is recognized by autoantibodies present in the synovial fluids of patients affected by juvenile rheumatoid arthritis/juvenile idiopathic arthritis. These findings point to a crucial role of poly(ADP-ribosyl)ation in shaping DEK's autoantigenic properties and in its function as a promoter of cell survival.
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Affiliation(s)
- F Kappes
- University of Konstanz, Department of Biology, Box X911, D-78457 Konstanz, Germany
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Lavelle C, Salles B, Wiesmüller L. DNA repair, damage signaling and carcinogenesis. DNA Repair (Amst) 2008; 7:670-80. [PMID: 18221920 DOI: 10.1016/j.dnarep.2007.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2007] [Indexed: 12/14/2022]
Abstract
The First joint meeting of the German DGDR (German Society for Research on DNA Repair) and the French SFTG (French Society of Genotoxicology) on DNA Repair was held in Toulouse, France, from September 15 to 19, 2007. It was organized by Lisa Wiesmüller and Bernard Salles together with the scientific committee consisting of Gilbert de Murcia, Jean-Marc Egly, Frank Grosse, Karl-Peter Hopfner, Georges Iliakis, Bernd Kaina, Markus Löbrich, Bernard Lopez, Daniel Marzin and Alain Sarasin. This report summarizes information presented by the speakers (invited lectures and oral communications) during the seven plenary sessions, which include (1) excision repair, (2) DNA repair and carcinogenesis, (3) double-strand break repair, (4) replication in repair and lesion bypass, (5) cellular responses to genotoxic stress, (6) DNA repair machinery within the chromatin context and (7) genotoxicology and testing. A total of 23 plenary lectures, 32 oral communications and 66 posters were presented in this rather intense 4 days meeting, which stimulated extensive discussions and highly interdisciplinary scientific exchanges among the approximately 250 participants.
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Chapter 17 Mass Spectrometry-Driven Approaches to Quantitative Proteomics and Beyond. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0166-526x(08)00217-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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