1
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Sundaram R, Gandhi S, Jonak C, Vasudevan D. Characterization of the Arabidopsis thaliana chromatin remodeler DEK3 for its interaction with histones and DNA. Biochimie 2024:S0300-9084(24)00177-9. [PMID: 39097158 DOI: 10.1016/j.biochi.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Chromatin structure and dynamics regulate all DNA-templated processes, such as transcription, replication, and repair. Chromatin binding factors, chromatin architectural proteins, and nucleosome remodelers modulate chromatin structure and dynamics and, thereby, the various DNA-dependent processes. Arabidopsis thaliana DEK3, a member of the evolutionarily conserved DEK domain-containing chromatin architectural proteins, is an important factor for chromatin structure and function, involved in transcriptional programming to regulate flowering time and abiotic stress tolerance. AtDEK3 contains an uncharacterized N-terminal domain, a middle SAF domain (winged helix-like domain), and a C-terminal DEK domain, but their role in the interaction of AtDEK3 with histones and DNA remained poorly understood. Using biochemical and biophysical analyses, we provide a comprehensive in vitro characterization of the different AtDEK3 domains for their interaction with histone H3/H4 and DNA. AtDEK3 directly interacts with histone H3/H4 tetramers through its N-terminal domain and the C-terminal DEK domain in a 1:1 stoichiometry. Upon interaction with H3/H4, the unstructured N-terminal domain of AtDEK3 undergoes a conformational change and adopts an alpha-helical conformation. In addition, the in-solution envelope structures of the AtDEK3 domains and their complex with H3/H4 have been characterized. The SAF and DEK domains associate with double-stranded and four-way junction DNA. As DEK3 possesses a histone-interacting domain at the N- and the C-terminus and a DNA-binding domain in the middle and at the C-terminus, the protein might play a complex role as a chromatin remodeler.
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Affiliation(s)
- Rajivgandhi Sundaram
- Institute of Life Sciences, Bhubaneswar, 751023, India; Manipal Academy of Higher Education, Manipal, 576104, India
| | - Surajit Gandhi
- Institute of Life Sciences, Bhubaneswar, 751023, India; Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Claudia Jonak
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Bioresources Unit, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Dileep Vasudevan
- Institute of Life Sciences, Bhubaneswar, 751023, India; Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, India.
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2
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Rodriguez-Rodriguez P, Arroyo-Garcia LE, Tsagkogianni C, Li L, Wang W, Végvári Á, Salas-Allende I, Plautz Z, Cedazo-Minguez A, Sinha SC, Troyanskaya O, Flajolet M, Yao V, Roussarie JP. A cell autonomous regulator of neuronal excitability modulates tau in Alzheimer's disease vulnerable neurons. Brain 2024; 147:2384-2399. [PMID: 38462574 PMCID: PMC11224620 DOI: 10.1093/brain/awae051] [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: 10/17/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 03/12/2024] Open
Abstract
Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer's disease. Gaining insight into the molecular mechanisms underlying this vulnerability will help reveal genes and pathways at play during incipient stages of the disease. Here, we use a data-driven functional genomics approach to model ECII neurons in silico and identify the proto-oncogene DEK as a regulator of tau pathology. We show that epigenetic changes caused by Dek silencing alter activity-induced transcription, with major effects on neuronal excitability. This is accompanied by the gradual accumulation of tau in the somatodendritic compartment of mouse ECII neurons in vivo, reactivity of surrounding microglia, and microglia-mediated neuron loss. These features are all characteristic of early Alzheimer's disease. The existence of a cell-autonomous mechanism linking Alzheimer's disease pathogenic mechanisms in the precise neuron type where the disease starts provides unique evidence that synaptic homeostasis dysregulation is of central importance in the onset of tau pathology in Alzheimer's disease.
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Affiliation(s)
| | | | - Christina Tsagkogianni
- Department of Neurobiology Care Sciences and Society, Karolinska Institutet, 17 164, Solna, Sweden
| | - Lechuan Li
- Department of Computer Science, Rice University, Houston, TX 77004, USA
| | - Wei Wang
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 164, Solna, Sweden
| | - Isabella Salas-Allende
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Zakary Plautz
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Angel Cedazo-Minguez
- Department of Neurobiology Care Sciences and Society, Karolinska Institutet, 17 164, Solna, Sweden
| | - Subhash C Sinha
- Helen and Robert Appel Alzheimer’s Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olga Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065, USA
| | - Vicky Yao
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 164, Solna, Sweden
| | - Jean-Pierre Roussarie
- Department of Anatomy & Neurobiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
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3
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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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4
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Pierzynska-Mach A, Diaspro A, Cella Zanacchi F. Super-resolution microscopy reveals the nanoscale cluster architecture of the DEK protein cancer biomarker. iScience 2023; 26:108277. [PMID: 38026229 PMCID: PMC10660485 DOI: 10.1016/j.isci.2023.108277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 09/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
DEK protein, a key chromatin regulator, is strongly overexpressed in various forms of cancer. While conventional microscopy revealed DEK as uniformly distributed within the cell nucleus, advanced super-resolution techniques uncovered cluster-like structures. However, a comprehensive understanding of DEK's cellular distribution and its implications in cancer and cell growth remained elusive. To bridge this gap, we employed single-molecule localization microscopy (SMLM) to dissect DEK's nanoscale organization in both normal-like and aggressive breast cancer cell lines. Our investigation included characteristics such as localizations per cluster, cluster areas, and intra-cluster localization densities (ICLDs). We elucidated how cluster features align with different breast cell types and how chromatin decompaction influences DEK clusters in these contexts. Our results indicate that DEK's intra-cluster localization density and nano-organization remain preserved and not significantly influenced by protein overexpression or chromatin compaction changes. This study advances the understanding of DEK's role in cancer and underscores its stable nanoscale behavior.
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Affiliation(s)
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, 16152 Genoa, Italy
- Department of Physics (DIFILAB), Department of Physics, University of Genoa, 16146 Genoa, Italy
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, 16152 Genoa, Italy
- Physics Department E. Fermi, University of Pisa, 56127 Pisa, Italy
- Centro per l’Integrazione della Strumentazione dell’Università di Pisa (CISUP), University of Pisa, 56127 Pisa, Italy
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5
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Naef P, Radpour R, Jaeger-Ruckstuhl CA, Bodmer N, Baerlocher GM, Doehner H, Doehner K, Riether C, Ochsenbein AF. IL-33-ST2 signaling promotes stemness in subtypes of myeloid leukemia cells through the Wnt and Notch pathways. Sci Signal 2023; 16:eadd7705. [PMID: 37643244 DOI: 10.1126/scisignal.add7705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/10/2023] [Indexed: 08/31/2023]
Abstract
Cell stemness is characterized by quiescence, pluripotency, and long-term self-renewal capacity. Therapy-resistant leukemic stem cells (LSCs) are the primary cause of relapse in patients with chronic and acute myeloid leukemia (CML and AML). However, the same signaling pathways frequently support stemness in both LSCs and normal hematopoietic stem cells (HSCs), making LSCs difficult to therapeutically target. In cell lines and patient samples, we found that interleukin-33 (IL-33) signaling promoted stemness only in leukemia cells in a subtype-specific manner. The IL-33 receptor ST2 was abundant on the surfaces of CD34+ BCR/ABL1 CML and CD34+ AML cells harboring AML1/ETO and DEK/NUP214 translocations or deletion of chromosome 9q [del(9q)]. The cell surface abundance of ST2, which was lower or absent on other leukemia subtypes and HSCs, correlated with stemness, activated Wnt signaling, and repressed Notch signaling. IL-33-ST2 signaling promoted the maintenance and expansion of AML1/ETO-, DEK/NUP214-, and BCR/ABL1-positive LSCs in culture and in mice by activating Wnt, MAPK, and NF-κB signaling. Wnt signaling and its inhibition of the Notch pathway up-regulated the expression of the gene encoding ST2, thus forming a cell-autonomous loop. IL-33-ST2 signaling promoted the resistance of CML cells to the tyrosine kinase inhibitor (TKI) nilotinib and of AML cells to standard chemotherapy. Thus, inhibiting IL-33-ST2 signaling may target LSCs to overcome resistance to chemotherapy or TKIs in these subtypes of leukemia.
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Affiliation(s)
- Pascal Naef
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Ramin Radpour
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
| | - Carla A Jaeger-Ruckstuhl
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
| | - Nils Bodmer
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
| | - Gabriela M Baerlocher
- Laboratory for Hematopoiesis and Molecular Genetics, Experimental Hematology, Department of BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
| | - Hartmut Doehner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm 89081, Germany
| | - Konstanze Doehner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm 89081, Germany
| | - Carsten Riether
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
| | - Adrian F Ochsenbein
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
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6
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Pierzynska-Mach A, Cainero I, Oneto M, Ferrando-May E, Lanzanò L, Diaspro A. Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model. Sci Rep 2023; 13:12749. [PMID: 37550322 PMCID: PMC10406876 DOI: 10.1038/s41598-023-38685-7] [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: 07/11/2022] [Accepted: 07/12/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic dysregulation of chromatin is one of the hallmarks of cancer development and progression, and it is continuously investigated as a potential general bio-marker of this complex disease. One of the nuclear factors involved in gene regulation is the unique DEK protein-a histone chaperon modulating chromatin topology. DEK expression levels increase significantly from normal to cancer cells, hence raising the possibility of using DEK as a tumor marker. Although DEK is known to be implicated in epigenetic and transcriptional regulation, the details of these interactions and their relevance in cancer development remain largely elusive. In this work, we investigated the spatial correlation between the nuclear distribution of DEK and chromatin patterns-alongside breast cancer progression-leveraging image cross-correlation spectroscopy (ICCS) coupled with Proximity Ligation Assay (PLA) analysis. We performed our study on the model based on three well-established human breast cell lines to consider this tumor's heterogeneity (MCF10A, MCF7, and MDA-MB-231 cells). Our results show that overexpression of DEK correlates with the overall higher level of spatial proximity between DEK and histone marks corresponding to gene promoters regions (H3K9ac, H3K4me3), although it does not correlate with spatial proximity between DEK and gene enhancers (H3K27ac). Additionally, we observed that colocalizing fractions of DEK and histone marks are lower for the non-invasive cell subtype than for the highly invasive cell line (MDA-MB-231). Thus, this study suggests that the role of DEK on transcriptionally active chromatin regions varies depending on the subtype of the breast cancer cell line.
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Affiliation(s)
| | - Isotta Cainero
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Michele Oneto
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
| | - Elisa Ferrando-May
- Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Luca Lanzanò
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy.
- DIFILAB, Department of Physics, University of Genoa, Genoa, Italy.
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7
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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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8
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Greene AN, Solomon MB, Privette Vinnedge LM. Novel molecular mechanisms in Alzheimer's disease: The potential role of DEK in disease pathogenesis. Front Aging Neurosci 2022; 14:1018180. [PMID: 36275000 PMCID: PMC9582447 DOI: 10.3389/fnagi.2022.1018180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease and age-related dementias (AD/ADRD) are debilitating diseases that exact a significant physical, emotional, cognitive, and financial toll on the individual and their social network. While genetic risk factors for early-onset AD have been identified, the molecular and genetic drivers of late-onset AD, the most common subtype, remain a mystery. Current treatment options are limited for the 35 million people in the United States with AD/ADRD. Thus, it is critically important to identify novel molecular mechanisms of dementia-related pathology that may be targets for the development of new interventions. Here, we summarize the overarching concepts regarding AD/ADRD pathogenesis. Then, we highlight one potential molecular driver of AD/ADRD, the chromatin remodeling protein DEK. We discuss in vitro, in vivo, and ex vivo findings, from our group and others, that link DEK loss with the cellular, molecular, and behavioral signatures of AD/ADRD. These include associations between DEK loss and cellular and molecular hallmarks of AD/ADRD, including apoptosis, Tau expression, and Tau hyperphosphorylation. We also briefly discuss work that suggests sex-specific differences in the role of DEK in AD/ADRD pathogenesis. Finally, we discuss future directions for exploiting the DEK protein as a novel player and potential therapeutic target for the treatment of AD/ADRD.
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Affiliation(s)
- Allie N. Greene
- Neuroscience Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Matia B. Solomon
- Neuroscience Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Department of Psychology, University of Cincinnati, Cincinnati, OH, United States
| | - Lisa M. Privette Vinnedge
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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9
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Yang YS, Jia XZ, Lu QY, Cai SL, Huang XT, Yang SH, Wood C, Wang YH, Zhou JJ, Chen YD, Yang JS, Yang WJ. Exosomal DEK removes chemoradiotherapy resistance by triggering quiescence exit of breast cancer stem cells. Oncogene 2022; 41:2624-2637. [PMID: 35351996 DOI: 10.1038/s41388-022-02278-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/11/2022] [Indexed: 02/07/2023]
Abstract
Tumor therapeutics often target the primary tumor bulk but fail to eradicate therapy-resistant cancer stem cells (CSCs) in quiescent state. These can then become activated to initiate recurrence and/or metastasis beyond therapy. Here, we identified and isolated chemoradiotherapy-resistant CSCs in quiescent state with high capacity of tumor-initiation and tumorsphere formation from three types of breast tumors in mice. Experiments of knockdown and rescue revealed DEK, a nuclear protein, as essential for CSC activation. Exogenous DEK was then used to trigger quiescence exit of CSCs. ChIP-seq and ATAC-seq showed that DEK directly binds to chromatin, facilitating its genome-wide accessibility. The resulting epigenetic events upregulate the expression of cellular activation-related genes including MYC targets, whereas cellular quiescence-related genes including the p53 signaling pathway are silenced. However, twinned with DEK-induced activation, formerly resistant CSCs were then destroyed by chemotherapy in vitro. In mice, traditional chemoradiotherapy concurrent with the injection of DEK-containing exosomes resulted in eradication of primary tumors together with formerly resistant CSCs without recurrence or metastasis. Our findings advance knowledge of the mechanism of quiescent CSC activation and may provide novel clinical opportunities for removal of quiescence-linked therapy resistance.
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Affiliation(s)
- Yao-Shun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xi-Zheng Jia
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Yun Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sun-Li Cai
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xue-Ting Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shu-Hua Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chris Wood
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yue-Hong Wang
- Department of Respiratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiao-Jiao Zhou
- Department of Surgical Oncology, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yi-Ding Chen
- Department of Surgical Oncology, The Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jin-Shu Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Jun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Lai CY, Hsieh MC, Yeh CM, Yang PS, Cheng JK, Wang HH, Lin KH, Nie ST, Lin TB, Peng HY. MicroRNA-489-3p attenuates neuropathic allodynia by regulating oncoprotein DEK/TET1-dependent epigenetic modification in the dorsal horn. Neuropharmacology 2022; 210:109028. [PMID: 35304174 DOI: 10.1016/j.neuropharm.2022.109028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/18/2022]
Abstract
Originally characterized as an oncoprotein overexpressed in many forms of cancer that participates in numerous cellular pathways, DEK has since been well described regarding the regulation of epigenetic markers and transcription factors in neurons. However, its role in neuropathic allodynia processes remain elusive and intriguingly complex. Here, we show that DEK, which is induced in spinal dorsal horn neurons after spinal nerve ligation (SNL), is regulated by miR-489-3p. Moreover, SNL-induced decrease in miR-489-3p expression increased the expression of DEK, which recruited TET1 to the promoter fragments of the Bdnf, Grm5, and Stat3 genes, thereby enhancing their transcription in the dorsal horn. Remarkably, these effects were also induced by intrathecally administering naïve animals with miR-489-3p inhibitor, which could be inhibited by knockdown of TET1 siRNA or DEK siRNA. Conversely, delivery of intrathecal miR-489-3p-mimic into SNL rats attenuated allodynia behavior and reversed protein expression coupled to the promoter segments in the dorsal horn. Thus, a spinal miR-489-3p/DEK/TET1 transcriptional axis may contribute to neuropathic allodynia. These results may provide a new target for treating neuropathic allodynia.
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Affiliation(s)
- Cheng-Yuan Lai
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Ming-Chun Hsieh
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Chou-Ming Yeh
- Division of Thoracic Surgery, Department of Health, Taichung Hospital, Executive Yuan, Taichung, Taiwan
| | - Po-Sheng Yang
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan; Department of Surgery, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jen-Kun Cheng
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan; Department of Anesthesiology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Hsueh-Hsiao Wang
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Kuan-Hung Lin
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan; Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Siao-Tong Nie
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Tzer-Bin Lin
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan
| | - Hsien-Yu Peng
- Department of Medicine, Mackay Medical College, New Taipei, Taiwan.
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11
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Zong W, Zhao B, Xi Y, Bordiya Y, Mun H, Cerda NA, Kim DH, Sung S. DEK domain-containing proteins control flowering time in Arabidopsis. THE NEW PHYTOLOGIST 2021; 231:182-192. [PMID: 33774831 PMCID: PMC8985477 DOI: 10.1111/nph.17366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/20/2021] [Indexed: 05/07/2023]
Abstract
Evolutionarily conserved DEK domain-containing proteins have been implicated in multiple chromatin-related processes, mRNA splicing and transcriptional regulation in eukaryotes. Here, we show that two DEK proteins, DEK3 and DEK4, control the floral transition in Arabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors, FLOWERING LOCUS C (FLC), and its two homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, to promote their expression. The binding of DEK3 and DEK4 to a histone octamer in vivo affects histone modifications at FLC, MAF4 and MAF5 loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II with FLC, MAF4 and MAF5 chromatin to promote their expression. Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering in Arabidopsis.
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Affiliation(s)
- Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yanpeng Xi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Hyungwon Mun
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Nicholas A Cerda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Dong-Hwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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12
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Chen Z, Huo D, Li L, Liu Z, Li Z, Xu S, Huang Y, Wu W, Zhou C, Liu Y, Kuang M, Wu F, Li H, Qian P, Song G, Wu X, Chen J, Hou Y. Nuclear DEK preserves hematopoietic stem cells potential via NCoR1/HDAC3-Akt1/2-mTOR axis. J Exp Med 2021; 218:e20201974. [PMID: 33755722 PMCID: PMC7992411 DOI: 10.1084/jem.20201974] [Citation(s) in RCA: 9] [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: 09/11/2020] [Revised: 01/16/2021] [Accepted: 02/18/2021] [Indexed: 12/14/2022] Open
Abstract
The oncogene DEK is found fused with the NUP214 gene creating oncoprotein DEK-NUP214 that induces acute myeloid leukemia (AML) in patients, and secreted DEK protein functions as a hematopoietic cytokine to regulate hematopoiesis; however, the intrinsic role of nuclear DEK in hematopoietic stem cells (HSCs) remains largely unknown. Here, we show that HSCs lacking DEK display defects in long-term self-renew capacity, eventually resulting in impaired hematopoiesis. DEK deficiency reduces quiescence and accelerates mitochondrial metabolism in HSCs, in part, dependent upon activating mTOR signaling. At the molecular level, DEK recruits the corepressor NCoR1 to repress acetylation of histone 3 at lysine 27 (H3K27ac) and restricts the chromatin accessibility of HSCs, governing the expression of quiescence-associated genes (e.g., Akt1/2, Ccnb2, and p21). Inhibition of mTOR activity largely restores the maintenance and potential of Dek-cKO HSCs. These findings highlight the crucial role of nuclear DEK in preserving HSC potential, uncovering a new link between chromatin remodelers and HSC homeostasis, and have clinical implications.
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Affiliation(s)
- Zhe Chen
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Dawei Huo
- Department of Cell Biology, Tianjin Medical University, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin, China
| | - Lei Li
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Zhilong Liu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Zhigang Li
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuangnian Xu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yongxiu Huang
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Weiru Wu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Chengfang Zhou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuanyuan Liu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Mei Kuang
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Feng Wu
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hui Li
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guanbin Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Xudong Wu
- Department of Cell Biology, Tianjin Medical University, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin, China
| | - Jieping Chen
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yu Hou
- Department of Hematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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13
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Maluchenko NV, Koshkina DO, Feofanov AV, Studitsky VM, Kirpichnikov MP. Poly(ADP-Ribosyl) Code Functions. Acta Naturae 2021; 13:58-69. [PMID: 34377556 PMCID: PMC8327145 DOI: 10.32607/actanaturae.11089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/10/2020] [Indexed: 01/14/2023] Open
Abstract
Poly(ADP-ribosyl)ation plays a key role in cellular metabolism. Covalent poly(ADP-ribosyl)ation affects the activity of the proteins engaged in DNA repair, chromatin structure regulation, gene expression, RNA processing, ribosome biogenesis, and protein translation. Non-covalent PAR-dependent interactions are involved in the various types of cellular response to stress and viral infection, such as inflammation, hormonal signaling, and the immune response. The review discusses how structurally different poly(ADP-ribose) (PAR) molecules composed of identical monomers can differentially participate in various cellular processes acting as the so-called "PAR code." The article describes the ability of PAR polymers to form functional biomolecular clusters through a phase-separation in response to various signals. This phase-separation contributes to rapid spatial segregation of biochemical processes and effective recruitment of the necessary components. The cellular PAR level is tightly controlled by a network of regulatory proteins: PAR code writers, readers, and erasers. Impaired PAR metabolism is associated with the development of pathological processes causing oncological, cardiovascular, and neurodegenerative diseases. Pharmacological correction of the PAR level may represent a new approach to the treatment of various diseases.
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Affiliation(s)
- N. V. Maluchenko
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
| | - D. O. Koshkina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
| | - A. V. Feofanov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - V. M. Studitsky
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Fox Chase Cancer Center, Philadelphia, PA, 19111-2497 USA
| | - M. P. Kirpichnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
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14
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Pease NA, Shephard MS, Sertorio M, Waltz SE, Vinnedge LMP. DEK Expression in Breast Cancer Cells Leads to the Alternative Activation of Tumor Associated Macrophages. Cancers (Basel) 2020; 12:cancers12071936. [PMID: 32708944 PMCID: PMC7409092 DOI: 10.3390/cancers12071936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer deaths among women. DEK is a known oncoprotein that is highly expressed in over 60% of breast cancers and is an independent marker of poor prognosis. However, the molecular mechanisms by which DEK promotes tumor progression are poorly understood. To identify novel oncogenic functions of DEK, we performed RNA-Seq analysis on isogenic Dek-knockout and complemented murine BC cells. Gene ontology analyses identified gene sets associated with immune system regulation and cytokine-mediated signaling and differential cytokine and chemokine expression was confirmed across Dek-proficient versus Dek-deficient cells. By exposing murine bone marrow-derived macrophages (BMDM) to tumor cell conditioned media (TCM) to mimic a tumor microenvironment, we showed that Dek-expressing breast cancer cells produce a cytokine milieu, including up-regulated Tslp and Ccl5 and down-regulated Cxcl1, Il-6, and GM-CSF, that drives the M2 polarization of macrophages. We validated this finding in primary murine mammary tumors and show that Dek expression in vivo is also associated with increased expression of M2 macrophage markers in murine tumors. Using TCGA data, we verified that DEK expression in primary human breast cancers correlates with the expression of several genes identified by RNA-Seq in our murine model and with M2 macrophage phenotypes. Together, our data demonstrate that by regulating the production of multiple secreted factors, DEK expression in BC cells creates a potentially immune suppressed tumor microenvironment, particularly by inducing M2 tumor associated macrophage (TAM) polarization.
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Affiliation(s)
- Nicholas A. Pease
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (N.A.P.); (M.S.S.); (M.S.)
- Molecular and Cellular Biology Program, Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Miranda S. Shephard
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (N.A.P.); (M.S.S.); (M.S.)
| | - Mathieu Sertorio
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (N.A.P.); (M.S.S.); (M.S.)
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Susan E. Waltz
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH 45267, USA
| | - Lisa M. Privette Vinnedge
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA; (N.A.P.); (M.S.S.); (M.S.)
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-513-636-1155
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15
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DEK terminates diapause by activation of quiescent cells in the crustacean Artemia. Biochem J 2019; 476:1753-1769. [PMID: 31189566 DOI: 10.1042/bcj20190169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/24/2022]
Abstract
To cope with harsh environments, the Artemia shrimp produces gastrula embryos in diapause, a state of obligate dormancy, having cellular quiescence and suppressed metabolism. The mechanism behind these cellular events remains largely unknown. Here, we study the regulation of cell quiescence using diapause embryos of Artemia We found that Artemia DEK (Ar-DEK), a nuclear factor protein, was down-regulated in the quiescent cells of diapause embryos and enriched in the activated cells of post-diapause embryos. Knockdown of Ar-DEK induced the production of diapause embryos whereas the control Artemia released free-swimming nuaplii. Our results indicate that Ar-DEK correlated with the termination of cellular quiescence via the increase in euchromatin and decrease in heterochromatin. The phenomena of quiescence have many implications beyond shrimp ecology. In cancer cells, for example, knockdown of DEK also induced a short period of cellular quiescence and increased resistance to environmental stress in MCF-7 and MKN45 cancer cell lines. Analysis of RNA sequences in Artemia and in MCF-7 revealed that the Wnt and AURKA signaling pathways were all down-regulated and the p53 signaling pathway was up-regulated upon inhibition of DEK expression. Our results provide insight into the functions of Ar-DEK in the activation of cellular quiescence during diapause formation in Artemia.
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16
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Mendes A, Fahrenkrog B. NUP214 in Leukemia: It's More than Transport. Cells 2019; 8:cells8010076. [PMID: 30669574 PMCID: PMC6356203 DOI: 10.3390/cells8010076] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/10/2019] [Accepted: 01/17/2019] [Indexed: 12/15/2022] Open
Abstract
NUP214 is a component of the nuclear pore complex (NPC) with a key role in protein and mRNA nuclear export. Chromosomal translocations involving the NUP214 locus are recurrent in acute leukemia and frequently fuse the C-terminal region of NUP214 with SET and DEK, two chromatin remodeling proteins with roles in transcription regulation. SET-NUP214 and DEK-NUP214 fusion proteins disrupt protein nuclear export by inhibition of the nuclear export receptor CRM1, which results in the aberrant accumulation of CRM1 protein cargoes in the nucleus. SET-NUP214 is primarily associated with acute lymphoblastic leukemia (ALL), whereas DEK-NUP214 exclusively results in acute myeloid leukemia (AML), indicating different leukemogenic driver mechanisms. Secondary mutations in leukemic blasts may contribute to the different leukemia outcomes. Additional layers of complexity arise from the respective functions of SET and DEK in transcription regulation and chromatin remodeling, which may drive malignant hematopoietic transformation more towards ALL or AML. Another, less frequent fusion protein involving the C terminus of NUP214 results in the sequestosome-1 (SQSTM1)-NUP214 chimera, which was detected in ALL. SQSTM1 is a ubiquitin-binding protein required for proper autophagy induction, linking the NUP214 fusion protein to yet another cellular mechanism. The scope of this review is to summarize the general features of NUP214-related leukemia and discuss how distinct chromosomal translocation partners can influence the cellular effects of NUP214 fusion proteins in leukemia.
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Affiliation(s)
- Adélia Mendes
- Institute of Biology and Molecular Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium.
| | - Birthe Fahrenkrog
- Institute of Biology and Molecular Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium.
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17
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Cifdaloz M, Osterloh L, Graña O, Riveiro-Falkenbach E, Ximénez-Embún P, Muñoz J, Tejedo C, Calvo TG, Karras P, Olmeda D, Miñana B, Gómez-López G, Cañon E, Eyras E, Guo H, Kappes F, Ortiz-Romero PL, Rodríguez-Peralto JL, Megías D, Valcárcel J, Soengas MS. Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1. Nat Commun 2017; 8:2249. [PMID: 29269732 PMCID: PMC5740069 DOI: 10.1038/s41467-017-02353-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 11/23/2017] [Indexed: 12/19/2022] Open
Abstract
Melanomas are well-known for their altered mRNA expression profiles. Yet, the specific contribution of mRNA binding proteins (mRBPs) to melanoma development remains unclear. Here we identify a cluster of melanoma-enriched genes under the control of CUGBP Elav-like family member 1 (CELF1). CELF1 was discovered with a distinct prognostic value in melanoma after mining the genomic landscape of the 692 known mRBPs across different cancer types. Genome-wide transcriptomic, proteomic, and RNA-immunoprecipitation studies, together with loss-of-function analyses in cell lines, and histopathological evaluation in clinical biopsies, revealed an intricate repertoire of CELF1-RNA interactors with minimal overlap with other malignancies. This systems approach uncovered the oncogene DEK as an unexpected target and downstream effector of CELF1. Importantly, CELF1 and DEK were found to represent early-induced melanoma genes and adverse indicators of overall patient survival. These results underscore novel roles of CELF1 in melanoma, illustrating tumor type-restricted functions of RBPs in cancer.
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Affiliation(s)
- Metehan Cifdaloz
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Lisa Osterloh
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | | | - Erica Riveiro-Falkenbach
- Instituto de Investigación i+12, Hospital 12 de Octubre Medical School, Universidad Complutense, 28041, Madrid, Spain
| | | | | | - Cristina Tejedo
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Tonantzin G Calvo
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Panagiotis Karras
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - David Olmeda
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Belén Miñana
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | | | - Estela Cañon
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain
| | - Eduardo Eyras
- Department of Experimental and Health Sciences, Universidad Pompeu Fabra, Barcelona, 08002, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
| | - Haihong Guo
- Institute of Biochemistry and Molecular Biology; Medical School, RWTH Aachen University, Aachen, 52074, Germany
| | - Ferdinand Kappes
- Institute of Biochemistry and Molecular Biology; Medical School, RWTH Aachen University, Aachen, 52074, Germany
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, No. 111, Ren Ai Road, Dushu Lake Higher Education Town, Suzhou Industrial Park (SIP), Suzhou, 215123, China
| | - Pablo L Ortiz-Romero
- Instituto de Investigación i+12, Hospital 12 de Octubre Medical School, Universidad Complutense, 28041, Madrid, Spain
| | - Jose L Rodríguez-Peralto
- Instituto de Investigación i+12, Hospital 12 de Octubre Medical School, Universidad Complutense, 28041, Madrid, Spain
| | - Diego Megías
- Confocal Microscopy Unit, (CNIO), Madrid, 28029, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
| | - María S Soengas
- Melanoma Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), 28029, Madrid, Spain.
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18
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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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19
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Gupta S, Johnson SH, Vasmatzis G, Porath B, Rustin JG, Rao P, Costello BA, Leibovich BC, Thompson RH, Cheville JC, Sukov WR. TFEB-VEGFA (6p21.1) co-amplified renal cell carcinoma: a distinct entity with potential implications for clinical management. Mod Pathol 2017; 30:998-1012. [PMID: 28338654 DOI: 10.1038/modpathol.2017.24] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/27/2017] [Accepted: 01/29/2017] [Indexed: 12/22/2022]
Abstract
A subset of renal cell carcinomas shows TFEB overexpression secondary to MALAT1-TFEB gene fusion. As alternate mechanisms of TFEB overexpression are likely to have the same effect, we sought to determine the frequency of amplification of TFEB and the adjacent VEGFA gene at 6p21.1. As patients with metastatic renal cell carcinomas are managed with anti-VEGF therapies, we retrospectively assessed therapeutic response in patients with amplified tumors. Amplification status was analyzed for 875 renal cell carcinomas from our institution, a consultative case and 794 cases from The Cancer Genome Atlas. Cases were classified as having low level (5-10 copies), and high-level amplification (>10 copies), and were further analyzed for adjacent oncogene copy number status (n=6; 3 single-nucleotide polymorphism genomic microarray, 3 The Cancer Genome Atlas) and structural rearrangements (n=1; mate-pair sequencing). These were then reviewed for histopathology, immunophenotype, and response to VEGF-targeted therapy on follow-up. In all, 10/875 (1.1%) institutional cases, 1 consultative case, and 3/794 (0.4%) of The Cancer Genome Atlas cases showed TFEB high-level amplification, while 14/875 (1.6%) cases showed TFEB low-level amplification. All cases had associated VEGFA amplification. This was confirmed with evaluation for copy number changes (n=6). The 6p21.1 high and low-level amplified tumors occurred in adults (mean age: 66), with over half being ≥pT3 (13/25, 52%), and most showed oncocytic, tubulopapillary features and high grade (≥grade 3: 20/22, 91%). These were aggressive tumors with metastasis and death from renal cell carcinoma in 11 (of 24, 46%) cases. Four patients received targeted therapy and had a mean survival of 31 months (range: 17-50) post nephrectomy. In summary, a group of aggressive renal cell carcinomas show genomic amplification of the 6p21.1 region including TFEB and VEGFA genes and share morphologic features. Additional studies are warranted to determine whether these patients respond to anti-VEGF therapy.
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Affiliation(s)
- Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Binu Porath
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jeannette G Rustin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Priya Rao
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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20
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Matrka MC, Watanabe M, Muraleedharan R, Lambert PF, Lane AN, Romick-Rosendale LE, Wells SI. Overexpression of the human DEK oncogene reprograms cellular metabolism and promotes glycolysis. PLoS One 2017; 12:e0177952. [PMID: 28558019 PMCID: PMC5448751 DOI: 10.1371/journal.pone.0177952] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/05/2017] [Indexed: 12/12/2022] Open
Abstract
The DEK oncogene is overexpressed in many human malignancies including at early tumor stages. Our reported in vitro and in vivo models of squamous cell carcinoma have demonstrated that DEK contributes functionally to cellular and tumor survival and to proliferation. However, the underlying molecular mechanisms remain poorly understood. Based on recent RNA sequencing experiments, DEK expression was necessary for the transcription of several metabolic enzymes involved in anabolic pathways. This identified a possible mechanism whereby DEK may drive cellular metabolism to enable cell proliferation. Functional metabolic Seahorse analysis demonstrated increased baseline and maximum extracellular acidification rates, a readout of glycolysis, in DEK-overexpressing keratinocytes and squamous cell carcinoma cells. DEK overexpression also increased the maximum rate of oxygen consumption and therefore increased the potential for oxidative phosphorylation (OxPhos). To detect small metabolites that participate in glycolysis and the tricarboxylic acid cycle (TCA) that supplies substrate for OxPhos, we carried out NMR-based metabolomics studies. We found that high levels of DEK significantly reprogrammed cellular metabolism and altered the abundances of amino acids, TCA cycle intermediates and the glycolytic end products lactate, alanine and NAD+. Taken together, these data support a scenario whereby overexpression of the human DEK oncogene reprograms keratinocyte metabolism to fulfill energy and macromolecule demands required to enable and sustain cancer cell growth.
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Affiliation(s)
- Marie C. Matrka
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Miki Watanabe
- NMR-Based Metabolomics Core Facility, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Ranjithmenon Muraleedharan
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Andrew N. Lane
- Center for Environmental Systems Biochemistry, Dept. Toxicology and Cancer Biology and Markey Cancer Center, Lexington, Kentucky, United States of America
| | - Lindsey E. Romick-Rosendale
- NMR-Based Metabolomics Core Facility, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Susanne I. Wells
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio, United States of America
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21
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Sun J, Bi F, Yang Y, Zhang Y, Jin A, Li J, Lin Z. DEK protein overexpression predicts poor prognosis in pancreatic ductal adenocarcinoma. Oncol Rep 2017; 37:857-864. [PMID: 27959420 DOI: 10.3892/or.2016.5302] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/25/2016] [Indexed: 11/06/2022] Open
Abstract
DEK, a transcription factor, is involved in mRNA splicing, transcriptional control, cell division and differentiation. Recent studies suggest that DEK overexpression can promote tumorigenesis in a wide range of cancer cell types. However, little is known concerning the status of DEK in pancreatic ductal adenocarcinoma (PDAC). Based on the microarray data from Gene Expression Omnibus (GEO), the expression levels of DEK mRNA in PDAC tissues were significantly higher than levels in the adjacent non-tumor tissues. To explore the clinical features of DEK overexpression in PDAC, 87 PDAC and 52 normal pancreas tissues were selected for immunoenzyme staining of the DEK protein. Localization of the DEK protein was detected in PANC-1 pancreatic cancer cells using immunofluorescence (IF) staining. The correlations between DEK overexpression and the clinical features of PDAC were evaluated using the Chi-squared (χ2) and Fisher's exact tests. The survival rates were calculated by the Kaplan-Meier method, and the relationship between prognostic factors and patient survival was also analyzed by the Cox proportional hazard models. The expression levels of DEK mRNA in PDAC tissues were significantly higher than that in the adjacent non‑tumor tissues. The DEK protein showed a primarily nuclear staining pattern in PDAC. The positive rate of the DEK protein was 52.9% (46/87) in PDAC, which was significantly higher than that in the adjacent normal pancreatic tissues (7.7%, 4/52). DEK overexpression in PDAC was correlated with tumor size, histological grade, tumor‑node‑metastasis (TNM) stage and overall survival (OS) rates. In addition, multivariate analysis demonstrated that DEK overexpression was an independent prognostic factor along with histological grade and TNM stage in patients with PDAC. In conclusion, DEK overexpression is associated with PDAC progression and may be a potential biomarker for poor prognostic evaluation in PDAC.
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Affiliation(s)
- Jie Sun
- Department of Pathology and Cancer Research Center, Yanbian University Medical College, Yanji, Jilin 133002, P.R. China
| | - Fangfang Bi
- Department of Pathology and Cancer Research Center, Yanbian University Medical College, Yanji, Jilin 133002, P.R. China
| | - Yang Yang
- Department of Pathology and Cancer Research Center, Yanbian University Medical College, Yanji, Jilin 133002, P.R. China
| | - Yuan Zhang
- Department of Pathology and Cancer Research Center, Yanbian University Medical College, Yanji, Jilin 133002, P.R. China
| | - Aihua Jin
- Department of Internal Medicine, Yanbian University Hospital, Yanji, Jilin 133002, P.R. China
| | - Jinzi Li
- Department of Pediatrics, Yanbian University Hospital, Yanji, Jilin 133002, P.R. China
| | - Zhenhua Lin
- Department of Pathology and Cancer Research Center, Yanbian University Medical College, Yanji, Jilin 133002, P.R. China
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22
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Ullmark T, Järvstråt L, Sandén C, Montano G, Jernmark-Nilsson H, Lilljebjörn H, Lennartsson A, Fioretos T, Drott K, Vidovic K, Nilsson B, Gullberg U. Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells. Haematologica 2016; 102:336-345. [PMID: 27612989 DOI: 10.3324/haematol.2016.149815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/05/2016] [Indexed: 12/29/2022] Open
Abstract
The zinc finger transcription factor Wilms tumor gene 1 (WT1) acts as an oncogene in acute myeloid leukemia. A naturally occurring alternative splice event between zinc fingers three and four, removing or retaining three amino acids (±KTS), is believed to change the DNA binding affinity of WT1, although there are conflicting data regarding the binding affinity and motifs of the different isoforms. Increased expression of the WT1 -KTS isoform at the expense of the WT1 +KTS isoform is associated with poor prognosis in acute myeloid leukemia. We determined the genome-wide binding pattern of WT1 -KTS and WT1 +KTS in leukemic K562 cells by chromatin immunoprecipitation and deep sequencing. We discovered that the WT1 -KTS isoform predominantly binds close to transcription start sites and to enhancers, in a similar fashion to other transcription factors, whereas WT1 +KTS binding is enriched within gene bodies. We observed a significant overlap between WT1 -KTS and WT1 +KTS target genes, despite the binding sites being distinct. Motif discovery revealed distinct binding motifs for the isoforms, some of which have been previously reported as WT1 binding sites. Additional analyses showed that both WT1 -KTS and WT1 +KTS target genes are more likely to be transcribed than non-targets, and are involved in cell proliferation, cell death, and development. Our study provides evidence that WT1 -KTS and WT1 +KTS share target genes yet still bind distinct locations, indicating isoform-specific regulation in transcription of genes related to cell proliferation and differentiation, consistent with the involvement of WT1 in acute myeloid leukemia.
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Affiliation(s)
- Tove Ullmark
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Linnea Järvstråt
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Carl Sandén
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Giorgia Montano
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Helena Jernmark-Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Kristina Drott
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Karina Vidovic
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Björn Nilsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
| | - Urban Gullberg
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden
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23
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Wu X, Wu G, Wu Z, Yao X, Li G. MiR-200a Suppresses the Proliferation and Metastasis in Pancreatic Ductal Adenocarcinoma through Downregulation of DEK Gene. Transl Oncol 2016; 9:25-31. [PMID: 26947878 PMCID: PMC4800058 DOI: 10.1016/j.tranon.2015.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 12/24/2022] Open
Abstract
MiR-200a has been reported to be able to suppress the epithelial-mesenchymal transition process in pancreatic cancer stem cells, suggesting that miR-200a could suppress the metastasis of pancreatic ductal adenocarcinoma (PDAC). However, its role in proliferation and metastasis of PDAC and the underlying mechanism by which miR-200a works in PDAC have not been elucidated. In our study, we for the first time identified that DEK gene is a direct downstream target of miR-200a. It was found that overexpression of miR-200a decreased DEK expression, suppressing the proliferation, migration, and invasion of PDAC cells. Meanwhile, knockdown of miR-200a can increase DEK level, promoting the proliferation, migration, and invasion of PDAC cells. Our study demonstrated that miR-200a suppresses the metastasis in pancreatic PDAC through downregulation of DEK, suggesting that miR-200a may be used as a novel potential marker in prediction of metastasis of PDAC.
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Affiliation(s)
- Xiaoyu Wu
- Department of Surgical Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, PR China
| | - Guannan Wu
- Department of Surgical Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, PR China
| | - Zhenfeng Wu
- Department of Surgical Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, PR China
| | - Xuequan Yao
- Department of Surgical Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, PR China
| | - Gang Li
- Department of General Surgery, Jiangsu Cancer Hospital, Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing 210009, PR China
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24
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Adams AK, Bolanos LC, Dexheimer PJ, Karns RA, Aronow BJ, Komurov K, Jegga AG, Casper KA, Patil YJ, Wilson KM, Starczynowski DT, Wells SI. IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival. Oncotarget 2015; 6:43395-407. [PMID: 26527316 PMCID: PMC4791239 DOI: 10.18632/oncotarget.6028] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
The chromatin-binding DEK protein was recently reported to promote the growth of HPV+ and HPV- head and neck squamous cell carcinomas (HNSCCs). Relevant cellular and molecular mechanism(s) controlled by DEK in HNSCC remain poorly understood. While DEK is known to regulate specific transcriptional targets, global DEK-dependent gene networks in HNSCC are unknown. To identify DEK transcriptional signatures we performed RNA-Sequencing (RNA-Seq) in HNSCC cell lines that were either proficient or deficient for DEK. Bioinformatic analyses and subsequent validation revealed that IRAK1, a regulator of inflammatory signaling, and IRAK1-dependent regulatory networks were significantly repressed upon DEK knockdown in HNSCC. According to TCGA data, 14% of HNSCC specimens overexpressed IRAK1, thus supporting possible oncogenic functions. Furthermore, genetic or pharmacologic inhibition of IRAK1 in HNSCC cell lines was sufficient to attenuate downstream signaling such as ERK1/2 and to induce HNSCC cell death by apoptosis. Finally, targeting DEK and IRAK1 simultaneously enhanced cell death as compared to targeting either alone. Our findings reveal that IRAK1 promotes cell survival and is an attractive therapeutic target in HNSCC cells. Thus, we propose a model wherein IRAK1 stimulates tumor signaling and phenotypes both independently and in conjunction with DEK.
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Affiliation(s)
- Allie K. Adams
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lyndsey C. Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Phillip J. Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rebekah A. Karns
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kakajan Komurov
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Keith A. Casper
- Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Yash J. Patil
- Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Keith M. Wilson
- Department of Otolaryngology, Head and Neck Surgery, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel T. Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Susanne I. Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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25
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Lohmann F, Dangeti M, Soni S, Chen X, Planutis A, Baron MH, Choi K, Bieker JJ. The DEK Oncoprotein Is a Critical Component of the EKLF/KLF1 Enhancer in Erythroid Cells. Mol Cell Biol 2015; 35:3726-38. [PMID: 26303528 PMCID: PMC4589598 DOI: 10.1128/mcb.00382-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 05/06/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023] Open
Abstract
Understanding how transcriptional regulators are themselves controlled is important in attaining a complete picture of the intracellular effects that follow signaling cascades during early development and cell-restricted differentiation. We have addressed this issue by focusing on the regulation of EKLF/KLF1, a zinc finger transcription factor that plays a necessary role in the global regulation of erythroid gene expression. Using biochemical affinity purification, we have identified the DEK oncoprotein as a critical factor that interacts with an essential upstream enhancer element of the EKLF promoter and exerts a positive effect on EKLF levels. This element also binds a core set of erythroid transcription factors, suggesting that DEK is part of a tissue-restricted enhanceosome that contains BMP4-dependent and -independent components. Together with local enrichment of properly coded histones and an open chromatin domain, optimal transcriptional activation of the EKLF locus can be established.
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Affiliation(s)
- Felix Lohmann
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Mohan Dangeti
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Shefali Soni
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Xiaoyong Chen
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Antanas Planutis
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Margaret H Baron
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York, USA Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, USA Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
| | - Kyunghee Choi
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - James J Bieker
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York, USA Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, USA
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26
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Dissecting the Potential Interplay of DEK Functions in Inflammation and Cancer. JOURNAL OF ONCOLOGY 2015; 2015:106517. [PMID: 26425120 PMCID: PMC4575739 DOI: 10.1155/2015/106517] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/05/2015] [Indexed: 12/12/2022]
Abstract
There is a long-standing correlation between inflammation, inflammatory cell signaling pathways, and tumor formation. Understanding the mechanisms behind inflammation-driven tumorigenesis is of great research and clinical importance. Although not entirely understood, these mechanisms include a complex interaction between the immune system and the damaged epithelium that is mediated by an array of molecular signals of inflammation—including reactive oxygen species (ROS), cytokines, and NFκB signaling—that are also oncogenic. Here, we discuss the association of the unique DEK protein with these processes. Specifically, we address the role of DEK in chronic inflammation via viral infections and autoimmune diseases, the overexpression and oncogenic activity of DEK in cancers, and DEK-mediated regulation of NFκB signaling. Combined, evidence suggests that DEK may play a complex, multidimensional role in chronic inflammation and subsequent tumorigenesis.
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27
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Sandén C, Gullberg U. The DEK oncoprotein and its emerging roles in gene regulation. Leukemia 2015; 29:1632-6. [PMID: 25765544 DOI: 10.1038/leu.2015.72] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/08/2015] [Accepted: 03/03/2015] [Indexed: 02/06/2023]
Abstract
The DEK oncogene is highly expressed in cells from most human tissues and overexpressed in a large and growing number of cancers. It also fuses with the NUP214 gene to form the DEK-NUP214 fusion gene in a subset of acute myeloid leukemia. Originally characterized as a member of this translocation, DEK has since been implicated in epigenetic and transcriptional regulation, but its role in these processes is still elusive and intriguingly complex. Similarly multifaceted is its contribution to cellular transformation, affecting multiple cellular processes such as self-renewal, proliferation, differentiation, senescence and apoptosis. Recently, the roles of the DEK and DEK-NUP214 proteins have been elucidated by global analysis of DNA binding and gene expression, as well as multiple functional studies. This review outlines recent advances in the understanding of the basic functions of the DEK protein and its role in leukemogenesis.
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Affiliation(s)
- C Sandén
- Department of Hematology, Lund University, Lund, Sweden
| | - U Gullberg
- Department of Hematology, Lund University, Lund, Sweden
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28
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Sandén C, Nilsson HJ, Gullberg U. The DEK oncoprotein is upregulated by multiple leukemia-associated fusion genes. Blood Cells Mol Dis 2015; 54:284-5. [PMID: 25524609 DOI: 10.1016/j.bcmd.2014.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/15/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Carl Sandén
- Department of Hematology, Lund University, Lund, Sweden.
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