1
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Lü Y, Cho T, Mukherjee S, Suarez CF, Gonzalez-Foutel NS, Malik A, Martinez S, Dervovic D, Oh RH, Langille E, Al-Zahrani KN, Hoeg L, Lin ZY, Tsai R, Mbamalu G, Rotter V, Ashton-Prolla P, Moffat J, Chemes LB, Gingras AC, Oren M, Durocher D, Schramek D. Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability. Mol Syst Biol 2024; 20:719-740. [PMID: 38580884 PMCID: PMC11148184 DOI: 10.1038/s44320-024-00032-x] [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: 09/12/2022] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024] Open
Abstract
Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.
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Affiliation(s)
- YiQing Lü
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Department of Biology, Suffolk University, Boston, MA, 02108, USA
| | - Tiffany Cho
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Saptaparna Mukherjee
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Carmen Florencia Suarez
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Nicolas S Gonzalez-Foutel
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Sebastien Martinez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Dzana Dervovic
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Robin Hyunseo Oh
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ellen Langille
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Khalid N Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Lisa Hoeg
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Zhen Yuan Lin
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Geraldine Mbamalu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Patricia Ashton-Prolla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul and Serviço de Genetica Médica HCPA, Porto Alegre, Brasil
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S3G9, Canada
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Lucia Beatriz Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Anne-Claude Gingras
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Durocher
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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2
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Ester L, Cabrita I, Ventzke M, Kieckhöfer E, Christodoulou M, Mandel AM, Diefenhardt P, Fabretti F, Benzing T, Habbig S, Schermer B. The role of the FSGS disease gene product and nuclear pore protein NUP205 in regulating nuclear localization and activity of transcriptional regulators YAP and TAZ. Hum Mol Genet 2023; 32:3153-3165. [PMID: 37565816 PMCID: PMC10630254 DOI: 10.1093/hmg/ddad135] [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: 06/20/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
Mutations in genes encoding nuclear pore proteins (NUPs) lead to the development of steroid-resistant nephrotic syndrome and focal segmental glomerulosclerosis (FSGS). However, the precise molecular mechanisms by which NUP dysfunction contributes to podocyte injury preceding FSGS remain unclear. The tightly regulated activity of Yes-associated protein (YAP) and WW-domain-containing transcription regulator 1 (TAZ), the transcriptional effectors of the Hippo pathway, is crucial for podocytes and the maintenance of the glomerular filter. In this study, we investigate the impact of NUPs on the regulation of YAP/TAZ nuclear import and activity in podocytes. In unbiased interactome studies using quantitative label-free mass spectrometry, we identify the FSGS disease gene products NUP107, NUP133, NUP205, and Exportin-5 (XPO5) as components of YAP and TAZ protein complexes in podocytes. Moreover, we demonstrate that NUP205 is essential for YAP/TAZ nuclear import. Consistently, both the nuclear interaction of YAP/TAZ with TEA domain transcription factor 1 and their transcriptional activity were dependent on NUP205 expression. Additionally, we elucidate a regulatory feedback mechanism whereby YAP activity is modulated in response to TAZ-mediated NUP205 expression. In conclusion, this study establishes a connection between the FSGS disease protein NUP205 and the activity of the transcriptional regulators and Hippo effectors YAP and TAZ and it proposes a potential pathological role of YAP/TAZ dysregulation in podocytes of patients with pathogenic NUP205 variants.
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Affiliation(s)
- Lioba Ester
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Inês Cabrita
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Michel Ventzke
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Emilia Kieckhöfer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Marita Christodoulou
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Amrei M Mandel
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Paul Diefenhardt
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Sandra Habbig
- Department of Pediatrics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Faculty of Medicine and University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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3
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Chen Y, Zhang Y, Zhou X. Non-classical functions of nuclear pore proteins in ciliopathy. Front Mol Biosci 2023; 10:1278976. [PMID: 37908226 PMCID: PMC10614291 DOI: 10.3389/fmolb.2023.1278976] [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: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Nucleoporins (NUPs) constitute integral nuclear pore protein (NPC) elements. Although traditional NUP functions have been extensively researched, evidence of additional vital non-NPC roles, referred to herein as non-classical NUP functions, is also emerging. Several NUPs localise at the ciliary base. Indeed, Nup188, Nup93 or Nup205 knockdown results in cilia loss, impacting cardiac left-right patterning in models and cell lines. Genetic variants of Nup205 and Nup188 have been identified in patients with congenital heart disease and situs inversus totalis or heterotaxy, a prevalent human ciliopathy. These findings link non-classical NUP functions to human diseases. This mini-review summarises pivotal NUP interactions with NIMA-related kinases or nephronophthisis proteins that regulate ciliary function and explores other NUPs potentially implicated in cilia-related disorders. Overall, elucidating the non-classical roles of NUPs will enhance comprehension of ciliopathy aetiology.
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Affiliation(s)
- Yan Chen
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
| | - Yuan Zhang
- Department of Assisted Reproduction, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangyu Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University Shanghai Medical College, Shanghai, China
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4
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Jacquet K, Rodrigue MA, Richard DE, Lavoie JN. The adenoviral protein E4orf4: a probing tool to decipher mechanical stress-induced nuclear envelope remodeling in tumor cells. Cell Cycle 2020; 19:2963-2981. [PMID: 33103553 DOI: 10.1080/15384101.2020.1836441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The human adenovirus (Ad) type 2/5 early region 4 (E4) ORF4 protein (E4orf4) exerts a remarkable tumor cell-selective killing activity in mammalian cells. This indicates that E4orf4 can target tumor cell-defining features and is a unique tool to probe cancer cell vulnerabilities. Recently, we found that E4orf4, through an interaction with the polarity protein PAR3, subverts nuclear envelope (NE) remodeling processes in a tumor cell-selective manner. In this Perspective, we outline mechanical signals that modify nuclear dynamics and tumor cell behavior to highlight potential mechanisms for E4orf4's tumoricidal activity. Through an analysis of E4orf4's cellular targets, we define a protein subnetwork that comprises phosphatase systems interconnected to polarity protein hubs, which could contribute to enhanced NE plasticity. We infer that elucidating E4orf4's protein network at a functional level could uncover key mechanisms of NE remodeling that define the tumor cell phenotype.
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Affiliation(s)
- Kévin Jacquet
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada
| | - Marc-Antoine Rodrigue
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada
| | - Darren E Richard
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval , Québec, Canada.,Endocrinology and Nephrology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada
| | - Josée N Lavoie
- Centre de Recherche sur le Cancer de l'Université Laval , Québec, Canada.,Oncology, Centre de Recherche du CHU de Québec-Université Laval , Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval , Québec, Canada
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5
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Kleinberger T. Biology of the adenovirus E4orf4 protein: from virus infection to cancer cell death. FEBS Lett 2019; 594:1891-1917. [DOI: 10.1002/1873-3468.13704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Tamar Kleinberger
- Department of Molecular Microbiology the Rappaport Faculty of Medicine Technion –Israel Institute of Technology Haifa Israel
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6
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Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach. Genomics 2019; 112:2041-2051. [PMID: 31770586 DOI: 10.1016/j.ygeno.2019.11.017] [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: 02/11/2019] [Revised: 05/29/2019] [Accepted: 11/22/2019] [Indexed: 11/21/2022]
Abstract
Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one of the costliest and widely exported agri-produce having global turnover of >10 billion USD. Mosaic/marble disease is one of the major impediments that requires understanding of disease at molecular level. Neither whole genome sequence nor any genomic resources are available, thus RNA seq approach can be a rapid and economical alternative. De novo transcriptome assembly was done with Illumina Hiseq data. A total of 5317 DEGs, 2267 TFs, 114 pathways and 175,952 genic region putative markers were obtained. Gene regulatory network analysis deciphered molecular events involved in marble disease. This is the first transcriptomic report revealing disease mechanism mediated by perturbation in auxin homeostasis and ethylene signalling leading to senescence. The web-genomic resource (SCMVTDb) catalogues putative molecular markers, candidate genes and transcript information. SCMVTDb can be used in germplasm improvement against mosaic disease in endeavour of small cardamom productivity. Availability of genomic resource, SCMVTDb: http://webtom.cabgrid.res.in/scmvtdb/.
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7
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Sales Gil R, de Castro IJ, Berihun J, Vagnarelli P. Protein phosphatases at the nuclear envelope. Biochem Soc Trans 2018; 46:173-182. [PMID: 29432143 PMCID: PMC5818667 DOI: 10.1042/bst20170139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022]
Abstract
The nuclear envelope (NE) is a unique topological structure formed by lipid membranes (Inner and Outer Membrane: IM and OM) interrupted by open channels (Nuclear Pore complexes). Besides its well-established structural role in providing a physical separation between the genome and the cytoplasm and regulating the exchanges between the two cellular compartments, it has become quite evident in recent years that the NE also represents a hub for localized signal transduction. Mechanical, stress, or mitogen signals reach the nucleus and trigger the activation of several pathways, many effectors of which are processed at the NE. Therefore, the concept of the NE acting just as a barrier needs to be expanded to embrace all the dynamic processes that are indeed associated with it. In this context, dynamic protein association and turnover coupled to reversible post-translational modifications of NE components can provide important clues on how this integrated cellular machinery functions as a whole. Reversible protein phosphorylation is the most used mechanism to control protein dynamics and association in cells. Keys to the reversibility of the system are protein phosphatases and the regulation of their activity in space and time. As the NE is clearly becoming an interesting compartment for the control and transduction of several signalling pathways, in this review we will focus on the role of Protein Phosphatases at the NE since the significance of this class of proteins in this context has been little explored.
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Affiliation(s)
- Raquel Sales Gil
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, U.K
| | - Ines J de Castro
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research (DZIF), Heidelberg 69120, Germany
| | - Jerusalem Berihun
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, U.K
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, U.K.
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8
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Chou CC, Zhang Y, Umoh ME, Vaughan SW, Lorenzini I, Liu F, Sayegh M, Donlin-Asp PG, Chen YH, Duong DM, Seyfried NT, Powers MA, Kukar T, Hales CM, Gearing M, Cairns NJ, Boylan KB, Dickson DW, Rademakers R, Zhang YJ, Petrucelli L, Sattler R, Zarnescu DC, Glass JD, Rossoll W. TDP-43 pathology disrupts nuclear pore complexes and nucleocytoplasmic transport in ALS/FTD. Nat Neurosci 2018; 21:228-239. [PMID: 29311743 PMCID: PMC5800968 DOI: 10.1038/s41593-017-0047-3] [Citation(s) in RCA: 343] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/07/2017] [Indexed: 12/13/2022]
Abstract
The cytoplasmic mislocalization and aggregation of TAR DNA-binding protein-43 (TDP-43) is a common histopathological hallmark of the amyotrophic lateral sclerosis and frontotemporal dementia disease spectrum (ALS/FTD). However, the composition of aggregates and their contribution to the disease process remain unknown. Here we used proximity-dependent biotin identification (BioID) to interrogate the interactome of detergent-insoluble TDP-43 aggregates and found them enriched for components of the nuclear pore complex and nucleocytoplasmic transport machinery. Aggregated and disease-linked mutant TDP-43 triggered the sequestration and/or mislocalization of nucleoporins and transport factors, and interfered with nuclear protein import and RNA export in mouse primary cortical neurons, human fibroblasts and induced pluripotent stem cell-derived neurons. Nuclear pore pathology is present in brain tissue in cases of sporadic ALS and those involving genetic mutations in TARDBP and C9orf72. Our data strongly implicate TDP-43-mediated nucleocytoplasmic transport defects as a common disease mechanism in ALS/FTD.
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Affiliation(s)
- Ching-Chieh Chou
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Yi Zhang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Xiangya Hospital and Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mfon E Umoh
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Spencer W Vaughan
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Ileana Lorenzini
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Feilin Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Department of Ophthalmology, the Second Hospital of Jilin University, Changchun, China
| | - Melissa Sayegh
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Paul G Donlin-Asp
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA.,Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Yu Han Chen
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Maureen A Powers
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Kukar
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.,Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chadwick M Hales
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Marla Gearing
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Nigel J Cairns
- Department of Pathology and Immunology, Washington University, St. Louis, MO, USA
| | - Kevin B Boylan
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Rita Sattler
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Daniela C Zarnescu
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Jonathan D Glass
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.,Emory ALS Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Wilfried Rossoll
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA. .,Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA. .,Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
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9
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Dongsheng H, Zhuo Z, Jiamin L, Hailan M, Lijuan H, Fan C, Dan Y, He Z, Yun X. Proteomic Analysis of the Peri-Infarct Area after Human Umbilical Cord Mesenchymal Stem Cell Transplantation in Experimental Stroke. Aging Dis 2016; 7:623-634. [PMID: 27699085 PMCID: PMC5036957 DOI: 10.14336/ad.2016.0121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/21/2016] [Indexed: 12/27/2022] Open
Abstract
Among various therapeutic approaches for stroke, treatment with human umbilical cord mesenchymal stem cells (hUC-MSCs) has acquired some promising results. However, the underlying mechanisms remain unclear. We analyzed the protein expression spectrum of the cortical peri-infarction region after ischemic stroke followed by treatment with hUC-MSCs, and found 16 proteins expressed differentially between groups treated with or without hUC-MSCs. These proteins were further determined by Gene Ontology term analysis and network with CD200-CD200R1, CCL21-CXCR3 and transcription factors. Three of them: Abca13, Grb2 and Ptgds were verified by qPCR and ELISA. We found the protein level of Abca13 and the mRNA level of Grb2 consistent with results from the proteomic analysis. Finally, the function of these proteins was described and the potential proteins that deserve to be further studied was also highlighted. Our data may provide possible underlying mechanisms for the treatment of stroke using hUC-MSCs.
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Affiliation(s)
- He Dongsheng
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Zhang Zhuo
- 4Department of Gastroenterology, Children's Hospital of Nanjing, Nanjing Medical University, Nanjing 210008, China
| | - Lao Jiamin
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Meng Hailan
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Han Lijuan
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Chen Fan
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Ye Dan
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Zhang He
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
| | - Xu Yun
- 1Department of Neurology, Affiliated Drum Tower Hospital, and; 2Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing 210008, China.; 3The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China; 5Jiangsu Province Stroke Center for Diagnosis and Therapy, Nanjing 210008, China; 6Nanjing Neuropsychiatry Clinic Medical Center, Nanjing 210008, China
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Activation of the Chicken Anemia Virus Apoptin Protein by Chk1/2 Phosphorylation Is Required for Apoptotic Activity and Efficient Viral Replication. J Virol 2016; 90:9433-45. [PMID: 27512067 DOI: 10.1128/jvi.00936-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Chicken anemia virus (CAV) is a single-stranded circular DNA virus that carries 3 genes, the most studied of which is the gene encoding VP3, also known as apoptin. This protein has been demonstrated to specifically kill transformed cells while leaving normal cells unharmed in a manner that is independent of p53 status. Although the mechanistic basis for this differential activity is unclear, it is evident that the subcellular localization of the protein is important for the difference. In normal cells, apoptin exists in filamentous networks in the cytoplasm, whereas in transformed cells, apoptin is present in the nucleus and appears as distinct foci. We have previously demonstrated that DNA damage signaling through the ataxia telangiectasia mutated (ATM) pathway induces the translocation of apoptin from the cytoplasm to the nucleus, where it induces apoptosis. We found that apoptin contains four checkpoint kinase consensus sites and that mutation of either threonine 56 or 61 to alanine restricts apoptin to the cytoplasm. Furthermore, treatment of tumor cells expressing apoptin with inhibitors of checkpoint kinase 1 (Chk1) and Chk2 causes apoptin to localize to the cytoplasm. Importantly, silencing of Chk2 rescues cancer cells from the cytotoxic effects of apoptin. Finally, treatment of virus-producing cells with Chk inhibitor protects them from virus-mediated toxicity and reduces the titer of progeny virus. Taken together, our results indicate that apoptin is a sensor of DNA damage signaling through the ATM-Chk2 pathway, which induces it to migrate to the nucleus during viral replication. IMPORTANCE The chicken anemia virus (CAV) protein apoptin is known to induce tumor cell-specific death when expressed. Therefore, understanding its regulation and mechanism of action could provide new insights into tumor cell biology. We have determined that checkpoint kinase 1 and 2 signaling is important for apoptin regulation and is a likely feature of both tumor cells and host cells producing virus progeny. Inhibition of checkpoint signaling prevents apoptin toxicity in tumor cells and attenuates CAV replication, suggesting it may be a future target for antiviral therapy.
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The Human Adenovirus Type 5 E4orf4 Protein Targets Two Phosphatase Regulators of the Hippo Signaling Pathway. J Virol 2015; 89:8855-70. [PMID: 26085163 DOI: 10.1128/jvi.03710-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/05/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED When expressed alone at high levels, the human adenovirus E4orf4 protein exhibits tumor cell-specific p53-independent toxicity. A major E4orf4 target is the B55 class of PP2A regulatory subunits, and we have shown recently that binding of E4orf4 inhibits PP2A(B55) phosphatase activity in a dose-dependent fashion by preventing access of substrates (M. Z. Mui et al., PLoS Pathog 9:e1003742, 2013, http://dx.doi.org/10.1371/journal.ppat.1003742). While interaction with B55 subunits is essential for toxicity, E4orf4 mutants exist that, despite binding B55 at high levels, are defective in cell killing, suggesting that other essential targets exist. In an attempt to identify additional targets, we undertook a proteomics approach to characterize E4orf4-interacting proteins. Our findings indicated that, in addition to PP2A(B55) subunits, ASPP-PP1 complex subunits were found among the major E4orf4-binding species. Both the PP2A and ASPP-PP1 phosphatases are known to positively regulate effectors of the Hippo signaling pathway, which controls the expression of cell growth/survival genes by dephosphorylating the YAP transcriptional coactivator. We find here that expression of E4orf4 results in hyperphosphorylation of YAP, suggesting that Hippo signaling is affected by E4orf4 interactions with PP2A(B55) and/or ASPP-PP1 phosphatases. Furthermore, knockdown of YAP1 expression was seen to enhance E4orf4 killing, again consistent with a link between E4orf4 toxicity and inhibition of the Hippo pathway. This effect may in fact contribute to the cancer cell specificity of E4orf4 toxicity, as many human cancer cells rely heavily on the Hippo pathway for their enhanced proliferation. IMPORTANCE The human adenovirus E4orf4 protein has been known for some time to induce tumor cell-specific death when expressed at high levels; thus, knowledge of its mode of action could be of importance for development of new cancer therapies. Although the B55 form of the phosphatase PP2A has long been known as an essential E4orf4 target, genetic analyses indicated that others must exist. To identify additional E4orf4 targets, we performed, for the first time, a large-scale affinity purification/mass spectrometry analysis of E4orf4 binding partners. Several additional candidates were detected, including key regulators of the Hippo signaling pathway, which enhances cell viability in many cancers, and results of preliminary studies suggested a link between inhibition of Hippo signaling and E4orf4 toxicity.
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Regulation of human adenovirus alternative RNA splicing by the adenoviral L4-33K and L4-22K proteins. Int J Mol Sci 2015; 16:2893-912. [PMID: 25636034 PMCID: PMC4346872 DOI: 10.3390/ijms16022893] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/06/2015] [Accepted: 01/22/2015] [Indexed: 01/12/2023] Open
Abstract
Adenovirus makes extensive use of alternative RNA splicing to produce a complex set of spliced viral mRNAs. Studies aimed at characterizing the interactions between the virus and the host cell RNA splicing machinery have identified three viral proteins of special significance for the control of late viral gene expression: L4-33K, L4-22K, and E4-ORF4. L4-33K is a viral alternative RNA splicing factor that controls L1 alternative splicing via an interaction with the cellular protein kinases Protein Kinase A (PKA) and DNA-dependent protein kinase (DNA-PK). L4-22K is a viral transcription factor that also has been implicated in the splicing of a subset of late viral mRNAs. E4-ORF4 is a viral protein that binds the cellular protein phosphatase IIA (PP2A) and controls Serine/Arginine (SR)-rich protein activity by inducing SR protein dephosphorylation. The L4-33K, and most likely also the L4-22K protein, are highly phosphorylated in vivo. Here we will review the function of these viral proteins in the post-transcriptional control of adenoviral gene expression and further discuss the significance of potential protein kinases phosphorylating the L4-33K and/or L4-22K proteins.
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