51
|
Targa A, Larrimore KE, Wong CK, Chong YL, Fung R, Lee J, Choi H, Rancati G. Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene. EMBO J 2021; 40:e107839. [PMID: 34528284 PMCID: PMC8561638 DOI: 10.15252/embj.2021107839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptive evolution to cellular stress is a process implicated in a wide range of biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic changes, which allow expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC; long-term adaptation and fitness recovery instead occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that early phenotypic plasticity allows later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and to dissect mechanisms of adaptation.
Collapse
Affiliation(s)
- Altea Targa
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Katherine E Larrimore
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Cheng Kit Wong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yu Lin Chong
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Ronald Fung
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Joseph Lee
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Hyungwon Choi
- Department of MedicineYong Loo Lin School of MedicineNUS and National University Health SystemSingaporeSingapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Skin Research Institute of Singapore (SRIS)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| |
Collapse
|
52
|
Stefanello ST, Luchtefeld I, Liashkovich I, Pethö Z, Azzam I, Bulk E, Rosso G, Döhlinger L, Hesse B, Oeckinghaus A, Shahin V. Impact of the Nuclear Envelope on Malignant Transformation, Motility, and Survival of Lung Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102757. [PMID: 34658143 PMCID: PMC8596107 DOI: 10.1002/advs.202102757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Indexed: 05/08/2023]
Abstract
Nuclear pore complexes (NPCs) selectively mediate all nucleocytoplasmic transport and engage in fundamental cell-physiological processes. It is hypothesized that NPCs are critical for malignant transformation and survival of lung cancer cells, and test the hypothesis in lowly and highly metastatic non-small human lung cancer cells (NSCLCs). It is shown that malignant transformation is paralleled by an increased NPCs density, and a balanced pathological weakening of the physiological stringency of the NPC barrier. Pharmacological interference using barrier-breaking compounds collapses the stringency. Concomitantly, it induces drastic overall structural changes of NSCLCs, terminating their migration. Moreover, the degree of malignancy is found to be paralleled by substantially decreased lamin A/C levels. The latter provides crucial structural and mechanical stability to the nucleus, and interacts with NPCs, cytoskeleton, and nucleoskeleton for cell maintenance, survival, and motility. The recent study reveals the physiological importance of the NPC barrier stringency for mechanical and structural resilience of normal cell nuclei. Hence, reduced lamin A/C levels in conjunction with controlled pathological weakening of the NPC barrier stringency may facilitate deformability of NSCLCs during the metastasis steps. Modulation of the NPC barrier presents a potential strategy for suppressing the malignant phenotype or enhancing the effectiveness of currently existing chemotherapeutics.
Collapse
Affiliation(s)
- Sílvio Terra Stefanello
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Isabelle Luchtefeld
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Ivan Liashkovich
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Zoltan Pethö
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Ihab Azzam
- Institute of Immunology, University of Münster, Röntgen-Str. 21, Münster, 48149, Germany
| | - Etmar Bulk
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Gonzalo Rosso
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Lilly Döhlinger
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Bettina Hesse
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| | - Andrea Oeckinghaus
- Institute of Molecular Tumor Biology, University of Münster, Robert-Koch-Str. 43, Münster, 48149, Germany
| | - Victor Shahin
- Institute of Physiology II, University of Münster, Robert-Koch-Str. 27b, Münster, 48149, Germany
| |
Collapse
|
53
|
Nallasivan MP, Haussmann IU, Civetta A, Soller M. Channel nuclear pore protein 54 directs sexual differentiation and neuronal wiring of female reproductive behaviors in Drosophila. BMC Biol 2021; 19:226. [PMID: 34666772 PMCID: PMC8527774 DOI: 10.1186/s12915-021-01154-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/15/2021] [Indexed: 11/23/2022] Open
Abstract
Background Female reproductive behaviors and physiology change profoundly after mating. The control of pregnancy-associated changes in physiology and behaviors are largely hard-wired into the brain to guarantee reproductive success, yet the gene expression programs that direct neuronal differentiation and circuit wiring at the end of the sex determination pathway in response to mating are largely unknown. In Drosophila, the post-mating response induced by male-derived sex-peptide in females is a well-established model to elucidate how complex innate behaviors are hard-wired into the brain. Here, we use a genetic approach to further characterize the molecular and cellular architecture of the sex-peptide response in Drosophila females. Results Screening for mutations that affect the sensitivity to sex-peptide, we identified the channel nuclear pore protein Nup54 gene as an essential component for mediating the sex-peptide response, with viable mutant alleles leading to the inability of laying eggs and reducing receptivity upon sex-peptide exposure. Nup54 directs correct wiring of eight adult brain neurons that express pickpocket and are required for egg-laying, while additional channel Nups also mediate sexual differentiation. Consistent with links of Nups to speciation, the Nup54 promoter is a hot spot for rapid evolution and promoter variants alter nucleo-cytoplasmic shuttling. Conclusions These results implicate nuclear pore functionality to neuronal wiring underlying the sex-peptide response and sexual differentiation as a response to sexual conflict arising from male-derived sex-peptide to direct the female post-mating response. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01154-6.
Collapse
Affiliation(s)
- Mohanakarthik P Nallasivan
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Department of Life Science, School of Health Sciences, Birmingham City University, Birmingham, B15 3TN, UK
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. .,Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
54
|
Wu S, Chen K, Xu T, Ma K, Gao L, Fu C, Zhang W, Jing C, Ren C, Deng M, Chen Y, Zhou Y, Pan W, Jia X. Tpr Deficiency Disrupts Erythroid Maturation With Impaired Chromatin Condensation in Zebrafish Embryogenesis. Front Cell Dev Biol 2021; 9:709923. [PMID: 34722501 PMCID: PMC8548687 DOI: 10.3389/fcell.2021.709923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Vertebrate erythropoiesis involves nuclear and chromatin condensation at the early stages of terminal differentiation, which is a unique process to distinguish mature erythrocytes from erythroblasts. However, the underlying mechanisms of chromatin condensation during erythrocyte maturation remain elusive. Here, we reported a novel zebrafish mutant cas7 with erythroid maturation deficiency. Positional cloning showed that a single base mutation in tprb gene, which encodes nucleoporin translocated promoter region (Tpr), is responsible for the disrupted erythroid maturation and upregulation of erythroid genes, including ae1-globin and be1-globin. Further investigation revealed that deficient erythropoiesis in tprb cas7 mutant was independent on HIF signaling pathway. The proportion of euchromatin was significantly increased, whereas the percentage of heterochromatin was markedly decreased in tprb cas7 mutant. In addition, TPR knockdown in human K562 cells also disrupted erythroid differentiation and dramatically elevated the expression of globin genes, which suggests that the functions of TPR in erythropoiesis are highly conserved in vertebrates. Taken together, this study revealed that Tpr played vital roles in chromatin condensation and gene regulation during erythroid maturation in vertebrates.
Collapse
Affiliation(s)
- Shuang Wu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Kai Chen
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Tao Xu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Central Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Ke Ma
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Lei Gao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Cong Fu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Wenjuan Zhang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Changbin Jing
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chunguang Ren
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Min Deng
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yi Chen
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhou
- Stem Cell Program, Hematology/Oncology Program at Children’s Hospital Boston, Harvard Medical School, Boston, MA, United States
| | - Weijun Pan
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoe Jia
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China
| |
Collapse
|
55
|
Lange J, Wood-Kaczmar A, Ali A, Farag S, Ghosh R, Parker J, Casey C, Uno Y, Kunugi A, Ferretti P, Andre R, Tabrizi SJ. Mislocalization of Nucleocytoplasmic Transport Proteins in Human Huntington's Disease PSC-Derived Striatal Neurons. Front Cell Neurosci 2021; 15:742763. [PMID: 34658796 PMCID: PMC8519404 DOI: 10.3389/fncel.2021.742763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene (HTT). Disease progression is characterized by the loss of vulnerable neuronal populations within the striatum. A consistent phenotype across HD models is disruption of nucleocytoplasmic transport and nuclear pore complex (NPC) function. Here we demonstrate that high content imaging is a suitable method for detecting mislocalization of lamin-B1, RAN and RANGAP1 in striatal neuronal cultures thus allowing a robust, unbiased, highly powered approach to assay nuclear pore deficits. Furthermore, nuclear pore deficits extended to the selectively vulnerable DARPP32 + subpopulation neurons, but not to astrocytes. Striatal neuron cultures are further affected by changes in gene and protein expression of RAN, RANGAP1 and lamin-B1. Lowering total HTT using HTT-targeted anti-sense oligonucleotides partially restored gene expression, as well as subtly reducing mislocalization of proteins involved in nucleocytoplasmic transport. This suggests that mislocalization of RAN, RANGAP1 and lamin-B1 cannot be normalized by simply reducing expression of CAG-expanded HTT in the absence of healthy HTT protein.
Collapse
Affiliation(s)
- Jenny Lange
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Alison Wood-Kaczmar
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Aneesa Ali
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Sahar Farag
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Rhia Ghosh
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jennifer Parker
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Caroline Casey
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Yumiko Uno
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Akiyoshi Kunugi
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Patrizia Ferretti
- Stem Cell and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ralph Andre
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Sarah J. Tabrizi
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- UK Dementia Research Institute, University College London, London, United Kingdom
| |
Collapse
|
56
|
Gao X, Yu S, Guan Y, Shen Y, Xu L. Nucleoporin 50 mediates Kcna4 transcription to regulate cardiac electrical activity. J Cell Sci 2021; 134:271877. [PMID: 34409458 DOI: 10.1242/jcs.256818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
Emerging evidence has demonstrated that nucleoporins (Nups) play a pivotal role in cell-type-specific gene regulation, but how they control the expression and activity of ion channel genes in the heart remains unclear. Here, we show that Nup50, which is localized in the nucleus of cardiomyocytes, selectively induces an increase in the transcription and translation of Kcna4. The Kcna4 gene encodes a K+ voltage-gated channel of shaker-related subfamily member 4 and is essential for regulating the action potential in cardiac membranes. Using immunofluorescence imaging, luciferase assays and chromatin immunoprecipitation assays, we identified that the direct binding of the FG-repeat domain within Nup50 to the proximity of the Kcna4 promoter was required to activate the transcription and subsequent translation of Kcna4. Functionally, Nup50 overexpression increased the currents of KCNA4-encoded Ito,s channels, and reverse knockdown of Nup50 resulted in a remarkable decrease in the amplitude of Ito,s currents in cardiomyocytes. Moreover, a positive correlation between Nup50 and Kcna4 mRNA and protein expression was observed in heart tissues subjected to ischemic insults. These findings provide insights into the homeostatic control of cardiac electrophysiology through Nup-mediated regulation.
Collapse
Affiliation(s)
- Xueting Gao
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Shuai Yu
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Yi Guan
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Yunli Shen
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China
| | - Liang Xu
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| |
Collapse
|
57
|
Wang E, Abdel-Wahab O. mRNA Export as a Novel Cancer-Specific Dependency. Cancer Discov 2021; 11:2129-2131. [PMID: 34479974 DOI: 10.1158/2159-8290.cd-21-0862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue, Malone and colleagues identified the nuclear mRNA export factor NXT1 as a novel genetic dependency in neuroblastoma as well as several additional pediatric cancers. These data highlight potential cell type-specific differences in the nuclear export machinery that may be exploited as cancer therapeutics.See related article by Malone et al., p. 2282.
Collapse
Affiliation(s)
- Eric Wang
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
58
|
Scoca V, Di Nunzio F. Membraneless organelles restructured and built by pandemic viruses: HIV-1 and SARS-CoV-2. J Mol Cell Biol 2021; 13:259-268. [PMID: 33760045 PMCID: PMC8083626 DOI: 10.1093/jmcb/mjab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Viruses hijack host functions to invade their target cells and spread to new cells. Specifically, viruses learned to usurp liquid‒liquid phase separation (LLPS), a newly exploited mechanism, used by the cell to concentrate enzymes to accelerate and confine a wide variety of cellular processes. LLPS gives rise to actual membraneless organelles (MLOs), which do not only increase reaction rates but also act as a filter to select molecules to be retained or to be excluded from the liquid droplet. This is exactly what seems to happen with the condensation of SARS-CoV-2 nucleocapsid protein to favor the packaging of intact viral genomes, excluding viral subgenomic or host cellular RNAs. Another older pandemic virus, HIV-1, also takes advantage of LLPS in the host cell during the viral cycle. Recent discoveries highlighted that HIV-1 RNA genome condensates in nuclear MLOs accompanied by specific host and viral proteins, breaking the dogma of retroviruses that limited viral synthesis exclusively to the cytoplasmic compartment. Intriguing fundamental properties of viral/host LLPS remain still unclear. Future studies will contribute to deeply understanding the role of pathogen-induced MLOs in the epidemic invasion of pandemic viruses.
Collapse
Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology, Pasteur Institute, Paris, France
- BioSPC Doctoral School, Universitè de Paris, Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology, Pasteur Institute, Paris, France
| |
Collapse
|
59
|
Coyne AN, Baskerville V, Zaepfel BL, Dickson DW, Rigo F, Bennett F, Lusk CP, Rothstein JD. Nuclear accumulation of CHMP7 initiates nuclear pore complex injury and subsequent TDP-43 dysfunction in sporadic and familial ALS. Sci Transl Med 2021; 13:eabe1923. [PMID: 34321318 PMCID: PMC9022198 DOI: 10.1126/scitranslmed.abe1923] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/02/2021] [Accepted: 06/09/2021] [Indexed: 01/29/2023]
Abstract
Alterations in the components [nucleoporins (Nups)] and function of the nuclear pore complex (NPC) have been implicated as contributors to the pathogenesis of genetic forms of neurodegeneration including C9orf72 amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). We hypothesized that Nup alterations and the consequential loss of NPC function may lie upstream of TDP-43 dysfunction and mislocalization widely observed in ALS, FTD, and related neurodegenerative diseases. Here, we provide evidence that CHMP7, a critical mediator of NPC quality control, is increased in nuclei of C9orf72 and sporadic ALS induced pluripotent stem cell (iPSC)-derived spinal neurons (iPSNs) and postmortem human motor cortex before the emergence of Nup alterations. Inhibiting the nuclear export of CHMP7 triggered Nup reduction and TDP-43 dysfunction and pathology in human neurons. Knockdown of CHMP7 alleviated disease-associated Nup alterations, deficits in Ran GTPase localization, defects in TDP-43-associated mRNA expression, and downstream glutamate-induced neuronal death. Thus, our data support a role for altered CHMP7-mediated Nup homeostasis as a prominent initiating pathological mechanism for familial and sporadic ALS and highlight the potential for CHMP7 as therapeutic target.
Collapse
Affiliation(s)
- Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Victoria Baskerville
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin L Zaepfel
- Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
60
|
Kwon H, Kim J, Jho EH. Role of the Hippo pathway and mechanisms for controlling cellular localization of YAP/TAZ. FEBS J 2021; 289:5798-5818. [PMID: 34173335 DOI: 10.1111/febs.16091] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/05/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022]
Abstract
The Hippo pathway is a crucial signaling mechanism that inhibits the growth of cells and organs during development and in disease. When the Hippo pathway is activated, YAP/TAZ transcriptional coactivators are phosphorylated by upstream kinases, preventing nuclear localization of YAP/TAZ. However, when the Hippo pathway is inhibited, YAP/TAZ localize mainly in the nucleus and induce the expression of target genes related to cell proliferation. Abnormal proliferation of cells is one of the hallmarks of cancer initiation, and activation of Hippo pathway dampens such cell proliferation. Various types of diseases including cancer can occur due to the dysregulation of the Hippo pathway. Therefore, a better understanding of the Hippo pathway signaling mechanisms, and in particular how YAP/TAZ exist in the nucleus, may lead to the identification of new therapeutic targets for treating cancer and other diseases. In this review, we summarize the overall Hippo pathway and discuss mechanisms related to nuclear localization of YAP/TAZ.
Collapse
Affiliation(s)
- Hyeryun Kwon
- Department of Life Science, University of Seoul, Korea
| | - Jiyoung Kim
- Department of Life Science, University of Seoul, Korea
| | - Eek-Hoon Jho
- Department of Life Science, University of Seoul, Korea
| |
Collapse
|
61
|
The human nucleoporin Tpr protects cells from RNA-mediated replication stress. Nat Commun 2021; 12:3937. [PMID: 34168151 PMCID: PMC8225803 DOI: 10.1038/s41467-021-24224-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/04/2021] [Indexed: 12/24/2022] Open
Abstract
Although human nucleoporin Tpr is frequently deregulated in cancer, its roles are poorly understood. Here we show that Tpr depletion generates transcription-dependent replication stress, DNA breaks, and genomic instability. DNA fiber assays and electron microscopy visualization of replication intermediates show that Tpr deficient cells exhibit slow and asymmetric replication forks under replication stress. Tpr deficiency evokes enhanced levels of DNA-RNA hybrids. Additionally, complementary proteomic strategies identify a network of Tpr-interacting proteins mediating RNA processing, such as MATR3 and SUGP2, and functional experiments confirm that their depletion trigger cellular phenotypes shared with Tpr deficiency. Mechanistic studies reveal the interplay of Tpr with GANP, a component of the TREX-2 complex. The Tpr-GANP interaction is supported by their shared protein level alterations in a cohort of ovarian carcinomas. Our results reveal links between nucleoporins, DNA transcription and replication, and the existence of a network physically connecting replication forks with transcription, splicing, and mRNA export machinery.
Collapse
|
62
|
Yoshizawa T, Guo L. Karyopherin-βs play a key role as a phase separation regulator. J Biochem 2021; 170:15-23. [PMID: 34223614 DOI: 10.1093/jb/mvab072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
Recent studies have revealed that cells utilize liquid-liquid phase separation (LLPS) as a mechanism in assembly of membrane-less organelles, such as RNP granules. The nucleus is a well-known membrane-bound organelle surrounded by the nuclear envelope; the nuclear pore complex on the nuclear envelope likely applies LLPS in the central channel to facilitate selective biological macromolecule exchange. Karyopherin-β family proteins exclusively pass through the central channel with cargos by dissolving the phase separated hydrogel formed by the phenylalanine-glycine (FG) repeats-containing nucleoporins. Karyopherin-βs also exhibit dissolution activity for the phase separation of cargo proteins. Many cargos, including RNA-binding proteins containing intrinsically disordered regions (IDRs), undergo phase separation; however, aberrant phase separation is linked to fatal neurodegenerative diseases. Multiple weak interactions between karyopherin-βs and phase separation-prone proteins, such as FG repeats-containing nucleoporins or IDR-containing karyopherin-β cargos, are likely to be important for passing through the nuclear pore complex and maintaining the soluble state of cargo, respectively. In this review, we discuss how karyopherin-βs regulate phase separation to function.
Collapse
Affiliation(s)
- Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu-shi, Shiga 525-8577, Japan
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA 19107, USA
| |
Collapse
|
63
|
Amemiya S. Nanoelectrochemical Study of Molecular Transport through the Nuclear Pore Complex. CHEM REC 2021; 21:1430-1441. [PMID: 33502100 PMCID: PMC8217113 DOI: 10.1002/tcr.202000175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 11/10/2022]
Abstract
The nuclear pore complex (NPC) is the proteinaceous nanopore that solely mediates the transport of both small molecules and macromolecules between the nucleus and cytoplasm of a eukaryotic cell to regulate gene expression. In this personal account, we introduce recent progress in our nanoelectrochemical study of molecular transport through the NPC. Our work represents the importance of chemistry in understanding and controlling of NPC-mediated molecular transport to enable the efficient and safe delivery of genetic therapeutics into the nucleus, thereby fundamentally contributing to human health. Specifically, we employ nanoscale scanning electrochemical microscopy to test our hypothesis that the nanopore of the NPC is divided by transport barriers concentrically into peripheral and central routes to efficiently mediate the bimodal traffic of protein transport and RNA export, respectively, through cooperative hydrophobic and electrostatic interactions.
Collapse
Affiliation(s)
- Shigeru Amemiya
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, 15260, PA
| |
Collapse
|
64
|
Havrdová M, Urbančič I, Bartoň Tománková K, Malina L, Štrancar J, Bourlinos AB. Self-Targeting of Carbon Dots into the Cell Nucleus: Diverse Mechanisms of Toxicity in NIH/3T3 and L929 Cells. Int J Mol Sci 2021; 22:ijms22115608. [PMID: 34070594 PMCID: PMC8198156 DOI: 10.3390/ijms22115608] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
It is important to understand the nanomaterials intracellular trafficking and distribution and investigate their targeting into the nuclear area in the living cells. In our previous study, we firstly observed penetration of nonmodified positively charged carbon dots decorated with quaternary ammonium groups (QCDs) into the nucleus of mouse NIH/3T3 fibroblasts. Thus, in this work, we focused on deeper study of QCDs distribution inside two healthy mouse NIH/3T3 and L929 cell lines by fluorescence microspectroscopy and performed a comprehensive cytotoxic and DNA damage measurements. Real-time penetration of QCDs across the plasma cell membrane was recorded, concentration dependent uptake was determined and endocytic pathways were characterized. We found out that the QCDs concentration of 200 µg/mL is close to saturation and subsequently, NIH/3T3 had a different cell cycle profile, however, no significant changes in viability (not even in the case with QCDs in the nuclei) and DNA damage. In the case of L929, the presence of QCDs in the nucleus evoked a cellular death. Intranuclear environment of NIH/3T3 cells affected fluorescent properties of QCDs and evoked fluorescence blue shifts. Studying the intracellular interactions with CDs is essential for development of future applications such as DNA sensing, because CDs as DNA probes have not yet been developed.
Collapse
Affiliation(s)
- Markéta Havrdová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Correspondence: ; Tel.: +420-58-563-4384
| | - Iztok Urbančič
- Laboratory of Biophysics, Condensed Matter Physics Department, “Jozef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia; (I.U.); (J.Š.)
| | - Kateřina Bartoň Tománková
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Institute of Translation Medicine, Palacký University in Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic; (K.B.T.); (L.M.)
| | - Lukáš Malina
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Institute of Translation Medicine, Palacký University in Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic; (K.B.T.); (L.M.)
| | - Janez Štrancar
- Laboratory of Biophysics, Condensed Matter Physics Department, “Jozef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia; (I.U.); (J.Š.)
| | | |
Collapse
|
65
|
Bensidoun P, Zenklusen D, Oeffinger M. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1660. [PMID: 33938148 DOI: 10.1002/wrna.1660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Pierre Bensidoun
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada
| | - Marlene Oeffinger
- Systems Biology, Institut de Recherches Cliniques de Montréal, Montréal, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de médecine, Université de Montréal, Montréal, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Canada
| |
Collapse
|
66
|
Liang Y, Song C, Liu M, Gong P, Zhou C, Knöpfel T. Cortex-Wide Dynamics of Intrinsic Electrical Activities: Propagating Waves and Their Interactions. J Neurosci 2021; 41:3665-3678. [PMID: 33727333 PMCID: PMC8055070 DOI: 10.1523/jneurosci.0623-20.2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Cortical circuits generate patterned activities that reflect intrinsic brain dynamics that lay the foundation for any, including stimuli-evoked, cognition and behavior. However, the spatiotemporal organization properties and principles of this intrinsic activity have only been partially elucidated because of previous poor resolution of experimental data and limited analysis methods. Here we investigated continuous wave patterns in the 0.5-4 Hz (delta band) frequency range on data from high-spatiotemporal resolution optical voltage imaging of the upper cortical layers in anesthetized mice. Waves of population activities propagate in heterogeneous directions to coordinate neuronal activities between different brain regions. The complex wave patterns show characteristics of both stereotypy and variety. The location and type of wave patterns determine the dynamical evolution when different waves interact with each other. Local wave patterns of source, sink, or saddle emerge at preferred spatial locations. Specifically, "source" patterns are predominantly found in cortical regions with low multimodal hierarchy such as the primary somatosensory cortex. Our findings reveal principles that govern the spatiotemporal dynamics of spontaneous cortical activities and associate them with the structural architecture across the cortex.SIGNIFICANCE STATEMENT Intrinsic brain activities, as opposed to external stimulus-evoked responses, have increasingly gained attention, but it remains unclear how these intrinsic activities are spatiotemporally organized at the cortex-wide scale. By taking advantage of the high spatiotemporal resolution of optical voltage imaging, we identified five wave pattern types, and revealed the organization properties of different wave patterns and the dynamical mechanisms when they interact with each other. Moreover, we found a relationship between the emergence probability of local wave patterns and the multimodal structure hierarchy across cortical areas. Our findings reveal the principles of spatiotemporal wave dynamics of spontaneous activities and associate them with the underlying hierarchical architecture across the cortex.
Collapse
Affiliation(s)
- Yuqi Liang
- Department of Physics, Centre for Nonlinear Studies and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, People's Republic of China
- The HKBU Institute of Research and Continuing Education, Shenzhen 518000, People's Republic of China
| | - Chenchen Song
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mianxin Liu
- Department of Physics, Centre for Nonlinear Studies and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, People's Republic of China
- School of Biomedical Engineering, Shanghai Tech University, Shanghai 201210, People's Republic of China
| | - Pulin Gong
- School of Physics, University of Sydney, Sydney 2006, New South Wales, Australia
- Australian Research Council Centre of Excellence for Integrative Brain Function, University of Sydney, Sydney 2001, New South Wales, Australia
| | - Changsong Zhou
- Department of Physics, Centre for Nonlinear Studies and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, People's Republic of China
- The HKBU Institute of Research and Continuing Education, Shenzhen 518000, People's Republic of China
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China
- Beijing Computational Science Research Center, Beijing 100193, People's Republic of China
| | - Thomas Knöpfel
- Laboratory for Neuronal Circuit Dynamics, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
67
|
Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol 2021; 23:116-126. [PMID: 33558730 DOI: 10.1038/s41556-020-00630-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Alterations in nuclear shape are present in human diseases and ageing. A compromised nuclear lamina is molecularly interlinked to altered chromatin functions and genomic instability. Whether these alterations are a cause or a consequence of the pathological state are important questions in biology. Here, we summarize the roles of nuclear envelope components in chromatin organization, phase separation and transcriptional and epigenetic regulation. Examining these functions in healthy backgrounds will guide us towards a better understanding of pathological alterations.
Collapse
Affiliation(s)
- Adam Karoutas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Francis Crick Institute, London, UK
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| |
Collapse
|
68
|
Smeltzer S, Quadri Z, Miller A, Zamudio F, Hunter J, Stewart NJF, Saji S, Lee DC, Chaput D, Selenica MLB. Hypusination of Eif5a regulates cytoplasmic TDP-43 aggregation and accumulation in a stress-induced cellular model. Biochim Biophys Acta Mol Basis Dis 2021; 1867:165939. [PMID: 32882370 DOI: 10.1016/j.bbadis.2020.165939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/17/2020] [Indexed: 11/23/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is a nuclear RNA/DNA binding protein involved in mRNA metabolism. Aberrant mislocalization to the cytoplasm and formation of phosphorylated/aggregated TDP-43 inclusions remains the hallmark pathology in a spectrum of neurodegenerative diseases, including frontotemporal disorders and Alzheimer's disease. Eukaryotic Translation Initiation Factor 5A undergoes a unique post-translation modification of lysine to hypusine (K50), which determines eIF5A binding partners. We used a sodium arsenite-induced cellular stress model to investigate the role of hypusinated eIF5A (eIF5AHypK50) in governing TDP-43 cytoplasmic mislocalization and accumulation in stress granule. Our proteomics and functional data provide evidence that eIF5A interacts with TDP-43 in a hypusine-dependent manner. Additionally, we showed that following stress TDP-43 interactions with eIF5AHypK50 were induced both in the cytoplasm and stress granules. Pharmacological reduction of hypusination or mutations of lysine residues within the hypusine loop decreased phosphorylated and insoluble TDP-43 levels. The proteomic and biochemical analysis also identified nuclear pore complex importins KPNA1/2, KPNB1, and RanGTP as interacting partners of eIF5AHypK50. These findings are the first to provide a novel pathway and potential therapeutic targets that require further investigation in models of TDP-43 proteinopathies.
Collapse
Affiliation(s)
- Shayna Smeltzer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Zainuddin Quadri
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA; Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY, USA
| | - Abraian Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Frank Zamudio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Jordan Hunter
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Nicholas J F Stewart
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Sheba Saji
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Daniel C Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA; Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY, USA
| | - Dale Chaput
- Proteomics and Mass Spectrometry Core Facility, Florida Center of Excellence for Drug Discovery and Innovation (CDDI), University of South Florida, 3720 Spectrum Blvd, Suite 303, Tampa, FL 33612, USA
| | - Maj-Linda B Selenica
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA; Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY, USA.
| |
Collapse
|
69
|
Schuller AP, Wojtynek M, Mankus D, Tatli M, Kronenberg-Tenga R, Regmi SG, Dip PV, Lytton-Jean AKR, Brignole EJ, Dasso M, Weis K, Medalia O, Schwartz TU. The cellular environment shapes the nuclear pore complex architecture. Nature 2021; 598:667-671. [PMID: 34646014 PMCID: PMC8550940 DOI: 10.1038/s41586-021-03985-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/01/2021] [Indexed: 12/04/2022]
Abstract
Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE)1-3. These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel4-6. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.
Collapse
Affiliation(s)
- Anthony P. Schuller
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Matthias Wojtynek
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland ,grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - David Mankus
- grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Meltem Tatli
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Rafael Kronenberg-Tenga
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Saroj G. Regmi
- grid.94365.3d0000 0001 2297 5165Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD USA
| | - Phat V. Dip
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786MIT.nano, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Abigail K. R. Lytton-Jean
- grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Edward J. Brignole
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786MIT.nano, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Mary Dasso
- grid.94365.3d0000 0001 2297 5165Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD USA
| | - Karsten Weis
- grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ohad Medalia
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Thomas U. Schwartz
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| |
Collapse
|
70
|
Abstract
Nuclear pore complexes are multiprotein channels that span the nuclear envelope, which connects the nucleus to the cytoplasm. In addition to their main role in the regulation of nucleocytoplasmic molecule exchange, it has become evident that nuclear pore complexes and their components also have multiple transport-independent functions. In recent years, an increasing number of studies have reported the involvement of nuclear pore complex components in embryogenesis, cell differentiation and tissue-specific processes. Here, we review the findings that highlight the dynamic nature of nuclear pore complexes and their roles in many cell type-specific functions during development and tissue homeostasis.
Collapse
Affiliation(s)
- Valeria Guglielmi
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Maximiliano A D'Angelo
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| |
Collapse
|
71
|
Hong SH, Son KH, Ha SY, Wee TI, Choi SK, Won JE, Han HD, Ro Y, Park YM, Eun JW, Nam SW, Han JW, Kang K, You JS. Nucleoporin 210 Serves a Key Scaffold for SMARCB1 in Liver Cancer. Cancer Res 2020; 81:356-370. [PMID: 33239431 DOI: 10.1158/0008-5472.can-20-0568] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022]
Abstract
The roles of chromatin remodelers and their underlying mechanisms of action in cancer remain unclear. In this study, SMARCB1, known initially as a bona fide tumor suppressor gene, was investigated in liver cancer. SMARCB1 was highly upregulated in patients with liver cancer and was associated with poor prognosis. Loss- and gain-of-function studies in liver cells revealed that SMARCB1 loss led to reduced cell proliferation, wound healing capacity, and tumor growth in vivo. Although upregulated SMARCB1 appeared to contribute to switch/sucrose nonfermentable (SWI/SNF) complex stability and integrity, it did not act using its known pathways antagonism with EZH2 or association between TP53 or AMPK. SMARCB1 knockdown induced a mild reduction in global H3K27 acetylation, and chromatin immunoprecipitation sequencing of SMARCB1 and acetylated histone H3K27 antibodies before and after SMARCB1 loss identified Nucleoporin210 (NUP210) as a critical target of SMARCB1, which bound its enhancer and changed H3K27Ac enrichment and downstream gene expression, particularly cholesterol homeostasis and xenobiotic metabolism. Notably, NUP210 was not only a putative tumor supporter involved in liver cancer but also acted as a key scaffold for SMARCB1 and P300 to chromatin. Furthermore, SMARCB1 deficiency conferred sensitivity to doxorubicin and P300 inhibitor in liver cancer cells. These findings provide insights into mechanisms underlying dysregulation of chromatin remodelers and show novel associations between nucleoporins and chromatin remodelers in cancer. SIGNIFICANCE: This study reveals a novel protumorigenic role for SMARCB1 and describes valuable links between nucleoporins and chromatin remodelers in cancer by identifying NUP210 as a critical coregulator of SMARCB1 chromatin remodeling activity.
Collapse
Affiliation(s)
| | - Keun Hong Son
- College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae In Wee
- School of Medicine, Konkuk University, Seoul, Korea
| | | | - Ji Eun Won
- School of Medicine, Konkuk University, Seoul, Korea
| | - Hee Dong Han
- School of Medicine, Konkuk University, Seoul, Korea
| | - Youngtae Ro
- School of Medicine, Konkuk University, Seoul, Korea
| | | | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Suk Woo Nam
- Department of Pathology, College of Medicine, Catholic University, Seoul, Korea
| | - Jeung-Whan Han
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, Korea
| | - Keunsoo Kang
- College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Jueng Soo You
- School of Medicine, Konkuk University, Seoul, Korea.
- Research Institute of Medical Science, Konkuk University, Seoul, Korea
| |
Collapse
|
72
|
Coyne AN, Zaepfel BL, Hayes L, Fitchman B, Salzberg Y, Luo EC, Bowen K, Trost H, Aigner S, Rigo F, Yeo GW, Harel A, Svendsen CN, Sareen D, Rothstein JD. G 4C 2 Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD. Neuron 2020; 107:1124-1140.e11. [PMID: 32673563 PMCID: PMC8077944 DOI: 10.1016/j.neuron.2020.06.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 03/06/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023]
Abstract
Through mechanisms that remain poorly defined, defects in nucleocytoplasmic transport and accumulations of specific nuclear-pore-complex-associated proteins have been reported in multiple neurodegenerative diseases, including C9orf72 Amyotrophic Lateral Sclerosis and Frontotemporal Dementia (ALS/FTD). Using super-resolution structured illumination microscopy, we have explored the mechanism by which nucleoporins are altered in nuclei isolated from C9orf72 induced pluripotent stem-cell-derived neurons (iPSNs). Of the 23 nucleoporins evaluated, we observed a reduction in a subset of 8, including key components of the nuclear pore complex scaffold and the transmembrane nucleoporin POM121. Reduction in POM121 appears to initiate a decrease in the expression of seven additional nucleoporins, ultimately affecting the localization of Ran GTPase and subsequent cellular toxicity in C9orf72 iPSNs. Collectively, our data suggest that the expression of expanded C9orf72 ALS/FTD repeat RNA alone affects nuclear POM121 expression in the initiation of a pathological cascade affecting nucleoporin levels within neuronal nuclei and ultimately downstream neuronal survival.
Collapse
Affiliation(s)
- Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin L Zaepfel
- Biochemistry, Cellular, and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lindsey Hayes
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Boris Fitchman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Yuval Salzberg
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - En-Ching Luo
- Bioengineering Graduate Program, University of California San Diego College of Engineering, La Jolla, CA 92037, USA
| | - Kelly Bowen
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hannah Trost
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stefan Aigner
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Gene W Yeo
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA 92037, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
73
|
Tamura K. Nuclear pore complex-mediated gene expression in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2020; 133:449-455. [PMID: 32170459 DOI: 10.1007/s10265-020-01177-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/08/2020] [Indexed: 05/20/2023]
Abstract
Nuclear pore complexes (NPCs) are large multi-protein complexes that control bidirectional trafficking of macromolecules between the nucleus and cytoplasm. This trafficking is highly regulated and participates in a considerably broader range of cellular activities, including defense responses against pathogens in plants. Recently, NPC is emerging as a platform to physically associate the underlying chromatin with the nuclear periphery, thus regulating chromatin structure and gene expression. For instance, NPC components have been shown to promote the formation of specific genomics loops, which is linked to transcriptional memory for rapid reactivation of genes. With newly developed techniques and tools, our insight in this area has been substantially advanced. This review summarizes recent works on the molecular function of NPC machinery as hubs for transcriptional regulation and compares systems between plant and non-plant organisms.
Collapse
Affiliation(s)
- Kentaro Tamura
- Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| |
Collapse
|
74
|
Zhang A, Wang S, Kim J, Yan J, Yan X, Pang Q, Hua J. Nuclear pore complex components have temperature-influenced roles in plant growth and immunity. PLANT, CELL & ENVIRONMENT 2020; 43:1452-1466. [PMID: 32022936 DOI: 10.1111/pce.13741] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/19/2020] [Accepted: 02/01/2020] [Indexed: 05/28/2023]
Abstract
Nuclear pore complexes (NPCs) are main channels controlling nucleocytoplasmic transport and are composed of approximately 30 nucleoporins (NUPs). Emerging evidence suggests that some NUP genes have specialized functions that challenge the traditional view of NPCs as structures of uniform composition. Here, we analysed the role of six outer-ring components of NPC at normal and warm growth temperatures by examining their loss-of-function mutants in Arabidopsis thaliana. All six NUP subunits, NUP85, NUP96, NUP 133, NUP 160, SEH1 and HOS1, have a non-redundant temperature-influenced function in one or more of the processes, including rosette growth, leaf architecture and intracellular immune receptor-mediated disease resistance. At the molecular level, NUP85 and NUP133 are required for mRNA export only at warm temperature and play a larger role in the localization of transcription factor at warm temperature. In addition, NUP96 and HOS1 are essential for the expression of high temperature-responsive genes, which is correlated with their larger activity in facilitating nuclear accumulation of the transcription factor PIF4 at warm temperature. Our results show that subunits of NPC have differential roles at different temperatures, suggesting the existence of temperature-influenced NPC complexes and activities.
Collapse
Affiliation(s)
- Aiqin Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| | - Shuai Wang
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Jitae Kim
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| | - Jiapei Yan
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| | - Xiufeng Yan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Jian Hua
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, New York
| |
Collapse
|
75
|
Abstract
The Hippo pathway plays a pivotal role in tissue homeostasis and tumor suppression. YAP and TAZ are downstream effectors of the Hippo pathway, and their activities are tightly suppressed by phosphorylation-dependent cytoplasmic retention. However, the molecular mechanisms governing YAP/TAZ nuclear localization have not been fully elucidated. Here, we report that Mastermind-like 1 and 2 (MAML1/2) are indispensable for YAP/TAZ nuclear localization and transcriptional activities. Ectopic expression or depletion of MAML1/2 induces nuclear translocation or cytoplasmic retention of YAP/TAZ, respectively. Additionally, mutation of the MAML nuclear localization signal, as well as its YAP/TAZ interacting region, both abolish nuclear localization and transcriptional activity of YAP/TAZ. Importantly, we demonstrate that the level of MAML1 messenger RNA (mRNA) is regulated by microRNA-30c (miR-30c) in a cell-density-dependent manner. In vivo and clinical results suggest that MAML potentiates YAP/TAZ oncogenic function and positively correlates with YAP/TAZ activation in human cancer patients, suggesting pathological relevance in the context of cancer development. Overall, our study not only provides mechanistic insight into the regulation of YAP/TAZ subcellular localization, but it also strongly suggests that the miR30c-MAML-YAP/TAZ axis is a potential therapeutic target for developing novel cancer treatments.
Collapse
|
76
|
Bishop PJ, Kinoshita Y, Lopes NN, Ward AS, Kohtz DS. Changes in Nup62 content affect contact-induced differentiation of cultured myoblasts. Differentiation 2020; 114:27-35. [PMID: 32554220 DOI: 10.1016/j.diff.2020.05.001] [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: 10/01/2019] [Revised: 03/21/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Differentiation of cultured skeletal myoblasts is induced by extrinsic signals that include reduction in ambient mitogen concentration and increased cell density. Using an established murine myoblast cell line (C2C12), we have found that experimental reduction of the nucleoporin p62 (Nup62) content of myoblasts enhances differentiation in high-mitogen medium, while forced expression of Nup62 inhibits density-induced differentiation. In contrast, differentiation of myoblasts induced by low-mitogen medium was unaffected by ectopic Nup62 expression. Further analyses suggested that Nup62 content affects density-induced myoblast differentiation through a mechanism involving activation of p38 MAP kinase. Nuclear pore complex (NPC) composition, in particular changes in NUP62 content, may be altered during viral infection, differentiation, and in neoplastic growth. The results support a functional role for changes in Nup62 composition in NPCs and density-induced myogenic differentiation, and suggest a link between loss of Nup62 content and induction of an intracellular stress signaling pathways.
Collapse
Affiliation(s)
- Patrick J Bishop
- Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, 48859, USA.
| | - Yayoi Kinoshita
- Department of Pathology, Icahn School of Medicine, One Gustave Levy Place, New York, NY, 10029, USA.
| | - N Natalie Lopes
- Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, 48859, USA.
| | - Avery S Ward
- Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, 48859, USA.
| | - D Stave Kohtz
- Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, 48859, USA.
| |
Collapse
|
77
|
Fernandez J, Arhel NJ. [Transportin-1 orchestrates HIV-1 uncoating and nuclear entry]. Med Sci (Paris) 2020; 36:203-206. [PMID: 32228833 DOI: 10.1051/medsci/2020031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Juliette Fernandez
- Institut de recherche en infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| | - Nathalie J Arhel
- Institut de recherche en infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, 1919 route de Mende, 34293 Montpellier, France
| |
Collapse
|
78
|
Zou R, Xu Y, Feng Y, Shen M, Yuan F, Yuan Y. YAP nuclear‐cytoplasmic translocation is regulated by mechanical signaling, protein modification, and metabolism. Cell Biol Int 2020; 44:1416-1425. [DOI: 10.1002/cbin.11345] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/12/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Rong Zou
- Department of Ophthalmology, Zhongshan HospitalFudan University 180# Fenglin Road 200032 Shanghai China
| | - Yahui Xu
- Department of Ophthalmology, Zhongshan HospitalFudan University 180# Fenglin Road 200032 Shanghai China
| | - Yifan Feng
- Department of Ophthalmology, Zhongshan HospitalFudan University 180# Fenglin Road 200032 Shanghai China
| | - Minqian Shen
- Department of Ophthalmology, Zhongshan HospitalFudan University 180# Fenglin Road 200032 Shanghai China
| | - Fei Yuan
- Department of Ophthalmology, Zhongshan HospitalFudan University 180# Fenglin Road 200032 Shanghai China
| | - Yuanzhi Yuan
- Department of Ophthalmology, Zhongshan HospitalFudan University 180# Fenglin Road 200032 Shanghai China
| |
Collapse
|
79
|
Masaki K, Sonobe Y, Ghadge G, Pytel P, Lépine P, Pernin F, Cui QL, Antel JP, Zandee S, Prat A, Roos RP. RNA-binding protein altered expression and mislocalization in MS. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2020; 7:7/3/e704. [PMID: 32217641 PMCID: PMC7176246 DOI: 10.1212/nxi.0000000000000704] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Objective To determine whether there are nuclear depletion and cellular mislocalization of RNA-binding proteins (RBPs) transactivation response DNA-binding protein of 43 kDa (TDP-43), fused in sarcoma (FUS), and polypyrimidine tract–binding protein (PTB) in MS, as is the case in amyotrophic lateral sclerosis (ALS) and oligodendrocytes infected with Theiler murine encephalomyelitis virus (TMEV), we examined MS lesions and in vitro cultured primary human brain–derived oligodendrocytes. Methods Nuclear depletion and mislocalization of TDP-43, FUS, and PTB are thought to contribute to the pathogenesis of ALS and TMEV demyelination. The latter findings prompted us to investigate these RBPs in the demyelinated lesions of MS and in in vitro cultured human brain–derived oligodendrocytes under metabolic stress conditions. Results We found (1) mislocalized TDP-43 in oligodendrocytes in active lesions in some patients with MS; (2) decreased PTB1 expression in oligodendrocytes in mixed active/inactive demyelinating lesions; (3) decreased nuclear expression of PTB2 in neurons in cortical demyelinating lesions; and (4) nuclear depletion of TDP-43 in oligodendrocytes under metabolic stress induced by low glucose/low nutrient conditions compared with optimal culture conditions. Conclusion TDP-43 has been found to have a key role in oligodendrocyte function and viability, whereas PTB is important in neuronal differentiation, suggesting that altered expression and mislocalization of these RBPs in MS lesions may contribute to the pathogenesis of demyelination and neurodegeneration. Our findings also identify nucleocytoplasmic transport as a target for treatment.
Collapse
Affiliation(s)
- Katsuhisa Masaki
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Yoshifumi Sonobe
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Ghanashyam Ghadge
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Peter Pytel
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Paula Lépine
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Florian Pernin
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Qiao-Ling Cui
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Jack P Antel
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Stephanie Zandee
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Alexandre Prat
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada
| | - Raymond P Roos
- From the Department of Neurology (K.M., Y.S., G.G., R.P.R.) and Department of Pathology (P.P.), University of Chicago Medical Center, IL; Neuroimmunology Research Laboratory (P.L., S.Z., A.P.), Centre du Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), QC, Canada; and Neuroimmunology Unit (F.P., Q.-L.C., J.P.A.), Montreal Neurological Institute, McGill University, QC, Canada.
| |
Collapse
|
80
|
Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell 2020; 177:1384-1403. [PMID: 31150619 DOI: 10.1016/j.cell.2019.05.016] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field.
Collapse
Affiliation(s)
- Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
81
|
Dewi FRP, Jiapaer S, Kobayashi A, Hazawa M, Ikliptikawati DK, Hartono, Sabit H, Nakada M, Wong RW. Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma. Autophagy 2020; 17:1001-1012. [PMID: 32207633 PMCID: PMC8078762 DOI: 10.1080/15548627.2020.1741318] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Children with ependymoma have high mortality rates because ependymoma is resistant to conventional therapy. Genomic and transcriptomic studies have identified potential targets as significantly altered genes in ependymoma patients. Although several candidate oncogenes in ependymoma were recently reported, the detailed mechanisms for the roles of these candidate oncogenes in ependymoma progression remain unclear. Here, we report an oncogenic role of the nucleoporin TPR (translocated promoter region, nuclear basket protein) in regulating HSF1 (heat shock transcription factor 1) mRNA trafficking, maintaining MTORC1 activity to phosphorylate ULK1, and preventing macroautophagy/autophagy induction in ependymoma. High expression of TPR were associated with increased HSF1 and HSPA/HSP70 expression in ependymoma patients. In an ependymoma mouse xenograft model, MTOR inhibition by rapamycin therapeutically suppressed TPR expression and reduced tumor size in vivo. Together, these results suggest that TPR may act as a biomarker for ependymoma, and pharmacological interventions targeting TPR-HSF1-MTOR may have therapeutic potential for ependymoma treatment. Abbreviations: ATG: autophagy related; BECN1: beclin 1; BSA: bovine serum albumin; CQ: chloroquine; DMSO: dimethyl sulfoxide; GEO: gene expression omnibus; GFP: green fluorescence protein; HSF1: heat shock transcription factor 1; HSPA/HSP70: heat shock protein family A (Hsp70); LMNB1: lamin B1; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; MAPK8/JNK: mitogen-activated protein kinase 8; MTORC1: mechanistic target of rapamycin kinase complex 1; NPC: nuclear pore complex; NUP: nucleoporin; PBS: phosphate-buffered saline; q-PCR: quantitative real time PCR; SDS: sodium dodecyl sulfate; SQSTM1: sequestosome 1; STED: stimulated emission depletion microscopy; STX17: syntaxin 17; TCGA: the cancer genome atlas; TPR: translocated promoter region, nuclear basket protein; ULK1: unc-51 like autophagy activating kinase 1.
Collapse
Affiliation(s)
- Firli Rahmah Primula Dewi
- WPI Nano Life Science Institute (WPI-nanoLSI) & Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Shabierjiang Jiapaer
- Department of Neurosurgery, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Akiko Kobayashi
- WPI Nano Life Science Institute (WPI-nanoLSI) & Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Masaharu Hazawa
- WPI Nano Life Science Institute (WPI-nanoLSI) & Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Dini Kurnia Ikliptikawati
- WPI Nano Life Science Institute (WPI-nanoLSI) & Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Hartono
- WPI Nano Life Science Institute (WPI-nanoLSI) & Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Hemragul Sabit
- Department of Neurosurgery, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Richard W Wong
- WPI Nano Life Science Institute (WPI-nanoLSI) & Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
82
|
Burdine RD, Preston CC, Leonard RJ, Bradley TA, Faustino RS. Nucleoporins in cardiovascular disease. J Mol Cell Cardiol 2020; 141:43-52. [PMID: 32209327 DOI: 10.1016/j.yjmcc.2020.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/01/2023]
Abstract
Cardiovascular disease is a pressing health problem with significant global health, societal, and financial burdens. Understanding the molecular basis of polygenic cardiac pathology is thus essential to devising novel approaches for management and treatment. Recent identification of uncharacterized regulatory functions for a class of nuclear envelope proteins called nucleoporins offers the opportunity to understand novel putative mechanisms of cardiac disease development and progression. Consistent reports of nucleoporin deregulation associated with ischemic and dilated cardiomyopathies, arrhythmias and valvular disorders suggests that nucleoporin impairment may be a significant but understudied variable in cardiopathologic disorders. This review discusses and converges existing literature regarding nuclear pore complex proteins and their association with cardiac pathologies, and proposes a role for nucleoporins as facilitators of cardiac disease.
Collapse
Affiliation(s)
- Ryan D Burdine
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; School of Health Sciences, University of South Dakota, 414 E Clark St, Vermillion, SD 57069, United States of America
| | - Claudia C Preston
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Riley J Leonard
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Tyler A Bradley
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America
| | - Randolph S Faustino
- Genetics and Genomics Group, Sanford Research, 2301 E. 60(th) Street N., Sioux Falls, SD 57104, United States of America; Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22(nd) Street, Sioux Falls, SD 57105, United States of America.
| |
Collapse
|
83
|
Leonard RJ, Preston CC, Gucwa ME, Afeworki Y, Selya AS, Faustino RS. Protein Subdomain Enrichment of NUP155 Variants Identify a Novel Predicted Pathogenic Hotspot. Front Cardiovasc Med 2020; 7:8. [PMID: 32118046 PMCID: PMC7019101 DOI: 10.3389/fcvm.2020.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/17/2020] [Indexed: 01/05/2023] Open
Abstract
Functional variants in nuclear envelope genes are implicated as underlying causes of cardiopathology. To examine the potential association of single nucleotide variants of nucleoporin genes with cardiac disease, we employed a prognostic scoring approach to investigate variants of NUP155, a nucleoporin gene clinically linked with atrial fibrillation. Here we implemented bioinformatic profiling and predictive scoring, based on the gnomAD, National Heart Lung and Blood Institute-Exome Sequencing Project (NHLBI-ESP) Exome Variant Server, and dbNSFP databases to identify rare single nucleotide variants (SNVs) of NUP155 potentially associated with cardiopathology. This predictive scoring revealed 24 SNVs of NUP155 as potentially cardiopathogenic variants located primarily in the N-terminal crescent-shaped domain of NUP155. In addition, a predicted NUP155 R672G variant prioritized in our study was mapped to a region within the alpha helical stack of the crescent domain of NUP155. Bioinformatic analysis of inferred protein-protein interactions of NUP155 revealed over representation of top functions related to molecular transport, RNA trafficking, and RNA post-transcriptional modification. Topology analysis revealed prioritized hubs critical for maintaining network integrity and informational flow that included FN1, SIRT7, and CUL7 with nodal enrichment of RNA helicases in the topmost enriched subnetwork. Furthermore, integration of the top 5 subnetworks to capture network topology of an expanded framework revealed that FN1 maintained its hub status, with elevation of EED, CUL3, and EFTUD2. This is the first study to report novel discovery of a NUP155 subdomain hotspot that enriches for allelic variants of NUP155 predicted to be clinically damaging, and supports a role for RNA metabolism in cardiac disease and development.
Collapse
Affiliation(s)
- Riley J. Leonard
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
- Department of Biology, College of St. Benedict/St. John's University, Collegeville, MN, United States
| | - Claudia C. Preston
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
| | - Melanie E. Gucwa
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
- Department of Biology, Carthage College, Kenosha, WI, United States
| | - Yohannes Afeworki
- Functional Genomics & Bioinformatics Core Facility, Sanford Research, Sioux Falls, SD, United States
| | - Arielle S. Selya
- Behavioral Sciences Group, Sanford Research, Sioux Falls, SD, United States
| | - Randolph S. Faustino
- Genetics and Genomics Group, Sanford Research, Sioux Falls, SD, United States
- Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, United States
| |
Collapse
|
84
|
Okazaki R, Yamazoe K, Inoue YH. Nuclear Export of Cyclin B Mediated by the Nup62 Complex Is Required for Meiotic Initiation in Drosophila Males. Cells 2020; 9:E270. [PMID: 31979075 PMCID: PMC7072204 DOI: 10.3390/cells9020270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The central channel of the nuclear pore complex plays an important role in the selective transport of proteins between the nucleus and cytoplasm. Previous studies have demonstrated that the depletion of the Nup62 complex, constructing the nuclear pore channel in premeiotic Drosophila cells, resulted in the absence of meiotic cells. We attempted to understand the mechanism underlying the cell cycle arrest before meiosis. METHODS We induced dsRNAs against the nucleoporin mRNAs using the Gal4/UAS system in Drosophila. RESULTS The cell cycle of the Nup62-depleted cells was arrested before meiosis without CDK1 activation. The ectopic over-expression of CycB, but not constitutively active CDK1, resulted in partial rescue from the arrest. CycB continued to exist in the nuclei of Nup62-depleted cells and cells depleted of exportin encoded by emb. Protein complexes containing CycB, Emb, and Nup62 were observed in premeiotic spermatocytes. CycB, which had temporally entered the nucleus, was associated with Emb, and the complex was transported back to the cytoplasm through the central channel, interacting with the Nup62 complex. Conclusion: We proposed that CycB is exported with Emb through the channel interacting with the Nup62 complex before the onset of meiosis. The nuclear export ensures the modification and formation of sufficient CycB-CDK1 in the cytoplasm.
Collapse
Affiliation(s)
| | | | - Yoshihiro H. Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Kyoto, Japan; (R.O.); (K.Y.)
| |
Collapse
|
85
|
Gomar-Alba M, Mendoza M. Modulation of Cell Identity by Modification of Nuclear Pore Complexes. Front Genet 2020; 10:1301. [PMID: 31969901 PMCID: PMC6960265 DOI: 10.3389/fgene.2019.01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 11/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) are protein assemblies that form channels across the nuclear envelope to mediate communication between the nucleus and the cytoplasm. Additionally, NPCs interact with chromatin and influence the position and expression of multiple genes. Interestingly, the composition of NPCs can vary in different cell-types, tissues, and developmental states. Here, we review recent findings suggesting that modifications of NPC composition, including post-translational modifications, play an instructive role in cell fate establishment. In particular, we focus on the role of cell-specific NPC deacetylation in asymmetrically dividing budding yeast, which modulates transport-dependent and transport-independent NPC functions to determine the time of commitment to a new division cycle in daughter cells. By modulating protein localization and gene expression, NPCs are therefore emerging as central regulators of cell identity.
Collapse
Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| |
Collapse
|
86
|
Hightower RM, Reid AL, Gibbs DE, Wang Y, Widrick JJ, Kunkel LM, Kastenschmidt JM, Villalta SA, van Groen T, Chang H, Gornisiewicz S, Landesman Y, Tamir S, Alexander MS. The SINE Compound KPT-350 Blocks Dystrophic Pathologies in DMD Zebrafish and Mice. Mol Ther 2020; 28:189-201. [PMID: 31628052 PMCID: PMC6952030 DOI: 10.1016/j.ymthe.2019.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/23/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked muscle wasting disease that is caused by the loss of functional dystrophin protein in cardiac and skeletal muscles. DMD patient muscles become weakened, leading to eventual myofiber breakdown and replacement with fibrotic and adipose tissues. Inflammation drives the pathogenic processes through releasing inflammatory cytokines and other factors that promote skeletal muscle degeneration and contributing to the loss of motor function. Selective inhibitors of nuclear export (SINEs) are a class of compounds that function by inhibiting the nuclear export protein exportin 1 (XPO1). The XPO1 protein is an important regulator of key inflammatory and neurological factors that drive inflammation and neurotoxicity in various neurological and neuromuscular diseases. Here, we demonstrate that SINE compound KPT-350 can ameliorate dystrophic-associated pathologies in the muscles of DMD models of zebrafish and mice. Thus, SINE compounds are a promising novel strategy for blocking dystrophic symptoms and could be used in combinatorial treatments for DMD.
Collapse
Affiliation(s)
- Rylie M Hightower
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA; UAB Center for Exercise Medicine (UCEM), Birmingham, AL 35294, USA
| | - Andrea L Reid
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
| | - Devin E Gibbs
- Division of Genetics and Genomics at Boston Children's Hospital, Boston, MA 02115, USA
| | - Yimin Wang
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA
| | - Jeffrey J Widrick
- Division of Genetics and Genomics at Boston Children's Hospital, Boston, MA 02115, USA
| | - Louis M Kunkel
- Division of Genetics and Genomics at Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics at Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; The Manton Center for Orphan Disease Research at Boston Children's Hospital, Boston, MA 02115, USA
| | - Jenna M Kastenschmidt
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA; Institute for Immunology, University of California-Irvine, Irvine, CA 92697, USA
| | - S Armando Villalta
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA; Institute for Immunology, University of California-Irvine, Irvine, CA 92697, USA
| | - Thomas van Groen
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hua Chang
- Karyopharm Therapeutics, Newton, MA 02459, USA
| | | | | | | | - Matthew S Alexander
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham and Children's of Alabama, Birmingham, AL 35294, USA; UAB Center for Exercise Medicine (UCEM), Birmingham, AL 35294, USA; Department of Genetics at the University of Alabama at Birmingham, Birmingham, AL 35294, USA; Civitan International Research Center at the University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
87
|
King GA, Ünal E. The dynamic nuclear periphery as a facilitator of gamete health and rejuvenation. Curr Genet 2020; 66:487-493. [PMID: 31915924 DOI: 10.1007/s00294-019-01050-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/26/2022]
Abstract
The nuclear periphery is a hotspot for the accumulation of age-induced damage in eukaryotic cells. The types of damage that occur at the periphery and their phenotypic consequences have begun to be characterized; however, the mechanisms by which cells repair or eliminate nuclear damage remain poorly understood. Using budding yeast meiosis as a natural system to study cellular rejuvenation, we recently discovered a novel nuclear quality control event, in which age-induced damage is sequestered away from dividing chromosomes to a discarded nuclear compartment that we term the GUNC (for "Gametogenesis Uninherited Nuclear Compartment"). Interestingly, extensive nuclear remodeling occurs even in young cells, including a surprising modularity of the nuclear pore complex, suggesting a general contribution to gamete fitness. In this review, we discuss these findings in the context of recent evidence that the nuclear periphery is a highly dynamic region critical for cellular health.
Collapse
Affiliation(s)
- Grant A King
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, 94720, USA.
| |
Collapse
|
88
|
Kuhn TM, Capelson M. Nuclear Pore Proteins in Regulation of Chromatin State. Cells 2019; 8:cells8111414. [PMID: 31717499 PMCID: PMC6912232 DOI: 10.3390/cells8111414] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/31/2022] Open
Abstract
Nuclear pore complexes (NPCs) are canonically known to regulate nucleocytoplasmic transport. However, research efforts over the last decade have demonstrated that NPCs and their constituent nucleoporins (Nups) also interact with the genome and perform important roles in regulation of gene expression. It has become increasingly clear that many Nups execute these roles specifically through regulation of chromatin state, whether through interactions with histone modifiers and downstream changes in post-translational histone modifications, or through relationships with chromatin-remodeling proteins that can result in physical changes in nucleosome occupancy and chromatin compaction. This review focuses on these findings, highlighting the functional connection between NPCs/Nups and regulation of chromatin structure, and how this connection can manifest in regulation of transcription.
Collapse
|
89
|
Lindholm Carlström E, Halvardson J, Etemadikhah M, Wetterberg L, Gustavson KH, Feuk L. Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family. BMC Med Genomics 2019; 12:156. [PMID: 31694657 PMCID: PMC6833288 DOI: 10.1186/s12920-019-0606-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/18/2019] [Indexed: 01/20/2023] Open
Abstract
Background Non-syndromic intellectual disability is genetically heterogeneous with dominant, recessive and complex forms of inheritance. We have performed detailed genetic studies in a large multi-generational Swedish family, including several members diagnosed with non-syndromic intellectual disability. Linkage analysis was performed on 22 family members, nine affected with mild to moderate intellectual disability and 13 unaffected family members. Methods Family members were analyzed with Affymetrix Genome-Wide Human SNP Array 6.0 and the genetic data was used to detect copy number variation and to perform genome wide linkage analysis with the SNP High Throughput Linkage analysis system and the Merlin software. For the exome sequencing, the samples were prepared using the Sure Select Human All Exon Kit (Agilent Technologies, Santa Clara, CA, USA) and sequenced using the Ion Proton™ System. Validation of identified variants was performed with Sanger sequencing. Results The linkage analysis results indicate that intellectual disability in this family is genetically heterogeneous, with suggestive linkage found on chromosomes 1q31-q41, 4q32-q35, 6p25 and 14q24-q31 (LOD scores of 2.4, simulated p-value of 0.000003 and a simulated genome-wide p-value of 0.06). Exome sequencing was then performed in 14 family members and 7 unrelated individuals from the same region. The analysis of coding variation revealed a pathogenic and candidate variants in different branches of the family. In three patients we find a known homozygous pathogenic mutation in the Homo sapiens solute carrier family 17 member 5 (SLC17A5), causing Salla disease. We also identify a deletion overlapping KDM3B and a duplication overlapping MAP3K4 and AGPAT4, both overlapping variants previously reported in developmental disorders. Conclusions DNA samples from the large family analyzed in this study were initially collected based on a hypothesis that affected members shared a major genetic risk factor. Our results show that a complex phenotype such as mild intellectual disability in large families from genetically isolated populations may show considerable genetic heterogeneity.
Collapse
Affiliation(s)
- Eva Lindholm Carlström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden.
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Mitra Etemadikhah
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Lennart Wetterberg
- Department of Clinical Neuroscience (CNS), K8, Karolinska Institutet, Stockholm, Sweden
| | - Karl-Henrik Gustavson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Box 815, SE-751 08, Uppsala, Sweden
| |
Collapse
|
90
|
Chanukuppa V, Paul D, Taunk K, Chatterjee T, Sharma S, Kumar S, Santra MK, Rapole S. XPO1 is a critical player for bortezomib resistance in multiple myeloma: A quantitative proteomic approach. J Proteomics 2019; 209:103504. [PMID: 31465861 DOI: 10.1016/j.jprot.2019.103504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/26/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023]
Abstract
Among the blood cancers, 13% mortality is caused by Multiple myeloma (MM) type of hematological malignancy. In spite of therapeutic advances in chemotherapy treatment, still MM remains an incurable disease is mainly due to emergence of chemoresistance. At present time, FDA approved bortezomib is the first line drug for MM treatment. However, like other chemotherapy, MM patients are acquiring resistance against bortezomib. The present study aims to identify and validate bortezomib resistant protein targets in MM using iTRAQ and label free quantitative proteomic approaches. 112 differentially expressed proteins were commonly found in both approaches with similar differential expression pattern. Exportin-1 (XPO1) protein was selected for further validation as its significant high expression was observed in both iTRAQ and label free analysis. Bioinformatic analysis of these common differentially expressed proteins showed a clear cluster of proteins such as SMC1A, RCC2, CSE1, NUP88, NUP50, TPR, HSPA14, DYNLL1, RAD21 and RANBP2 being associated with XPO1. Functional studies like cell count assay, flow cytometry assay and soft agar assay proved that XPO1 knock down in RPMI 8226R cell line results in re-sensitization to bortezomib drug. The mass spectrometry data are available via ProteomeXchange with identifier PXD013859. BIOLOGICAL SIGNIFICANCE: Multiple myeloma (MM) is a type of hematological malignancy which constitutes about 13% of all blood cell related malignancies. Chemoresistance is one of the major obstacles for the successful treatment for MM. Bortezomib is a first proteasome inhibitor drug, widely used in MM treatment. The present study aims to identify and validate bortezomib resistant protein targets in MM. Here, we identified 112 candidate proteins to be associated with bortezomib resistance using global quantitative proteomic analysis. Among these candidate proteins, we show that XPO1 plays crucial role in emerging bortezomib resistance using functional studies like cell count assay, flow cytometry assay and soft agar assay. XPO1 could be a potential therapeutic target for MM and development of inhibitors of XPO1 might help to cure MM.
Collapse
Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India
| | - Debasish Paul
- Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India; Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | | | | | - Saravanan Kumar
- Thermo Fisher Scientific India Pvt. Ltd, Whitefield, Bangalore 560066, KA, India
| | - Manas K Santra
- Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India.
| |
Collapse
|
91
|
Hampoelz B, Schwarz A, Ronchi P, Bragulat-Teixidor H, Tischer C, Gaspar I, Ephrussi A, Schwab Y, Beck M. Nuclear Pores Assemble from Nucleoporin Condensates During Oogenesis. Cell 2019; 179:671-686.e17. [PMID: 31626769 PMCID: PMC6838685 DOI: 10.1016/j.cell.2019.09.022] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 08/09/2019] [Accepted: 09/20/2019] [Indexed: 02/02/2023]
Abstract
The molecular events that direct nuclear pore complex (NPC) assembly toward nuclear envelopes have been conceptualized in two pathways that occur during mitosis or interphase, respectively. In gametes and embryonic cells, NPCs also occur within stacked cytoplasmic membrane sheets, termed annulate lamellae (AL), which serve as NPC storage for early development. The mechanism of NPC biogenesis at cytoplasmic membranes remains unknown. Here, we show that during Drosophila oogenesis, Nucleoporins condense into different precursor granules that interact and progress into NPCs. Nup358 is a key player that condenses into NPC assembly platforms while its mRNA localizes to their surface in a translation-dependent manner. In concert, Microtubule-dependent transport, the small GTPase Ran and nuclear transport receptors regulate NPC biogenesis in oocytes. We delineate a non-canonical NPC assembly mechanism that relies on Nucleoporin condensates and occurs away from the nucleus under conditions of cell cycle arrest.
Collapse
Affiliation(s)
- Bernhard Hampoelz
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Andre Schwarz
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Paolo Ronchi
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, Heidelberg, Germany
| | | | - Christian Tischer
- Center for Bioimage Analysis, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Imre Gaspar
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Anne Ephrussi
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Yannick Schwab
- European Molecular Biology Laboratory, Electron Microscopy Core Facility, Heidelberg, Germany; European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Max Planck Institute of Biophysics, Frankfurt am Main, Germany; European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
| |
Collapse
|
92
|
Aho V, Mäntylä E, Ekman A, Hakanen S, Mattola S, Chen JH, Weinhardt V, Ruokolainen V, Sodeik B, Larabell C, Vihinen-Ranta M. Quantitative Microscopy Reveals Stepwise Alteration of Chromatin Structure during Herpesvirus Infection. Viruses 2019; 11:v11100935. [PMID: 31614678 PMCID: PMC6832731 DOI: 10.3390/v11100935] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/24/2022] Open
Abstract
During lytic herpes simplex virus 1 (HSV-1) infection, the expansion of the viral replication compartments leads to an enrichment of the host chromatin in the peripheral nucleoplasm. We have shown previously that HSV-1 infection induces the formation of channels through the compacted peripheral chromatin. Here, we used three-dimensional confocal and expansion microscopy, soft X-ray tomography, electron microscopy, and random walk simulations to analyze the kinetics of host chromatin redistribution and capsid localization relative to their egress site at the nuclear envelope. Our data demonstrated a gradual increase in chromatin marginalization, and the kinetics of chromatin smoothening around the viral replication compartments correlated with their expansion. We also observed a gradual transfer of capsids to the nuclear envelope. Later in the infection, random walk modeling indicated a gradually faster transport of capsids to the nuclear envelope that correlated with an increase in the interchromatin channels in the nuclear periphery. Our study reveals a stepwise and time-dependent mechanism of herpesvirus nuclear egress, in which progeny viral capsids approach the egress sites at the nuclear envelope via interchromatin spaces.
Collapse
Affiliation(s)
- Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (V.A.); (E.M.); (S.H.); (S.M.); (V.R.)
| | - Elina Mäntylä
- Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (V.A.); (E.M.); (S.H.); (S.M.); (V.R.)
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, 33014 Tampere, Finland
| | - Axel Ekman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.E.); (J.-H.C.); (V.W.); (C.L.)
| | - Satu Hakanen
- Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (V.A.); (E.M.); (S.H.); (S.M.); (V.R.)
| | - Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (V.A.); (E.M.); (S.H.); (S.M.); (V.R.)
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.E.); (J.-H.C.); (V.W.); (C.L.)
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.E.); (J.-H.C.); (V.W.); (C.L.)
| | - Visa Ruokolainen
- Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (V.A.); (E.M.); (S.H.); (S.M.); (V.R.)
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany;
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.E.); (J.-H.C.); (V.W.); (C.L.)
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, University of Jyvaskyla, 40014 Jyvaskyla, Finland; (V.A.); (E.M.); (S.H.); (S.M.); (V.R.)
- Correspondence:
| |
Collapse
|
93
|
The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat Cell Biol 2019; 21:1248-1260. [PMID: 31576060 DOI: 10.1038/s41556-019-0397-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022]
Abstract
While nuclear lamina abnormalities are hallmarks of human diseases, their interplay with epigenetic regulators and precise epigenetic landscape remain poorly understood. Here, we show that loss of the lysine acetyltransferase MOF or its associated NSL-complex members KANSL2 or KANSL3 leads to a stochastic accumulation of nuclear abnormalities with genomic instability patterns including chromothripsis. SILAC-based MOF and KANSL2 acetylomes identified lamin A/C as an acetylation target of MOF. HDAC inhibition or acetylation-mimicking lamin A derivatives rescue nuclear abnormalities observed in MOF-deficient cells. Mechanistically, loss of lamin A/C acetylation resulted in its increased solubility, defective phosphorylation dynamics and impaired nuclear mechanostability. We found that nuclear abnormalities include EZH2-dependent histone H3 Lys 27 trimethylation and loss of nascent transcription. We term this altered epigenetic landscape "heterochromatin enrichment in nuclear abnormalities" (HENA). Collectively, the NSL-complex-dependent lamin A/C acetylation provides a mechanism that maintains nuclear architecture and genome integrity.
Collapse
|
94
|
Shukla E, Chauhan R. Host-HIV-1 Interactome: A Quest for Novel Therapeutic Intervention. Cells 2019; 8:cells8101155. [PMID: 31569640 PMCID: PMC6830350 DOI: 10.3390/cells8101155] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
The complex nature and structure of the human immunodeficiency virus has rendered the cure for HIV infections elusive. The advances in antiretroviral treatment regimes and the development of highly advanced anti-retroviral therapy, which primarily targets the HIV enzymes, have dramatically changed the face of the HIV epidemic worldwide. Despite this remarkable progress, patients treated with these drugs often witness inadequate efficacy, compound toxicity and non-HIV complications. Considering the limited inventory of druggable HIV proteins and their susceptibility to develop drug resistance, recent attempts are focussed on targeting HIV-host interactomes that are essential for viral reproduction. Noticeably, unlike other viruses, HIV subverts the host nuclear pore complex to enter into and exit through the nucleus. Emerging evidence suggests a crucial role of interactions between HIV-1 proteins and host nucleoporins that underlie the import of the pre-integration complex into the nucleus and export of viral RNAs into the cytoplasm during viral replication. Nevertheless, the interaction of HIV-1 with nucleoporins has been poorly described and the role of nucleoporins during nucleocytoplasmic transport of HIV-1 still remains unclear. In this review, we highlight the advances and challenges in developing a more effective antiviral arsenal by exploring critical host-HIV interactions with a special focus on nuclear pore complex (NPC) and nucleoporins.
Collapse
Affiliation(s)
- Ekta Shukla
- National Center for Cell Science, S.P Pune University, Pune-411007, Maharashtra, India.
| | - Radha Chauhan
- National Center for Cell Science, S.P Pune University, Pune-411007, Maharashtra, India.
| |
Collapse
|
95
|
Capitanchik C, Dixon CR, Swanson SK, Florens L, Kerr ARW, Schirmer EC. Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins. Nucleus 2019; 9:410-430. [PMID: 29912636 PMCID: PMC7000147 DOI: 10.1080/19491034.2018.1469351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Laminopathies yield tissue-specific pathologies, yet arise from mutation of ubiquitously-expressed genes. A little investigated hypothesis to explain this is that the mutated proteins or their partners have tissue-specific splice variants. To test this, we analyzed RNA-Seq datasets, finding novel isoforms or isoform tissue-specificity for: Lap2, linked to cardiomyopathy; Nesprin 2, linked to Emery-Dreifuss muscular dystrophy and Lmo7, that regulates the Emery-Dreifuss muscular dystrophy linked emerin gene. Interestingly, the muscle-specific Lmo7 exon is rich in serine phosphorylation motifs, suggesting regulatory function. Muscle-specific splice variants in non-nuclear envelope proteins linked to other muscular dystrophies were also found. Nucleoporins tissue-specific variants were found for Nup54, Nup133, Nup153 and Nup358/RanBP2. RT-PCR confirmed novel Lmo7 and RanBP2 variants and specific knockdown of the Lmo7 variantreduced myogenic index. Nuclear envelope proteins were enriched for tissue-specific splice variants compared to the rest of the genome, suggesting that splice variants contribute to its tissue-specific functions.
Collapse
Affiliation(s)
- Charlotte Capitanchik
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Charles R Dixon
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Selene K Swanson
- b Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Laurence Florens
- b Stowers Institute for Medical Research , Kansas City , MO , USA
| | - Alastair R W Kerr
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| | - Eric C Schirmer
- a The Wellcome Centre for Cell Biology and Institute of Cell Biology , University of Edinburgh , Edinburgh , UK
| |
Collapse
|
96
|
Abstract
Nuclear pore complexes (NPCs), the channels connecting the nucleus with the cytoplasm, are the largest protein structures of the nuclear envelope. In addition to their role in regulating nucleocytoplasmic transport, increasing evidence shows that these multiprotein structures play central roles in the regulation of gene activity. In light of recent discoveries, NPCs are emerging as scaffolds that mediate the regulation of specific gene sets at the nuclear periphery. The function of NPCs as genome organizers and hubs for transcriptional regulation provides additional evidence that the compartmentalization of genes and transcriptional regulators within the nuclear space is an important mechanism of gene expression regulation.
Collapse
Affiliation(s)
- Maximiliano A D'Angelo
- a Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, NCI-Designated Cancer Center , 10901 N. Torrey Pines Road, La Jolla , CA , United States
| |
Collapse
|
97
|
Pathirathna P, Balla RJ, Meng G, Wei Z, Amemiya S. Nanoscale electrostatic gating of molecular transport through nuclear pore complexes as probed by scanning electrochemical microscopy. Chem Sci 2019; 10:7929-7936. [PMID: 31673318 PMCID: PMC6788534 DOI: 10.1039/c9sc02356a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
The nuclear pore complex (NPC) is a large protein nanopore that solely mediates molecular transport between the nucleus and cytoplasm of a eukaryotic cell. There is a long-standing consensus that selective transport barriers of the NPC are exclusively based on hydrophobic repeats of phenylalanine and glycine (FG) of nucleoporins. Herein, we reveal experimentally that charged residues of amino acids intermingled between FG repeats can modulate molecular transport through the NPC electrostatically and in a pathway-dependent manner. Specifically, we investigate the NPC of the Xenopus oocyte nucleus to find that excess positive charges of FG-rich nucleoporins slow down passive transport of a polycationic peptide, protamine, without affecting that of a polyanionic pentasaccharide, Arixtra, and small monovalent ions. Protamine transport is slower with a lower concentration of electrolytes in the transport media, where the Debye length becomes comparable to the size of water-filled spaces among the gel-like network of FG repeats. Slow protamine transport is not affected by the binding of a lectin, wheat germ agglutinin, to the peripheral route of the NPC, which is already blocked electrostatically by adjacent nucleoporins that have more cationic residues than anionic residues and even FG dipeptides. The permeability of NPCs to the probe ions is measured by scanning electrochemical microscopy using ion-selective tips based on liquid/liquid microinterfaces and is analysed by effective medium theory to determine the sizes of peripheral and central routes with distinct protamine permeability. Significantly, nanoscale electrostatic gating at the NPC can be relevant not only chemically and biologically, but also biomedically for efficient nuclear import of genetically therapeutic substances.
Collapse
Affiliation(s)
- Pavithra Pathirathna
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Ryan J Balla
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Guanqun Meng
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Zemeng Wei
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Shigeru Amemiya
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| |
Collapse
|
98
|
Jin P, Jiang J, Xie N, Zhou L, Huang Z, Zhang L, Qin S, Fu S, Peng L, Gao W, Li B, Lei Y, Nice EC, Li C, Shao J, Xie K. MCT1 relieves osimertinib-induced CRC suppression by promoting autophagy through the LKB1/AMPK signaling. Cell Death Dis 2019; 10:615. [PMID: 31409796 PMCID: PMC6692318 DOI: 10.1038/s41419-019-1844-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 07/21/2019] [Accepted: 07/24/2019] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide. Development of novel chemotherapeutics is still required to enable successful treatment and improve survival for CRC patients. Here, we found that osimertinib (OSI) exhibits potent anti-CRC effects by inducing apoptosis, independent of its selective inhibitory activity targeting the EGFR T790M mutation. Intriguingly, OSI treatment triggers autophagic flux in CRC cells. Inhibition of autophagy markedly augments OSI-induced apoptosis and growth inhibition in CRC cells, suggesting a protective role of autophagy in response to OSI treatment. Mechanistically, OSI upregulates the expression of monocarboxylate transporter 1 (MCT1) and subsequently activates LKB1/AMPK signaling, leading to autophagy induction in CRC cells. Notably, OSI significantly exaggerates the sensitivity of CRC cells to the first-line drugs 5-fluorouracil or oxaliplatin. Taken together, our study unravels a novel mechanism of OSI-mediated protective autophagy involving MCT1/LKB1/AMPK signaling, and suggests the use of OSI as a potential agent for clinical CRC treatment.
Collapse
Affiliation(s)
- Ping Jin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Jingwen Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Na Xie
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Lu Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Siyuan Qin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Shuyue Fu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Liyuan Peng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Wei Gao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Bowen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, P. R. China
| | - Yunlong Lei
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jichun Shao
- Department of Urology, Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital), Chengdu, Sichuan, China.
| | - Ke Xie
- Department of Oncology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610054, P. R. China.
| |
Collapse
|
99
|
Pesce L, Cozzolino M, Lanzanò L, Diaspro A, Bianchini P. Measuring expansion from macro- to nanoscale using NPC as intrinsic reporter. JOURNAL OF BIOPHOTONICS 2019; 12:e201900018. [PMID: 30980601 PMCID: PMC7065622 DOI: 10.1002/jbio.201900018] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 05/22/2023]
Abstract
Expansion microscopy is a super-resolution method that allows expanding uniformly biological samples, by increasing the relative distances among fluorescent molecules labeling specific components. One of the main concerns in this approach regards the isotropic behavior at the nanoscale. The present study aims to determine the robustness of such a technique, quantifying the expansion parameters i.e. scale factor, isotropy, uniformity. Our focus is on the nuclear pore complex (NPC), as well-known nanoscale component endowed of a preserved and symmetrical structure localized on the nuclear envelope. Here, we show that Nup153 is a good reporter to quantitatively address the isotropy of the expansion process. The quantitative analysis carried out on NPCs, at different spatial scales, allows concluding that expansion microscopy can be used at the nanoscale to measure subcellular features with an accuracy from 10 to 5 nm. Therefore, it is an excellent method for structural studies of macromolecular complexes.
Collapse
Affiliation(s)
- Luca Pesce
- Nanoscopy and NIC Department, Istituto Italiano di TecnologiaGenoaItaly
- Department of PhysicsUniversity of GenoaGenoaItaly
| | - Marco Cozzolino
- Nanoscopy and NIC Department, Istituto Italiano di TecnologiaGenoaItaly
- Department of PhysicsUniversity of GenoaGenoaItaly
| | - Luca Lanzanò
- Nanoscopy and NIC Department, Istituto Italiano di TecnologiaGenoaItaly
| | - Alberto Diaspro
- Nanoscopy and NIC Department, Istituto Italiano di TecnologiaGenoaItaly
- Department of PhysicsUniversity of GenoaGenoaItaly
| | - Paolo Bianchini
- Nanoscopy and NIC Department, Istituto Italiano di TecnologiaGenoaItaly
| |
Collapse
|
100
|
Kindermann B, Valkova C, Krämer A, Perner B, Engelmann C, Behrendt L, Kritsch D, Jungnickel B, Kehlenbach RH, Oswald F, Englert C, Kaether C. The nuclear pore proteins Nup88/214 and T-cell acute lymphatic leukemia-associated NUP214 fusion proteins regulate Notch signaling. J Biol Chem 2019; 294:11741-11750. [PMID: 31186352 DOI: 10.1074/jbc.ra118.006357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/20/2019] [Indexed: 01/14/2023] Open
Abstract
The Notch receptor is a key mediator of developmental programs and cell-fate decisions. Imbalanced Notch signaling leads to developmental disorders and cancer. To fully characterize the Notch signaling pathway and exploit it in novel therapeutic interventions, a comprehensive view on the regulation and requirements of Notch signaling is needed. Notch is regulated at different levels, ranging from ligand binding, stability to endocytosis. Using an array of different techniques, including reporter gene assays, immunocytochemistry, and ChIP-qPCR we show here, to the best of our knowledge for the first time, regulation of Notch signaling at the level of the nuclear pore. We found that the nuclear pore protein Nup214 (nucleoporin 214) and its interaction partner Nup88 negatively regulate Notch signaling in vitro and in vivo in zebrafish. In mammalian cells, loss of Nup88/214 inhibited nuclear export of recombination signal-binding protein for immunoglobulin κJ region (RBP-J), the DNA-binding component of the Notch pathway. This inhibition increased binding of RBP-J to its cognate promoter regions, resulting in increased downstream Notch signaling. Interestingly, we also found that NUP214 fusion proteins, causative for certain cases of T-cell acute lymphatic leukemia, potentially contribute to tumorigenesis via a Notch-dependent mechanism. In summary, the nuclear pore components Nup88/214 suppress Notch signaling in vitro, and in zebrafish, nuclear RBP-J levels are rate-limiting factors for Notch signaling in mammalian cells, and regulation of nucleocytoplasmic transport of RBP-J may contribute to fine-tuning Notch activity in cells.
Collapse
Affiliation(s)
- Bastian Kindermann
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| | - Christina Valkova
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| | - Andreas Krämer
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| | - Birgit Perner
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| | - Christian Engelmann
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| | - Laura Behrendt
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| | - Daniel Kritsch
- Institut für Biochemie und Biophysik, Friedrich Schiller Universität Jena, 07745 Jena, Germany
| | - Berit Jungnickel
- Institut für Biochemie und Biophysik, Friedrich Schiller Universität Jena, 07745 Jena, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Universitätsmedizin Göttingen, 37073 Göttingen, Germany
| | - Franz Oswald
- Universitätsklinikum Ulm, Zentrum für Innere Medizin, Abteilung für Innere Medizin I, 89081 Ulm, Germany
| | - Christoph Englert
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany.,Institut für Biochemie und Biophysik, Friedrich Schiller Universität Jena, 07745 Jena, Germany
| | - Christoph Kaether
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, 07745 Jena, Germany
| |
Collapse
|