1
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Rondón Ortiz AN, Zhang L, Ash PEA, Basu A, Puri S, van der Spek SJF, Wang Z, Dorrian L, Emili A, Wolozin B. Proximity labeling reveals dynamic changes in the SQSTM1 protein network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571324. [PMID: 38168279 PMCID: PMC10760047 DOI: 10.1101/2023.12.12.571324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
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2
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Zhang L, Chen M, Wang Z, Zhong M, Chen H, Li T, Wang L, Zhao Z, Zhang XB, Ke G, Liu Y, Tan W. Spatiotemporal Regulation of Cell Fate in Living Systems Using Photoactivatable Artificial DNA Membraneless Organelles. ACS CENTRAL SCIENCE 2024; 10:1201-1210. [PMID: 38947212 PMCID: PMC11212128 DOI: 10.1021/acscentsci.4c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024]
Abstract
Coacervates formed by liquid-liquid phase separation emerge as important biomimetic models for studying the dynamic behaviors of membraneless organelles and synchronously motivating the creation of smart architectures with the regulation of cell fate. Despite continuous progress, it remains challenging to balance the trade-offs among structural stability, versatility, and molecular communication for regulation of cell fate and systemic investigation in a complex physiological system. Herein, we present a self-stabilizing and fastener-bound gain-of-function methodology to create a new type of synthetic DNA membraneless organelle (MO) with high stability and controlled bioactivity on the basis of DNA coacervates. Specifically, long single-strand DNA generated by rolling circle amplification (RCA) is selected as the scaffold that assembles into membraneless coacervates via phase separation. Intriguingly, the as-formed DNA MO can recruit RCA byproducts and other components to achieve self-stabilization, nanoscale condensation, and function encoding. As a proof of concept, photoactivatable DNA MO is constructed and successfully employed for time-dependent accumulation and spatiotemporal management of cancer in a mouse model. This study offers new, important insights into synthetic membraneless organelles for the basic understanding and manipulation of important life processes.
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Affiliation(s)
- Lili Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Mei Chen
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Materials Science and Engineering, Aptamer
Engineering Center of Hunan Province, Hunan
University, Changsha, Hunan 410082, China
| | - Zhiqiang Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Minjuan Zhong
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Hong Chen
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Ting Li
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Linlin Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhihui Zhao
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Xiao-Bing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Guoliang Ke
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Yanlan Liu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, College of Biology, Aptamer Engineering Center of Hunan
Province, Hunan University, Changsha, Hunan 410082, China
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Roesmann F, Sertznig H, Klaassen K, Wilhelm A, Heininger D, Heß S, Elsner C, Marschalek R, Santiago ML, Esser S, Sutter K, Dittmer U, Widera M. The interferon-regulated host factor hnRNPA0 modulates HIV-1 production by interference with LTR activity, mRNA trafficking, and programmed ribosomal frameshifting. J Virol 2024:e0053424. [PMID: 38899932 DOI: 10.1128/jvi.00534-24] [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: 03/23/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The interplay between host factors and viral components impacts viral replication efficiency profoundly. Members of the cellular heterogeneous nuclear ribonucleoprotein family (hnRNPs) have been extensively studied as HIV-1 host dependency factors, but whether they play a role in innate immunity is currently unknown. This study aimed to identify hnRNPA0 as a type I interferon (IFN)-repressed host factor in HIV-1-infected cells. Knockdown of hnRNPA0, a situation that mirrors conditions under IFN stimulation, increased LTR activity, export of unspliced HIV-1 mRNA, viral particle production, and thus, increased infectivity. Conversely, hnRNPA0 overexpression primarily reduced plasmid-driven and integrated HIV-1 long terminal repeat (LTR) activity, significantly decreasing total viral mRNA and protein levels. In addition, high levels of hnRNPA0 significantly reduced the HIV-1 programmed ribosomal frameshifting efficiency, resulting in a shift in the HIV-1 p55/p15 ratio. The HIV-1 alternative splice site usage remained largely unaffected by altered hnRNPA0 levels suggesting that the synergistic inhibition of the LTR activity and viral mRNA transcription, as well as impaired ribosomal frameshifting efficiency, are critical factors for efficient HIV-1 replication regulated by hnRNPA0. The pleiotropic dose-dependent effects under high or low hnRNPA0 levels were further confirmed in HIV-1-infected Jurkat cells. Finally, our study revealed that hnRNPA0 levels in PBMCs were lower in therapy-naive HIV-1-infected individuals compared to healthy controls. Our findings highlight a significant role for hnRNPA0 in HIV-1 replication and suggest that its IFN-I-regulated expression levels are critical for viral fitness allowing replication in an antiviral environment.IMPORTANCERNA-binding proteins, in particular, heterogeneous nuclear ribonucleoproteins (hnRNPs), have been extensively studied. Some act as host dependency factors for HIV-1 since they are involved in multiple cellular gene expression processes. Our study revealed hnRNPA0 as an IFN-regulated host factor, that is differently expressed after IFN-I treatment in HIV-1 target cells and lower expressed in therapy-naïve HIV-1-infected individuals. Our findings demonstrate the significant pleiotropic role of hnRNPA0 in viral replication: In high concentrations, hnRNPA0 limits viral replication by negatively regulating Tat-LTR transcription, retaining unspliced mRNA in the nucleus, and significantly impairing programmed ribosomal frameshifting. Low hnRNPA0 levels as observed in IFN-treated THP-1 cells, particularly facilitate HIV LTR activity and unspliced mRNA export, suggesting a role in innate immunity in favor of HIV replication. Understanding the mode of action between hnRNPA0 and HIV-1 gene expression might help to identify novel therapeutically strategies against HIV-1 and other viruses.
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Affiliation(s)
- Fabian Roesmann
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Katleen Klaassen
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Delia Heininger
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Stefanie Heß
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Mario L Santiago
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Stefan Esser
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Dermatology, HPSTD Outpatient Clinic, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV and AIDS-associated Diseases University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Frankfurt, Germany
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4
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Hashimoto Y, Greene C, Hanley N, Hudson N, Henshall D, Sweeney KJ, O'Brien DF, Campbell M. Pumilio-1 mediated translational control of claudin-5 at the blood-brain barrier. Fluids Barriers CNS 2024; 21:52. [PMID: 38898501 PMCID: PMC11188261 DOI: 10.1186/s12987-024-00553-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Claudin-5 is one of the most essential tight junction proteins at the blood-brain barrier. A single nucleotide polymorphism rs10314 is located in the 3'-untranslated region of claudin-5 and has been shown to be a risk factor for schizophrenia. Here, we show that the pumilio RNA-binding protein, pumilio-1, is responsible for rs10314-mediated claudin-5 regulation. The RNA sequence surrounding rs10314 is highly homologous to the canonical pumilio-binding sequence and claudin-5 mRNA with rs10314 produces 25% less protein due to its inability to bind to pumilio-1. Pumilio-1 formed cytosolic granules under stress conditions and claudin-5 mRNA appeared to preferentially accumulate in these granules. Added to this, we observed granular pumilio-1 in endothelial cells in human brain tissues from patients with psychiatric disorders or epilepsy with increased/accumulated claudin-5 mRNA levels, suggesting translational claudin-5 suppression may occur in a brain-region specific manner. These findings identify a key regulator of claudin-5 translational processing and how its dysregulation may be associated with neurological and neuropsychiatric disorders.
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Affiliation(s)
- Yosuke Hashimoto
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Chris Greene
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole Hanley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Natalie Hudson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Henshall
- Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, FutureNeuro, Royal College of Surgeons in Ireland (RCSI), University of Medicine and Health Sciences, Dublin, Ireland
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | - Matthew Campbell
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
- Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, FutureNeuro, Royal College of Surgeons in Ireland (RCSI), University of Medicine and Health Sciences, Dublin, Ireland.
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5
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Costa RG, Conceição A, Matos CA, Nóbrega C. The polyglutamine protein ATXN2: from its molecular functions to its involvement in disease. Cell Death Dis 2024; 15:415. [PMID: 38877004 PMCID: PMC11178924 DOI: 10.1038/s41419-024-06812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
A CAG repeat sequence in the ATXN2 gene encodes a polyglutamine (polyQ) tract within the ataxin-2 (ATXN2) protein, showcasing a complex landscape of functions that have been progressively unveiled over recent decades. Despite significant progresses in the field, a comprehensive overview of the mechanisms governed by ATXN2 remains elusive. This multifaceted protein emerges as a key player in RNA metabolism, stress granules dynamics, endocytosis, calcium signaling, and the regulation of the circadian rhythm. The CAG overexpansion within the ATXN2 gene produces a protein with an extended poly(Q) tract, inducing consequential alterations in conformational dynamics which confer a toxic gain and/or partial loss of function. Although overexpanded ATXN2 is predominantly linked to spinocerebellar ataxia type 2 (SCA2), intermediate expansions are also implicated in amyotrophic lateral sclerosis (ALS) and parkinsonism. While the molecular intricacies await full elucidation, SCA2 presents ATXN2-associated pathological features, encompassing autophagy impairment, RNA-mediated toxicity, heightened oxidative stress, and disruption of calcium homeostasis. Presently, SCA2 remains incurable, with patients reliant on symptomatic and supportive treatments. In the pursuit of therapeutic solutions, various studies have explored avenues ranging from pharmacological drugs to advanced therapies, including cell or gene-based approaches. These endeavours aim to address the root causes or counteract distinct pathological features of SCA2. This review is intended to provide an updated compendium of ATXN2 functions, delineate the associated pathological mechanisms, and present current perspectives on the development of innovative therapeutic strategies.
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Affiliation(s)
- Rafael G Costa
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal.
- PhD program in Biomedical Sciences, Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve (UAlg), Faro, Portugal.
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve (UAlg), Faro, Portugal.
| | - André Conceição
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- PhD program in Biomedical Sciences, Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve (UAlg), Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve (UAlg), Faro, Portugal
- Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, Lisbon, Portugal
| | - Carlos A Matos
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve (UAlg), Faro, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal.
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve (UAlg), Faro, Portugal.
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6
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Di Timoteo G, Giuliani A, Setti A, Biagi MC, Lisi M, Santini T, Grandioso A, Mariani D, Castagnetti F, Perego E, Zappone S, Lattante S, Sabatelli M, Rotili D, Vicidomini G, Bozzoni I. M 6A reduction relieves FUS-associated ALS granules. Nat Commun 2024; 15:5033. [PMID: 38866783 PMCID: PMC11169559 DOI: 10.1038/s41467-024-49416-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease due to gradual motoneurons (MN) degeneration. Among the processes associated to ALS pathogenesis, there is the formation of cytoplasmic inclusions produced by aggregation of mutant proteins, among which the RNA binding protein FUS. Here we show that, in neuronal cells and in iPSC-derived MN expressing mutant FUS, such inclusions are significantly reduced in number and dissolve faster when the RNA m6A content is diminished. Interestingly, stress granules formed in ALS conditions showed a distinctive transcriptome with respect to control cells, which reverted to similar to control after m6A downregulation. Notably, cells expressing mutant FUS were characterized by higher m6A levels suggesting a possible link between m6A homeostasis and pathological aggregates. Finally, we show that FUS inclusions are reduced also in patient-derived fibroblasts treated with STM-2457, an inhibitor of METTL3 activity, paving the way for its possible use for counteracting aggregate formation in ALS.
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Grants
- ERC-2019-SyG 855923-ASTRA EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- ERC-2018-CoG 818669-BrightEyes EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- AIRC IG 2019 Id. 23053 Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)
- PRIN 2017 2017P352Z4 Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- NextGenerationEU PNRR MUR Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "National Center for Gene Therapy and Drugbased on RNA Technology" (CN00000041) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "National Center for Gene Therapy and Drug based on RNA Technology" (CN00000041) Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- NextGenerationEU PNRR MUR Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)
- "Sapienza" Ateneo Project 2021 n. RM12117A61C811CE Sapienza Università di Roma (Sapienza University of Rome)
- Regione Lazio PROGETTI DI GRUPPI DI RICERCA 2020 - A0375-2020-36597 Regione Lazio (Region of Lazio)
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Andrea Giuliani
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Martina C Biagi
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy
| | - Michela Lisi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Alessia Grandioso
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Davide Mariani
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Francesco Castagnetti
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Eleonora Perego
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Sabrina Zappone
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Mario Sabatelli
- Section of Neurology, Department of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Adult NEMO Clinical Center, Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185, Rome, Italy
| | - Giuseppe Vicidomini
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy.
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy.
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy.
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7
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Sun H, Yang B, Li Q, Zhu X, Song E, Liu C, Song Y, Jiang G. Polystyrene nanoparticles trigger aberrant condensation of TDP-43 and amyotrophic lateral sclerosis-like symptoms. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01683-5. [PMID: 38849544 DOI: 10.1038/s41565-024-01683-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/23/2024] [Indexed: 06/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the dysfunction and progressive death of cerebral and spinal motor neurons. Preliminary epidemiological research has hinted at a relationship between environmental risks and the escalation of ALS, but the underlying reasons remain mostly mysterious. Here we show that nanosize polystyrene plastics (PS) induce ALS-like symptoms and illustrate the related molecular mechanism. When exposed to PS, cells endure internal oxidative stress, which leads to the aggregation of TAR DNA-binding protein 43 kDa (TDP-43), triggering ALS-like characteristics. In addition, the oxidized heat shock protein 70 fails to escort TDP-43 back to the nucleus. The cytoplasmic accumulation of TDP-43 facilitates the formation of a complex between PS and TDP-43, enhancing the condensation and solidification of TDP-43. These findings are corroborated through in silico and in vivo assays. Altogether, our work illustrates a unique toxicological mechanism induced by nanoparticles and provides insights into the connection between environmental pollution and neurodegenerative disorders.
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Affiliation(s)
- Hang Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Bingwei Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Qiong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Xiaokang Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Erqun Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Yang Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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8
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Islam M, Shen F, Regmi D, Petersen K, Karim MRU, Du D. Tau liquid-liquid phase separation: At the crossroads of tau physiology and tauopathy. J Cell Physiol 2024; 239:e30853. [PMID: 35980344 PMCID: PMC9938090 DOI: 10.1002/jcp.30853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 12/14/2022]
Abstract
Abnormal deposition of tau in neurons is a hallmark of Alzheimer's disease and several other neurodegenerative disorders. In the past decades, extensive efforts have been made to explore the mechanistic pathways underlying the development of tauopathies. Recently, the discovery of tau droplet formation by liquid-liquid phase separation (LLPS) has received a great deal of attention. It has been reported that tau condensates have a biological role in promoting and stabilizing microtubule (MT) assembly. Furthermore, it has been hypothesized that the transition of phase-separated tau droplets to a gel-like state and then to fibrils is associated with the pathology of neurodegenerative diseases. In this review, we outline LLPS, the structural disorder that facilitates tau droplet formation, the effects of posttranslational modification of tau on condensate formation, the physiological function of tau droplets, the pathways from droplet to toxic fibrils, and the therapeutic strategies for tauopathies that might evolve from toxic droplets. We expect a deeper understanding of tau LLPS will provide additional insights into tau physiology and tauopathies.
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Affiliation(s)
- Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Katherine Petersen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Md Raza Ul Karim
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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9
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Li X, Bedlack R. Evaluating emerging drugs in phase II & III for the treatment of amyotrophic lateral sclerosis. Expert Opin Emerg Drugs 2024; 29:93-102. [PMID: 38516735 DOI: 10.1080/14728214.2024.2333420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
INTRODUCTION Amyotrophic Lateral Sclerosis is a rapidly progressive motor neuron disorder causing severe disability and premature death. Owing to the advances in uncovering ALS pathophysiology, efficient clinical trial design and research advocacy program, several disease-modifying drugs have been approved for treating ALS. Despite this progress, ALS remains a rapidly disabling and life shortening condition. There is a critical need for more effective therapies. AREAS COVERED Here, we reviewed the emerging ALS therapeutics undergoing phase II & III clinical trials. To identify the investigational drugs, we searched ALS and phase II/III trials that are active and recruiting or not yet recruiting on clinicaltrials.gov and Pharmaprojects database. EXPERT OPINION The current pipeline is larger and more diverse than ever, with drugs targeting potential genetic and retroviral causes of ALS and drugs targeting a wide array of downstream pathways, including RNA metabolism, protein aggregation, integrated stress response and neuroinflammation.We remain most excited about those that target direct causes of ALS, e.g. antisense oligonucleotides targeting causative genes. Drugs that eliminate abnormal protein aggregates are also up-and-coming. Eventually, because of the heterogeneity of ALS pathophysiology, biomarkers that determine which biological events are most important for an individual ALS patient are needed.
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Affiliation(s)
- Xiaoyan Li
- Department of Neurology, Duke University, Durham, NC, USA
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10
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Liu S, Zhang X, Yao X, Wang G, Huang S, Chen P, Tang M, Cai J, Wu Z, Zhang Y, Xu R, Liu K, He K, Wang Y, Jiang L, Wang QA, Rui L, Liu J, Liu Y. Mammalian IRE1α dynamically and functionally coalesces with stress granules. Nat Cell Biol 2024; 26:917-931. [PMID: 38714852 DOI: 10.1038/s41556-024-01418-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 04/03/2024] [Indexed: 05/31/2024]
Abstract
Upon endoplasmic reticulum (ER) stress, activation of the ER-resident transmembrane protein kinase/endoribonuclease inositol-requiring enzyme 1 (IRE1) initiates a key branch of the unfolded protein response (UPR) through unconventional splicing generation of the transcription factor X-box-binding protein 1 (XBP1s). Activated IRE1 can form large clusters/foci, whose exact dynamic architectures and functional properties remain largely elusive. Here we report that, in mammalian cells, formation of IRE1α clusters is an ER membrane-bound phase separation event that is coupled to the assembly of stress granules (SGs). In response to different stressors, IRE1α clusters are dynamically tethered to SGs at the ER. The cytosolic linker portion of IRE1α possesses intrinsically disordered regions and is essential for its condensation with SGs. Furthermore, disruption of SG assembly abolishes IRE1α clustering and compromises XBP1 mRNA splicing, and such IRE1α-SG coalescence engenders enrichment of the biochemical components of the pro-survival IRE1α-XBP1 pathway during ER stress. Our findings unravel a phase transition mechanism for the spatiotemporal assembly of IRE1α-SG condensates to establish a more efficient IRE1α machinery, thus enabling higher stress-handling capacity.
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Affiliation(s)
- Songzi Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Xiaoge Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Xin Yao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Guan Wang
- Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Shijia Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Peng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Mingliang Tang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jie Cai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Clinical Research Center, the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhuyin Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yiliang Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Rongzhi Xu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Kai Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Kangmin He
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Lei Jiang
- Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Qiong A Wang
- Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, USA
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, CA, USA
| | - Liangyou Rui
- Department of Molecular and Integrative Physiology, the University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jianmiao Liu
- Cellular Signaling Laboratory, Key Laboratory of Molecular Biophysics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences; TaiKang Center for Life and Medical Sciences; the Institute for Advanced Studies; Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China.
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11
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Velázquez-Pérez L, Rodríguez-Labrada R, Gonzalez-Garcés Y, Canales-Ochoa N, Medrano-Montero J, Domínguez-Barrios Y, Carrillo-Rodes FJ, Ramírez-Bautista MB, Caballero-Laguna A, Gámez-Rodríguez O, Hernández-Oliver MO, Sosa-Cruz Y, Zayas-Hernández A, Vázquez-Mojena Y, Ziemann U, Auburger G. COVID-19 Impacts the Mental Health and Speech Function in Spinocerebellar Ataxia Type 2: Evidences from a Follow-Up Study. CEREBELLUM (LONDON, ENGLAND) 2024; 23:1101-1111. [PMID: 37861884 DOI: 10.1007/s12311-023-01612-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/30/2023] [Indexed: 10/21/2023]
Abstract
Limited evidence suggests that the SARS-CoV-2 infection can accelerate the progression of neurodegenerative diseases, but this has been not verified in the spinocerebellar ataxias (SCA). The objective of this study is to assess the impact of COVID-19 on the mental health and motor features of SCA2. A follow-up study was carried out in 170 Cuban SCA2 subjects and 87 community controls between 2020 and 2021. All subjects underwent a structured questionnaire to assess the risks of exposure to COVID-19, the confirmation of COVID-19 diagnosis, and the Hospital Anxiety and Depression Scale (HADS). Moreover, 36 subjects underwent the Scale for the Assessment and Rating of ataxia (SARA). The risk of exposure to SARS-CoV-2 and the frequency of COVID-19 were similar between the ataxia cohort and the community controls. Within the ataxia group, significantly increased HADS scores existed at the 2nd visit in both groups, but this increase was more evident for the infected group regarding the depression score. Moreover, a significant within-group increase of SARA score was observed in the infected group but not the non-infected group, which was mainly mediated by the significant increase of the speech item score in the infected group. Similar results were observed within the subgroup of preclinical carriers. Our study identified no selective vulnerability nor protection to COVID-19 in SCA2, but once infected, the patients experienced a deterioration of mental health and speech function, even at preclinical disease stage. These findings set rationales for tele-health approaches that minimize the detrimental effect of COVID-19 on SCA2 progression and identify SCA2 individuals as clinical model to elucidate the link between SARS-CoV-2 infection and neurodegeneration.
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Affiliation(s)
- Luis Velázquez-Pérez
- Centre for the Research and Rehabilitation of Hereditary Ataxias, Libertad 26, Holguín, Cuba.
- Cuban Academy of Sciences, Cuba St. 460, between Teniente Rey St., and Compostela St., Habana Vieja, 19100, Havana, Cuba.
| | - Roberto Rodríguez-Labrada
- Cuban Centre for Neuroscience, Playa. 198 St, between 27 and 25th Ave., 16 Cubanacan 19818, Playa, 11300, Havana, Cuba.
| | - Yasmany Gonzalez-Garcés
- Centre for the Research and Rehabilitation of Hereditary Ataxias, Libertad 26, Holguín, Cuba
| | - Nalia Canales-Ochoa
- Centre for the Research and Rehabilitation of Hereditary Ataxias, Libertad 26, Holguín, Cuba
| | | | - Yennis Domínguez-Barrios
- Clinical & Surgical Hospital "Calixto Garcia", Universidad avenue & J st, Vedado, 14 Plaza de la Revolución, 10400, Havana, Cuba
| | - Frank J Carrillo-Rodes
- Centre for the Research and Rehabilitation of Hereditary Ataxias, Libertad 26, Holguín, Cuba
| | | | | | - Osiel Gámez-Rodríguez
- University Hospital "Juan Bruno Zayas", Carretera del Caney Street. Pastorita, Santiago de Cuba, Cuba
| | | | | | | | - Yaimeé Vázquez-Mojena
- Cuban Centre for Neuroscience, Playa. 198 St, between 27 and 25th Ave., 16 Cubanacan 19818, Playa, 11300, Havana, Cuba
| | - Ulf Ziemann
- Department of Neurology and Stroke, Eberhard-Karls University of Tübingen, Hoppe-Seyler Str.3, 72076, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard-Karls University of Tübingen, 22 Hoppe-Seyler Str.3, 72076, Tübingen, Germany
| | - Georg Auburger
- Experimental Neurology, Faculty of Medicine, Goethe University, 24, 60590, Frankfurt, Germany
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12
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Wang JY, Liu YJ, Zhang XL, Liu YH, Jiang LL, Hu HY. PolyQ-expanded ataxin-2 aggregation impairs cellular processing-body homeostasis via sequestering the RNA helicase DDX6. J Biol Chem 2024; 300:107413. [PMID: 38810698 DOI: 10.1016/j.jbc.2024.107413] [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: 01/09/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 05/31/2024] Open
Abstract
Ataxin-2 (Atx2) is a polyglutamine (polyQ) tract-containing RNA-binding protein, while its polyQ expansion may cause protein aggregation that is implicated in the pathogenesis of neurodegenerative diseases such as spinocerebellar ataxia type 2 (SCA2). However, the molecular mechanism underlying how Atx2 aggregation contributes to the proteinopathies remains elusive. Here, we investigated the influence of Atx2 aggregation on the assembly and functionality of cellular processing bodies (P-bodies) by using biochemical and fluorescence imaging approaches. We have revealed that polyQ-expanded (PQE) Atx2 sequesters the DEAD-box RNA helicase (DDX6), an essential component of P-bodies, into aggregates or puncta via some RNA sequences. The N-terminal like-Sm (LSm) domain of Atx2 (residues 82-184) and the C-terminal helicase domain of DDX6 are responsible for the interaction and specific sequestration. Moreover, sequestration of DDX6 may aggravate pre-mRNA mis-splicing, and interfere with the assembly of cellular P-bodies, releasing the endoribonuclease MARF1 that promotes mRNA decay and translational repression. Rescuing the DDX6 protein level can recover the assembly and functionality of P-bodies, preventing targeted mRNA from degradation. This study provides a line of evidence for sequestration of the P-body components and impairment of the P-body homeostasis in dysregulating RNA metabolism, which is implicated in the disease pathologies and a potential therapeutic target.
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Affiliation(s)
- Jian-Yang Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Ya-Jun Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Xiang-Le Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Yin-Hu Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, PR China.
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13
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Pontifex CS, Zaman M, Fanganiello RD, Shutt TE, Pfeffer G. Valosin-Containing Protein (VCP): A Review of Its Diverse Molecular Functions and Clinical Phenotypes. Int J Mol Sci 2024; 25:5633. [PMID: 38891822 PMCID: PMC11172259 DOI: 10.3390/ijms25115633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
In this review we examine the functionally diverse ATPase associated with various cellular activities (AAA-ATPase), valosin-containing protein (VCP/p97), its molecular functions, the mutational landscape of VCP and the phenotypic manifestation of VCP disease. VCP is crucial to a multitude of cellular functions including protein quality control, endoplasmic reticulum-associated degradation (ERAD), autophagy, mitophagy, lysophagy, stress granule formation and clearance, DNA replication and mitosis, DNA damage response including nucleotide excision repair, ATM- and ATR-mediated damage response, homologous repair and non-homologous end joining. VCP variants cause multisystem proteinopathy, and pathology can arise in several tissue types such as skeletal muscle, bone, brain, motor neurons, sensory neurons and possibly cardiac muscle, with the disease course being challenging to predict.
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Affiliation(s)
- Carly S. Pontifex
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
| | - Mashiat Zaman
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Timothy E. Shutt
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Gerald Pfeffer
- Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada; (C.S.P.); (M.Z.); (T.E.S.)
- Alberta Child Health Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Heritage Medical Research Building 155, 3330 Hospital Dr NW, Calgary, AB T2N 4N1, Canada
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14
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Matera AG, Steiner RE, Mills CA, Herring LE, Garcia EL. Chaperoning the chaperones: Proteomic analysis of the SMN complex reveals conserved and etiologic connections to the proteostasis network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594402. [PMID: 38903116 PMCID: PMC11188114 DOI: 10.1101/2024.05.15.594402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Molecular chaperones and co-chaperones are highly conserved cellular components that perform variety of duties related to the proper three-dimensional folding of the proteome. The web of factors that carries out this essential task is called the proteostasis network (PN). Ribonucleoproteins (RNPs) represent an underexplored area in terms of the connections they make with the PN. The Survival Motor Neuron (SMN) complex is an RNP assembly chaperone and serves as a paradigm for studying how specific small nuclear (sn)RNAs are identified and paired with their client substrate proteins. SMN protein is the eponymous component of a large complex required for the biogenesis of uridine-rich small nuclear ribonucleoproteins (U-snRNPs) and localizes to distinct membraneless organelles in both the nucleus and cytoplasm of animal cells. SMN forms the oligomeric core of this complex, and missense mutations in its YG box self-interaction domain are known to cause Spinal Muscular Atrophy (SMA). The basic framework for understanding how snRNAs are assembled into U-snRNPs is known, the pathways and mechanisms used by cells to regulate their biogenesis are poorly understood. Given the importance of these processes to normal development as well as neurodegenerative disease, we set out to identify and characterize novel SMN binding partners. Here, we carried out affinity purification mass spectrometry (AP-MS) of SMN using stable fly lines exclusively expressing either wildtype or SMA-causing missense alleles. Bioinformatic analyses of the pulldown data, along with comparisons to proximity labeling studies carried out in human cells, revealed conserved connections to at least two other major chaperone systems including heat shock folding chaperones (HSPs) and histone/nucleosome assembly chaperones. Notably, we found that heat shock cognate protein Hsc70-4 and other HspA family members preferentially interacted with SMA-causing alleles of SMN. Hsc70-4 is particularly interesting because its mRNA is aberrantly sequestered by a mutant form of TDP-43 in mouse and Drosophila ALS (Amyotrophic Lateral Sclerosis) disease models. Most important, a missense allele of Hsc70-4 (HspA8 in mammals) was recently identified as a bypass suppressor of the SMA phenotype in mice. Collectively, these findings suggest that chaperone-related dysfunction lies at the etiological root of both ALS and SMA.
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Affiliation(s)
- A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill NC, USA
- Departments of Biology and Genetics, University of North Carolina at Chapel Hill
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina at Chapel Hill
| | - Rebecca E. Steiner
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill NC, USA
| | - C. Alison Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill
| | - Eric L. Garcia
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill NC, USA
- Department of Biology, University of Kentucky, Lexington KY, USA
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15
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Shang Z, Zhang S, Wang J, Zhou L, Zhang X, Billadeau DD, Yang P, Zhang L, Zhou F, Bai P, Jia D. TRIM25 predominately associates with anti-viral stress granules. Nat Commun 2024; 15:4127. [PMID: 38750080 PMCID: PMC11096359 DOI: 10.1038/s41467-024-48596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Stress granules (SGs) are induced by various environmental stressors, resulting in their compositional and functional heterogeneity. SGs play a crucial role in the antiviral process, owing to their potent translational repressive effects and ability to trigger signal transduction; however, it is poorly understood how these antiviral SGs differ from SGs induced by other environmental stressors. Here we identify that TRIM25, a known driver of the ubiquitination-dependent antiviral innate immune response, is a potent and critical marker of the antiviral SGs. TRIM25 undergoes liquid-liquid phase separation (LLPS) and co-condenses with the SG core protein G3BP1 in a dsRNA-dependent manner. The co-condensation of TRIM25 and G3BP1 results in a significant enhancement of TRIM25's ubiquitination activity towards multiple antiviral proteins, which are mainly located in SGs. This co-condensation is critical in activating the RIG-I signaling pathway, thus restraining RNA virus infection. Our studies provide a conceptual framework for better understanding the heterogeneity of stress granule components and their response to distinct environmental stressors.
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Affiliation(s)
- Zehua Shang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Jinrui Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Lili Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Xinyue Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China
| | - Daniel D Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Peiguo Yang
- School of Life Sciences, Westlake University, Hangzhou, 310024, 310030, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 100850, Beijing, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215000, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China.
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16
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Shelkovnikova TA, Hautbergue GM. RNP granules in ALS and neurodegeneration: From multifunctional membraneless organelles to therapeutic opportunities. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2024; 176:455-479. [PMID: 38802180 DOI: 10.1016/bs.irn.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and related neurodegenerative diseases are characterised by dysfunction of a host of RNA-binding proteins (RBPs) and a severely disrupted RNA metabolism. Recently, RBP-harbouring phase-separated complexes, ribonucleoprotein (RNP) granules, have come into the limelight as "crucibles" of neuronal pathology in ALS. RNP granules are indispensable for the multitude of regulatory processes underlying cellular RNA metabolism and serve as critical organisers of cellular biochemistry. Neurons, highly specialised cells, heavily rely on RNP granules for efficient trafficking, signalling and stress responses. Multiple RNP granule components, primarily RBPs such as TDP-43 and FUS, are affected by ALS mutations. However, even in the absence of mutations, RBP proteinopathies represent pathophysiological hallmarks of ALS. Given the high local concentrations of RBPs and RNAs, their weakened or enhanced interactions within RNP granules disrupt their homeostasis. Thus, the physiological process of phase separation and RNP granule formation, vital for maintaining the high-functioning state of neuronal cells, becomes their Achilles heel. Here, we will review the recent literature on the causes and consequences of abnormal RNP granule functioning in ALS and related disorders. In particular, we will summarise the evidence for the network-level dysfunction of RNP granules in these conditions and discuss considerations for therapeutic interventions to target RBPs, RNP granules and their network as a whole.
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Affiliation(s)
- Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom; Healthy Lifespan Institute (HELSI), University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
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17
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Koizumi T, Fujimoto A, Kawaguchi H, Kurosaki T, Kitamura A. Stress Granule Dysfunction via Chromophore-Associated Light Inactivation. ACS OMEGA 2024; 9:21298-21306. [PMID: 38764671 PMCID: PMC11097178 DOI: 10.1021/acsomega.4c01469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Stress granules (SGs) are cytoplasmic condensates composed of various proteins and RNAs that protect translation-associated machinery from harmful conditions during stress. However, the method of spatiotemporal inactivation of condensates such as SGs in live cells to study cellular phenotypes is still in the process of being demonstrated. Here, we show that the inactivation of SGs by chromophore-associated light inactivation (CALI) using a genetically encoded red fluorescence protein (SuperNova-Red) as a photosensitizer leads to differences in cell viability during recovery from hyperosmotic stress. CALI delayed the disassembly kinetics of SGs during recovery from hyperosmotic stress. Consequently, CALI could inactivate the SGs, and the cellular fate due to SGs could be analyzed. Furthermore, CALI is an effective spatiotemporal knockdown method for intracellular condensates/aggregates and would contribute to the elucidation of importance of such condensates/aggregates.
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Affiliation(s)
- Takumi Koizumi
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Ai Fujimoto
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Haruka Kawaguchi
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Tsumugi Kurosaki
- Laboratory
of Cellular and Molecular Sciences, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Akira Kitamura
- Laboratory
of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
- PRIME, Japan
Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-004, Japan
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18
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Lv J, Kou N, Li Y, Qiu K, Guo X, Zhang L, Zhang Z, He S, Yuan Y. Identification and Verification of Endoplasmic Reticulum Stress-Related Genes as Novel Signatures for Osteoarthritis Diagnosis and Therapy: A Bioinformatics Analysis-Oriented Pilot Study. Biochem Genet 2024:10.1007/s10528-024-10818-1. [PMID: 38734758 DOI: 10.1007/s10528-024-10818-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND AND PURPOSE Endoplasmic reticulum stress (ERS) has been reported to be closely associated with the development of osteoarthritis (OA), but the underlying mechanisms are not fully delineated. The present study was designed to investigate the involvement of ERS-related genes in regulating OA progression. METHODS The expression profiles of OA patients and normal people were downloaded from the gene expression omnibus (GEO) database. The differentially expressed genes (DEGs) in datasets GSE55457 and GSE55235 were screened and identified by R software with the construction of the protein-protein interaction (PPI) networks. Through the STRING and Venn diagram analysis, hub ERS-related genes were obtained. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed. Biomarkers with high diagnostic values of osteoarthritis (OA) were studied. The hematoxylin and eosin (H&E) staining and micro-CT were applied to evaluate the establishment of the OA model. The expression levels of biomarkers were validated with the use of reverse transcription‑quantitative polymerase chain reaction (RT-qPCR) and western blot. Finally, we evaluated the correlations of hub ERS-related genes with the immune infiltration cells via the CIBERSORT algorithm. RESULTS A total of 60 downregulated and 52 upregulated DEGs were identified, and the following GO and KEGG pathway analyses verified that those DEGs were mainly enriched in biological process (BP), cellular component (CC), molecular function (MF), and inflammation-associated signal pathways. Interestingly, among all the DEGs, six ER stress-associated genes, including activating transcription factor 3 (ATF3), DEAD-Box Helicase 3 X-Linked (DDX3X), AP-1 transcription factor subunit (JUN), eukaryotic initiation factor 4 (EIF4A1), KDEL endoplasmic reticulum protein retention receptor 3 (KDELR3), and vascular endothelial growth factor A (VEGFA), were found to be closely associated with OA progression, and the following RT-qPCR and Western Blot analysis confirmed that DDX3X, JUN, and VEGFA were upregulated, whereas KDELR3, EIF4A1, and ATF3 were downregulated in OA rats tissues compared to the normal tissues, which were in accordance with our bioinformatics findings. Furthermore, our receiver operating characteristic (ROC) curve analysis verified that the above six ER stress-associated genes could be used as ideal biomarkers for OA diagnosis and those genes also potentially regulated immune responses by influencing the biological functions of mast cells and macrophages. CONCLUSION Collectively, the present study firstly identified six ER stress-associated genes (ATF3, DDX3X, JUN, EIF4A1, KDELR3, and VEGFA) that may play critical role in regulating the progression of OA.
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Affiliation(s)
- Jia Lv
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Nannan Kou
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Yunxuan Li
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Kejia Qiu
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Xiang Guo
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Li Zhang
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Zhichao Zhang
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China
| | - Shaoxuan He
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China.
| | - Yong Yuan
- Department of Trauma Surgery, The Second Affiliated Hospital of Kunming Medical University, 374 Yunnan-Myanmar Avenue, Kunming, 650101, China.
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19
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Cui Q, Liu Z, Bai G. Friend or foe: The role of stress granule in neurodegenerative disease. Neuron 2024:S0896-6273(24)00286-1. [PMID: 38744273 DOI: 10.1016/j.neuron.2024.04.025] [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: 12/01/2023] [Revised: 03/12/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
Stress granules (SGs) are dynamic membraneless organelles that form in response to cellular stress. SGs are predominantly composed of RNA and RNA-binding proteins that assemble through liquid-liquid phase separation. Although the formation of SGs is considered a transient and protective response to cellular stress, their dysregulation or persistence may contribute to various neurodegenerative diseases. This review aims to provide a comprehensive overview of SG physiology and pathology. It covers the formation, composition, regulation, and functions of SGs, along with their crosstalk with other membrane-bound and membraneless organelles. Furthermore, this review discusses the dual roles of SGs as both friends and foes in neurodegenerative diseases and explores potential therapeutic approaches targeting SGs. The challenges and future perspectives in this field are also highlighted. A more profound comprehension of the intricate relationship between SGs and neurodegenerative diseases could inspire the development of innovative therapeutic interventions against these devastating diseases.
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Affiliation(s)
- Qinqin Cui
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China.
| | - Zongyu Liu
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ge Bai
- Department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Nanhu Brain-Computer Interface Institute, Hangzhou 311100, China; Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou 311121, China; NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China; Institute of Fundamental and Transdisciplinary Research, Zhejiang University, Hangzhou 310058, China.
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20
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Kim J, Kratz AF, Chen S, Sheng J, Kim HK, Zhang L, Singh BK, Chavez A. High-throughput tagging of endogenous loci for rapid characterization of protein function. SCIENCE ADVANCES 2024; 10:eadg8771. [PMID: 38691600 PMCID: PMC11062585 DOI: 10.1126/sciadv.adg8771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
To facilitate the interrogation of protein function at scale, we have developed high-throughput insertion of tags across the genome (HITAG). HITAG enables users to rapidly produce libraries of cells, each with a different protein of interest C-terminally tagged. HITAG is based on a modified strategy for performing Cas9-based targeted insertions, coupled with an improved approach for selecting properly tagged lines. Analysis of the resulting clones generated by HITAG reveals high tagging specificity, with most successful tagging events being indel free. Using HITAG, we fuse mCherry to a set of 167 stress granule-associated proteins and elucidate the features that drive a subset of proteins to strongly accumulate within these transient RNA-protein granules.
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Affiliation(s)
- Joonwon Kim
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander F. Kratz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shiye Chen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jenny Sheng
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hark Kyun Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liudeng Zhang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Brijesh Kumar Singh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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21
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Fang M, Liu Y, Huang C, Fan S. Targeting stress granules in neurodegenerative diseases: A focus on biological function and dynamics disorders. Biofactors 2024; 50:422-438. [PMID: 37966813 DOI: 10.1002/biof.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
Stress granules (SGs) are membraneless organelles formed by eukaryotic cells in response to stress to promote cell survival through their pleiotropic cytoprotective effects. SGs recruit a variety of components to enhance their physiological function, and play a critical role in the propagation of pathological proteins, a key factor in neurodegeneration. Recent advances indicate that SG dynamic disorders exacerbate neuronal susceptibility to stress in neurodegenerative diseases (NDs) including Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Huntington's disease (HD) and Parkinson's disease (PD). Here, we outline the biological functions of SGs, highlight SG dynamic disorders in NDs, and emphasize therapeutic approaches for enhancing SG dynamics to provide new insights into ND intervention.
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Affiliation(s)
- Minglv Fang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Liu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Cheng Huang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shengjie Fan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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22
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Petrauskas A, Fortunati DL, Kandi AR, Pothapragada SS, Agrawal K, Singh A, Huelsmeier J, Hillebrand J, Brown G, Chaturvedi D, Lee J, Lim C, Auburger G, VijayRaghavan K, Ramaswami M, Bakthavachalu B. Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation. PLoS Genet 2024; 20:e1011251. [PMID: 38768217 PMCID: PMC11166328 DOI: 10.1371/journal.pgen.1011251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 06/11/2024] [Accepted: 04/05/2024] [Indexed: 05/22/2024] Open
Abstract
Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) can function in translational activation, translational repression, mRNA stability and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which can help stimulate mRNA translation, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA Binding Proteins Identified by Editing (TRIBE), co-localization and immunoprecipitation experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA and protein content of Ataxin-2 mRNP granules. Experiments with transgenic Drosophila indicate that while the Atx2-LSm domain may protect against neurodegeneration, structured PAM2- and unstructured IDR- interactions both support Atx2-induced cytotoxicity. Taken together, the data lead to a proposal for how Ataxin-2 interactions are remodelled during translational control and how structured and non-structured interactions contribute differently to the specificity and efficiency of RNP granule condensation as well as to neurodegeneration.
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Affiliation(s)
- Arnas Petrauskas
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Daniel L. Fortunati
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Arvind Reddy Kandi
- School of Biosciences and Bioengineering, Indian Institute of Technology, Mandi, India
| | | | - Khushboo Agrawal
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam, Kerala, India
| | - Amanjot Singh
- National Centre for Biological Sciences, TIFR, Bangalore, India
- Manipal Institute of Regenerative Medicine, MAHE-Bengaluru, Govindapura, Bengaluru, India
| | - Joern Huelsmeier
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Jens Hillebrand
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Georgia Brown
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | | | - Jongbo Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, Republic of Korea
| | - Georg Auburger
- Experimental Neurology, Medical School, Goethe University, Frankfurt, Germany
| | | | - Mani Ramaswami
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Baskar Bakthavachalu
- School of Biosciences and Bioengineering, Indian Institute of Technology, Mandi, India
- Tata Institute for Genetics and Society Centre at inStem, Bellary Road, Bangalore, India
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23
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Lai CH, Ko KT, Fan PJ, Yu TA, Chang CF, Draczkowski P, Hsu STD. Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance. J Biol Chem 2024; 300:107230. [PMID: 38537699 PMCID: PMC11047754 DOI: 10.1016/j.jbc.2024.107230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024] Open
Abstract
Arsenite-induced stress granule (SG) formation can be cleared by the ubiquitin-proteasome system aided by the ATP-dependent unfoldase p97. ZFAND1 participates in this pathway by recruiting p97 to trigger SG clearance. ZFAND1 contains two An1-type zinc finger domains (ZF1 and ZF2), followed by a ubiquitin-like domain (UBL); but their structures are not experimentally determined. To shed light on the structural basis of the ZFAND1-p97 interaction, we determined the atomic structures of the individual domains of ZFAND1 by solution-state NMR spectroscopy and X-ray crystallography. We further characterized the interaction between ZFAND1 and p97 by methyl NMR spectroscopy and cryo-EM. 15N spin relaxation dynamics analysis indicated independent domain motions for ZF1, ZF2, and UBL. The crystal structure and NMR structure of UBL showed a conserved β-grasp fold homologous to ubiquitin and other UBLs. Nevertheless, the UBL of ZFAND1 contains an additional N-terminal helix that adopts different conformations in the crystalline and solution states. ZFAND1 uses the C-terminal UBL to bind to p97, evidenced by the pronounced line-broadening of the UBL domain during the p97 titration monitored by methyl NMR spectroscopy. ZFAND1 binding induces pronounced conformational heterogeneity in the N-terminal domain of p97, leading to a partial loss of the cryo-EM density of the N-terminal domain of p97. In conclusion, this work paved the way for a better understanding of the interplay between p97 and ZFAND1 in the context of SG clearance.
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Affiliation(s)
- Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuang-Ting Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Pei-Ju Fan
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | - Tsun-Ai Yu
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- High-Field Nuclear Magnetic Resonance Center, Academia Sinica, Taipei, Taiwan
| | | | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability With Knotted Chiral Meta Matter (SKCM(2)), Hiroshima University, Higashihiroshima, Japan.
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24
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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25
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Parker DM, Bublitz GR, Parker R. Shining light on DHX9: UV-induced stress granules illuminate protective mechanisms for daughter cell resilience. Mol Cell 2024; 84:1403-1405. [PMID: 38640893 DOI: 10.1016/j.molcel.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/21/2024]
Abstract
In a recent article in Cell, Zhou et al. investigate the origins, composition, and biological consequences of UV-induced stress granules. They find that UV-induced stress granules are triggered by the formation of RNA-protein crosslinks, uniquely contain DHX9 as a marker, form during mitosis independently of translation repression, and are enriched in intron-containing RNAs and splicing factors. Moreover, UV-induced granules contain double-stranded RNA (dsRNA) and trigger a dsRNA response. This work identifies a mechanism for resolving UV-damaged RNA and broadens the types of cytosolic "stress granules" that form.
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Affiliation(s)
- Dylan M Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Gaia R Bublitz
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
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26
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Shiramasa Y, Yamamoto R, Kashiwagi N, Sasaki F, Imai S, Ike M, Kitazawa S, Kameda T, Kitahara R. An aberrant fused in sarcoma liquid droplet of amyotrophic lateral sclerosis pathological variant, R495X, accelerates liquid-solid phase transition. Sci Rep 2024; 14:8914. [PMID: 38632300 PMCID: PMC11024109 DOI: 10.1038/s41598-024-59604-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
Intracellular aggregation of fused in sarcoma (FUS) is associated with the pathogenesis of familial amyotrophic lateral sclerosis (ALS). Under stress, FUS forms liquid droplets via liquid-liquid phase separation (LLPS). Two types of wild-type FUS LLPS exist in equilibrium: low-pressure LLPS (LP-LLPS) and high-pressure LLPS (HP-LLPS); the former dominates below 2 kbar and the latter over 2 kbar. Although several disease-type FUS variants have been identified, the molecular mechanism underlying accelerated cytoplasmic granule formation in ALS patients remains poorly understood. Herein, we report the reversible formation of the two LLPS states and the irreversible liquid-solid transition, namely droplet aging, of the ALS patient-type FUS variant R495X using fluorescence microscopy and ultraviolet-visible absorption spectroscopy combined with perturbations in pressure and temperature. Liquid-to-solid phase transition was accelerated in the HP-LLPS of R495X than in the wild-type variant; arginine slowed the aging of droplets at atmospheric conditions by inhibiting the formation of HP-LLPS more selectively compared to that of LP-LLPS. Our findings provide new insight into the mechanism by which R495X readily forms cytoplasmic aggregates. Targeting the aberrantly formed liquid droplets (the HP-LLPS state) of proteins with minimal impact on physiological functions could be a novel therapeutic strategy for LLPS-mediated protein diseases.
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Affiliation(s)
- Yutaro Shiramasa
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Ryu Yamamoto
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Norika Kashiwagi
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Fuka Sasaki
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Sawaka Imai
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Mikihito Ike
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ryo Kitahara
- Graduate School of Pharmacy, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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27
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Fiorentino J, Armaos A, Colantoni A, Tartaglia G. Prediction of protein-RNA interactions from single-cell transcriptomic data. Nucleic Acids Res 2024; 52:e31. [PMID: 38364867 PMCID: PMC11014251 DOI: 10.1093/nar/gkae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024] Open
Abstract
Proteins are crucial in regulating every aspect of RNA life, yet understanding their interactions with coding and noncoding RNAs remains limited. Experimental studies are typically restricted to a small number of cell lines and a limited set of RNA-binding proteins (RBPs). Although computational methods based on physico-chemical principles can predict protein-RNA interactions accurately, they often lack the ability to consider cell-type-specific gene expression and the broader context of gene regulatory networks (GRNs). Here, we assess the performance of several GRN inference algorithms in predicting protein-RNA interactions from single-cell transcriptomic data, and propose a pipeline, called scRAPID (single-cell transcriptomic-based RnA Protein Interaction Detection), that integrates these methods with the catRAPID algorithm, which can identify direct physical interactions between RBPs and RNA molecules. Our approach demonstrates that RBP-RNA interactions can be predicted from single-cell transcriptomic data, with performances comparable or superior to those achieved for the well-established task of inferring transcription factor-target interactions. The incorporation of catRAPID significantly enhances the accuracy of identifying interactions, particularly with long noncoding RNAs, and enables the identification of hub RBPs and RNAs. Additionally, we show that interactions between RBPs can be detected based on their inferred RNA targets. The software is freely available at https://github.com/tartaglialabIIT/scRAPID.
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Affiliation(s)
- Jonathan Fiorentino
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Alessio Colantoni
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Gian Gaetano Tartaglia
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Centre for Human Technologies (CHT), RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
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28
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Jin SW, Seong Y, Yoon D, Kwon YS, Song H. Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1. Nucleic Acids Res 2024; 52:3310-3326. [PMID: 38165001 PMCID: PMC11014241 DOI: 10.1093/nar/gkad1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/22/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
L1TD1 is a cytoplasmic RNA-binding protein specifically expressed in pluripotent stem cells and, unlike its mouse ortholog, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known protein-coding gene domesticated from a LINE-1 (L1) retroelement, the functional legacy of its ancestral protein, ORF1p of L1, and how it is manifested in L1TD1 are still unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs and localizes to high-density ribonucleoprotein (RNP) condensates. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. L1TD1 depletion promoted the formation of stress granules in embryonic stem cells. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain of L1TD1 facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatment of neurodegenerative diseases caused by disturbed stress granule dynamics.
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Affiliation(s)
- Sang Woo Jin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Youngmo Seong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Dayoung Yoon
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young-Soo Kwon
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Hoseok Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
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29
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Ren X, Cui Z, Zhang Q, Su Z, Xu W, Wu J, Jiang H. JunB condensation attenuates vascular endothelial damage under hyperglycemic condition. J Mol Cell Biol 2024; 15:mjad072. [PMID: 38140943 PMCID: PMC11080659 DOI: 10.1093/jmcb/mjad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 09/23/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Endothelial damage is the initial and crucial factor in the occurrence and development of vascular complications in diabetic patients, contributing to morbidity and mortality. Although hyperglycemia has been identified as a damaging effector, the detailed mechanisms remain elusive. In this study, identified by ATAC-seq and RNA-seq, JunB reverses the inhibition of proliferation and the promotion of apoptosis in human umbilical vein endothelial cells treated with high glucose, mainly through the cell cycle and p53 signaling pathways. Furthermore, JunB undergoes phase separation in the nucleus and in vitro, mediated by its intrinsic disordered region and DNA-binding domain. Nuclear localization and condensation behaviors are required for JunB-mediated proliferation and apoptosis. Thus, our study uncovers the roles of JunB and its coacervation in repairing vascular endothelial damage caused by high glucose, elucidating the involvement of phase separation in diabetes and diabetic endothelial dysfunction.
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Affiliation(s)
- Xuxia Ren
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zexu Cui
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiaoqiao Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhiguang Su
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Xu
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jinhui Wu
- Center of Geriatrics and Gerontology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Jiang
- Laboratory for Aging and Cancer Research, Frontiers Science Center Disease-related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
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30
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Maneix L, Iakova P, Lee CG, Moree SE, Lu X, Datar GK, Hill CT, Spooner E, King JCK, Sykes DB, Saez B, Di Stefano B, Chen X, Krause DS, Sahin E, Tsai FTF, Goodell MA, Berk BC, Scadden DT, Catic A. Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing. Nat Cell Biol 2024; 26:593-603. [PMID: 38553595 PMCID: PMC11021199 DOI: 10.1038/s41556-024-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Loss of protein function is a driving force of ageing. We have identified peptidyl-prolyl isomerase A (PPIA or cyclophilin A) as a dominant chaperone in haematopoietic stem and progenitor cells. Depletion of PPIA accelerates stem cell ageing. We found that proteins with intrinsically disordered regions (IDRs) are frequent PPIA substrates. IDRs facilitate interactions with other proteins or nucleic acids and can trigger liquid-liquid phase separation. Over 20% of PPIA substrates are involved in the formation of supramolecular membrane-less organelles. PPIA affects regulators of stress granules (PABPC1), P-bodies (DDX6) and nucleoli (NPM1) to promote phase separation and increase cellular stress resistance. Haematopoietic stem cell ageing is associated with a post-transcriptional decrease in PPIA expression and reduced translation of IDR-rich proteins. Here we link the chaperone PPIA to the synthesis of intrinsically disordered proteins, which indicates that impaired protein interaction networks and macromolecular condensation may be potential determinants of haematopoietic stem cell ageing.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Polina Iakova
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Charles G Lee
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Shannon E Moree
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xuan Lu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gandhar K Datar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Cedric T Hill
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Jordon C K King
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Borja Saez
- Center for Applied Medical Research, Hematology-Oncology Unit, Pamplona, Navarra, Spain
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Daniela S Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Ergun Sahin
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA
| | - Bradford C Berk
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Cell and Gene Therapy Program at the Dan L. Duncan Comprehensive Cancer Center, Houston, TX, USA.
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA.
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31
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Milani M, Della Valle I, Rossi S, Fabbrizio P, Margotta C, Nardo G, Cozzolino M, D'Ambrosi N, Apolloni S. Neuroprotective effects of niclosamide on disease progression via inflammatory pathways modulation in SOD1-G93A and FUS-associated amyotrophic lateral sclerosis models. Neurotherapeutics 2024; 21:e00346. [PMID: 38493058 PMCID: PMC11070272 DOI: 10.1016/j.neurot.2024.e00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease influenced by genetic, epigenetic, and environmental factors, resulting in dysfunction in cellular and molecular pathways. The limited efficacy of current treatments highlights the need for combination therapies targeting multiple aspects of the disease. Niclosamide, an anthelminthic drug listed as an essential medicine, has been repurposed in clinical trials for different diseases due to its anti-inflammatory and anti-fibrotic properties. Niclosamide can inhibit various molecular pathways (e.g., STAT3, mTOR) that are dysregulated in ALS, suggesting its potential to disrupt these altered mechanisms associated with the pathology. We administered niclosamide intraperitoneally to two transgenic murine models, SOD1-G93A and FUS mice, mimicking key pathological processes of ALS. The treatment was initiated at the onset of symptoms, and we assessed disease progression by neurological scores, rotarod and wire tests, and monitored survival. Furthermore, we investigated cellular and molecular mechanisms affected by niclosamide in the spinal cord and muscle of ALS mice. In both models, the administration of niclosamide resulted in a slowdown of disease progression, an increase in survival rates, and an improvement in tissue pathology. This was characterised by reduced gliosis, motor neuron loss, muscle atrophy, and inflammatory pathways. Based on these results, our findings demonstrate that niclosamide can impact multiple pathways involved in ALS. This multi-targeted approach leads to a slowdown in the progression of the disease, positioning niclosamide as a promising candidate for repurposing in the treatment of ALS.
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Affiliation(s)
- Martina Milani
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Program in Cellular and Molecular Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Ilaria Della Valle
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Program in Cellular and Molecular Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Simona Rossi
- Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
| | - Paola Fabbrizio
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Cassandra Margotta
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Giovanni Nardo
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Mauro Cozzolino
- Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
| | - Nadia D'Ambrosi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Savina Apolloni
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; UniCamillus-Saint Camillus International University of Health Sciences, Rome, Italy.
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Barrow ER, Valionyte E, Baxter CR, Yang Y, Herath S, O'Connell WA, Lopatecka J, Strachan A, Woznica W, Stephenson HN, Fejer G, Sharma V, Lu B, Luo S. Discovery of SQSTM1/p62-dependent P-bodies that regulate the NLRP3 inflammasome. Cell Rep 2024; 43:113935. [PMID: 38460129 DOI: 10.1016/j.celrep.2024.113935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/22/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024] Open
Abstract
Autophagy and ribonucleoprotein granules, such as P-bodies (PBs) and stress granules, represent vital stress responses to maintain cellular homeostasis. SQSTM1/p62 phase-separated droplets are known to play critical roles in selective autophagy; however, it is unknown whether p62 can exist as another form in addition to its autophagic droplets. Here, we found that, under stress conditions, including proteotoxicity, endotoxicity, and oxidation, autophagic p62 droplets are transformed to a type of enlarged PBs, termed p62-dependent P-bodies (pd-PBs). p62 phase separation is essential for the nucleation of pd-PBs. Mechanistically, pd-PBs are triggered by enhanced p62 droplet formation upon stress stimulation through the interactions between p62 and DDX6, a DEAD-box ATPase. Functionally, pd-PBs recruit the NLRP3 inflammasome adaptor ASC to assemble the NLRP3 inflammasome and induce inflammation-associated cytotoxicity. Our study shows that p62 droplet-to-PB transformation acts as a stress response to activate the NLRP3 inflammasome process, suggesting that persistent pd-PBs lead to NLRP3-dependent inflammation toxicity.
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Affiliation(s)
- Elizabeth R Barrow
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Evelina Valionyte
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Chris R Baxter
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Yi Yang
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Sharon Herath
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - William A O'Connell
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Justyna Lopatecka
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Alexander Strachan
- Plymouth Electron Microscopy Centre, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Waldemar Woznica
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Holly N Stephenson
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK
| | - Gyorgy Fejer
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Vikram Sharma
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Drake Circus, PL4 8AA Plymouth, UK
| | - Boxun Lu
- State Key Laboratory of Medical Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Shouqing Luo
- Peninsula Medical School, Faculty of Health, University of Plymouth, Research Way, PL6 8BU Plymouth, UK.
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33
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许 光, 高 安, 丛 斌. [Restraint stress induces blood-brain barrier injury in rat amygdala by activating the Rho/ROCK signaling pathway]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2024; 44:411-419. [PMID: 38597431 PMCID: PMC11006700 DOI: 10.12122/j.issn.1673-4254.2024.03.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Indexed: 04/11/2024]
Abstract
OBJECTIVE To investigate the role of Rho/ROCK signaling pathway in mediating restraint stress-induced blood-brain barrier (BBB) injury in the amygdala of rats. METHODS Sixty male SD rats were randomized equally into control group (with food and water deprivation for 6 h per day), restraint stress group (with restraint for 6 h per day), stress + fasudil treatment (administered by intraperitoneal injection at 1 mg/100 g 30 min before the 6-h restraint) group, and fasudil treatment alone group. The elevated plus-maze test was used to detect behavioral changes of the rats, serum corticosterone and S100B levels were determined with ELISA, and Evans Blue leakage in the brain tissue was examined to evaluate the changes in BBB permeability. The changes in expression levels of tight junction proteins in the amygdala were detected using immunofluorescence assay and Western blotting, and Rho/ROCK pathway activation was detected by Pull-down test and Western blotting. Ultrastructural changes of the cerebral microvascular endothelial cells were observed using transmission electron microscopy. RESULTS Compared with those in the control group, the rats in restrain stress group and stress+fasudil group showed obvious anxiety-like behavior with significantly increased serum corticosterone level (P<0.001). Compared with those in the control group and stress+fasudil group, the rat models of restrain stress showed more obvious Evans Blue leakage and higher S100B expression (P<0.01) but lower expressions of tight junction proteins in the amygdala. Pull-down test and Western blotting confirmed that the expression levels of RhoA-GTP, ROCK2 and P-MLC 2 were significantly higher in stress group than in the control group and stress + fasudil group (P<0.05). Transmission electron microscopy revealed obvious ultrastructural changes in the cerebral microvascular endothelial cells in the rat models of restrain stress. CONCLUSION Restraint stress induces BBB injury in the amygdala of rats by activating the Rho/ROCK signaling pathway.
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Affiliation(s)
- 光明 许
- 中央司法警官学院法医学教研室,河北 保定 071000Department of Forensic Medicine, National Police University for Criminal Justice, Baoding 071000, China
| | - 安迪 高
- 中央司法警官学院法医学教研室,河北 保定 071000Department of Forensic Medicine, National Police University for Criminal Justice, Baoding 071000, China
| | - 斌 丛
- 河北医科大学法医学院//河北省法医学重点实验室,河北 石家庄 050017College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
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34
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Jiang L, Roberts R, Wong M, Zhang L, Webber CJ, Libera J, Wang Z, Kilci A, Jenkins M, Ortiz AR, Dorrian L, Sun J, Sun G, Rashad S, Kornbrek C, Daley SA, Dedon PC, Nguyen B, Xia W, Saito T, Saido TC, Wolozin B. β-amyloid accumulation enhances microtubule associated protein tau pathology in an APP NL-G-F/MAPT P301S mouse model of Alzheimer's disease. Front Neurosci 2024; 18:1372297. [PMID: 38572146 PMCID: PMC10987964 DOI: 10.3389/fnins.2024.1372297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/01/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction The study of the pathophysiology study of Alzheimer's disease (AD) has been hampered by lack animal models that recapitulate the major AD pathologies, including extracellular -amyloid (A) deposition, intracellular aggregation of microtubule associated protein tau (MAPT), inflammation and neurodegeneration. Methods The humanized APPNL-G-F knock-in mouse line was crossed to the PS19 MAPTP301S, over-expression mouse line to create the dual APPNL-G-F/PS19 MAPTP301S line. The resulting pathologies were characterized by immunochemical methods and PCR. Results We now report on a double transgenic APPNL-G-F/PS19 MAPTP301S mouse that at 6 months of age exhibits robust A plaque accumulation, intense MAPT pathology, strong inflammation and extensive neurodegeneration. The presence of A pathology potentiated the other major pathologies, including MAPT pathology, inflammation and neurodegeneration. MAPT pathology neither changed levels of amyloid precursor protein nor potentiated A accumulation. Interestingly, study of immunofluorescence in cleared brains indicates that microglial inflammation was generally stronger in the hippocampus, dentate gyrus and entorhinal cortex, which are regions with predominant MAPT pathology. The APPNL-G-F/MAPTP301S mouse model also showed strong accumulation of N6-methyladenosine (m6A), which was recently shown to be elevated in the AD brain. m6A primarily accumulated in neuronal soma, but also co-localized with a subset of astrocytes and microglia. The accumulation of m6A corresponded with increases in METTL3 and decreases in ALKBH5, which are enzymes that add or remove m6A from mRNA, respectively. Discussion Our understanding of the pathophysiology of Alzheimer's disease (AD) has been hampered by lack animal models that recapitulate the major AD pathologies, including extracellular -amyloid (A) deposition, intracellular aggregation of microtubule associated protein tau (MAPT), inflammation and neurodegeneration. The APPNL-G-F/MAPTP301S mouse recapitulates many features of AD pathology beginning at 6 months of aging, and thus represents a useful new mouse model for the field.
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Affiliation(s)
- Lulu Jiang
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Department of Neuroscience, Center for Brain Immunology and Glia (BIG), School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Rebecca Roberts
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Melissa Wong
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Lushuang Zhang
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Chelsea Joy Webber
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Department of Pharmacology, Physiology and Biophysics, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Jenna Libera
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Zihan Wang
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Alper Kilci
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Matthew Jenkins
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Alejandro Rondón Ortiz
- Department of Pharmacology, Physiology and Biophysics, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Luke Dorrian
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore, Singapore
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sherif Rashad
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | | | - Sarah Anne Daley
- Department of Pharmacology, Physiology and Biophysics, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Geriatric Research Education and Clinical Center, Bedford VA Healthcare System, Bedford, MA, United States
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore, Singapore
| | - Brian Nguyen
- LifeCanvas Technologies, Cambridge, MA, United States
| | - Weiming Xia
- Department of Pharmacology, Physiology and Biophysics, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Geriatric Research Education and Clinical Center, Bedford VA Healthcare System, Bedford, MA, United States
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Takaomi C. Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Saitama, Japan
| | - Benjamin Wolozin
- Department of Anatomy and Neurobiology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Department of Pharmacology, Physiology and Biophysics, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Department of Neurology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA, United States
- Center for Systems Neuroscience, Boston University, Boston, MA, United States
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35
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Fakim H, Vande Velde C. The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2024; 156:176-189. [PMID: 37268555 DOI: 10.1016/j.semcdb.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
In recent years, there has been an emphasis on the role of phase-separated biomolecular condensates, especially stress granules, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). This is largely due to several ALS-associated mutations occurring in genes involved in stress granule assembly and observations that pathological inclusions detected in ALS patient neurons contain stress granule proteins, including the ALS-linked proteins TDP-43 and FUS. However, protein components of stress granules are also found in numerous other phase-separated biomolecular condensates under physiological conditions which are inadequately discussed in the context of ALS. In this review, we look beyond stress granules and describe the roles of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites, such as the nucleolus, Cajal bodies, paraspeckles and neuronal RNA transport granules. We also discuss the consequences of ALS-linked mutations in TDP-43 and FUS on their ability to phase separate into these stress-independent biomolecular condensates and perform their respective functions. Importantly, biomolecular condensates sequester multiple overlapping protein and RNA components, and their dysregulation could contribute to the observed pleiotropic effects of both sporadic and familial ALS on RNA metabolism.
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Affiliation(s)
- Hana Fakim
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada.
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36
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Uozumi R, Mori K, Gotoh S, Miyamoto T, Kondo S, Yamashita T, Kawabe Y, Tagami S, Akamine S, Ikeda M. PABPC1 mediates degradation of C9orf72-FTLD/ALS GGGGCC repeat RNA. iScience 2024; 27:109303. [PMID: 38444607 PMCID: PMC10914486 DOI: 10.1016/j.isci.2024.109303] [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: 09/01/2023] [Revised: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
GGGGCC hexanucleotide repeat expansion in C9orf72 causes frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Expanded GGGGCC repeat RNA accumulates within RNA foci and is translated into toxic dipeptide repeat proteins; thus, efficient repeat RNA degradation may alleviate diseases. hnRNPA3, one of the repeat RNA-binding proteins, has been implicated in the destabilization of repeat RNA. Using APEX2-mediated proximity biotinylation, here, we demonstrate PABPC1, a cytoplasmic poly (A)-binding protein, interacts with hnRNPA3. Knockdown of PABPC1 increased the accumulation of repeat RNA and RNA foci to the same extent as the knockdown of hnRNPA3. Proximity ligation assays indicated PABPC1-hnRNPA3 and PABPC1-RNA exosomes, a complex that degrades repeat RNA, preferentially co-localized when repeat RNA was present. Our results suggest that PABPC1 functions as a mediator of polyadenylated GGGGCC repeat RNA degradation through interactions with hnRNPA3 and RNA exosome complex.
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Affiliation(s)
- Ryota Uozumi
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kohji Mori
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shiho Gotoh
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tesshin Miyamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shizuko Kondo
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoko Yamashita
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuya Kawabe
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Psychiatry, Minoh Neuropsychiatric Hospital, Minoh, Osaka 562-0004, Japan
| | - Shinji Tagami
- Psychiatry, Minoh Neuropsychiatric Hospital, Minoh, Osaka 562-0004, Japan
- Health and Counseling Center, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shoshin Akamine
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Manabu Ikeda
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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37
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Freibaum BD, Messing J, Nakamura H, Yurtsever U, Wu J, Kim HJ, Hixon J, Lemieux RM, Duffner J, Huynh W, Wong K, White M, Lee C, Meyers RE, Parker R, Taylor JP. Identification of small molecule inhibitors of G3BP-driven stress granule formation. J Cell Biol 2024; 223:e202308083. [PMID: 38284934 PMCID: PMC10824102 DOI: 10.1083/jcb.202308083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Stress granule formation is triggered by the release of mRNAs from polysomes and is promoted by the action of the RNA-binding proteins G3BP1/2. Stress granules have been implicated in several disease states, including cancer and neurodegeneration. Consequently, compounds that limit stress granule formation or promote their dissolution have potential as both experimental tools and novel therapeutics. Herein, we describe two small molecules, G3BP inhibitor a and b (G3Ia and G3Ib), designed to bind to a specific pocket in G3BP1/2 that is targeted by viral inhibitors of G3BP1/2 function. In addition to disrupting the co-condensation of RNA, G3BP1, and caprin 1 in vitro, these compounds inhibit stress granule formation in cells treated prior to or concurrent with stress and dissolve pre-existing stress granules. These effects are consistent across multiple cell types and a variety of initiating stressors. Thus, these compounds represent powerful tools to probe the biology of stress granules and hold promise for therapeutic interventions designed to modulate stress granule formation.
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Affiliation(s)
- Brian D. Freibaum
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Haruko Nakamura
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ugur Yurtsever
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinjun Wu
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | | | | | | | | | | | | | | | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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38
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Sato K, Takayama KI, Inoue S. Stress granule-mediated RNA regulatory mechanism in Alzheimer's disease. Geriatr Gerontol Int 2024; 24 Suppl 1:7-14. [PMID: 37726158 DOI: 10.1111/ggi.14663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/20/2023] [Accepted: 08/27/2023] [Indexed: 09/21/2023]
Abstract
Living organisms experience a range of stresses. To cope effectively with these stresses, eukaryotic cells have evolved a sophisticated mechanism involving the formation of stress granules (SGs), which play a crucial role in protecting various types of RNA species under stress, such as mRNAs and long non-coding RNAs (lncRNAs). SGs are non-membranous cytoplasmic ribonucleoprotein (RNP) granules, and the RNAs they contain are translationally stalled. Importantly, SGs have been thought to contribute to the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD). SGs also contain multiple RNA-binding proteins (RBPs), several of which have been implicated in AD progression. SGs are transient structures that dissipate after stress relief. However, the chronic stresses associated with aging lead to the persistent formation of SGs and subsequently to solid-like pathological SGs, which could impair cellular RNA metabolism and also act as a nidus for the aberrant aggregation of AD-associated proteins. In this paper, we provide a comprehensive summary of the physical basis of SG-enriched RNAs and SG-resident RBPs. We then review the characteristics of AD-associated gene transcripts and their similarity to the SG-enriched RNAs. Furthermore, we summarize and discuss the functional implications of SGs in neuronal RNA metabolism and the aberrant aggregation of AD-associated proteins mediated by SG-resident RBPs in the context of AD pathogenesis. Geriatr Gerontol Int 2024; 24: 7-14.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- Integrated Research Initiative for Living Well with Dementia, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
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39
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Yan X, Zhang M, Wang D. Interplay between posttranslational modifications and liquid‒liquid phase separation in tumors. Cancer Lett 2024; 584:216614. [PMID: 38246226 DOI: 10.1016/j.canlet.2024.216614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a general phenomenon recently recognized to be critically involved in the regulation of a variety of cellular biological processes, such as transcriptional regulation, heterochromatin formation and signal transduction, through the compartmentalization of proteins or nucleic acids into droplet-like condensates. These processes are directly or indirectly related to tumor initiation and treatment. Posttranslational modifications (PTMs), which represent a rapid and reversible mechanism involved in the functional regulation of proteins, have emerged as key events in modulating LLPS under physiological or pathophysiological conditions, including tumorigenesis and antitumor therapy. In this review, we introduce the biological functions participated in cancer-associated LLPS, discuss the potential roles of LLPS during tumor onset or therapy, and emphasize the mechanistic characteristics of LLPS regulated by PTMs and its effects on tumor progression. We then provide a perspective on further studies on LLPS and its regulation by PTMs in cancer research. This review aims to broaden the understanding of the functions of LLPS and its regulation by PTMs under normal or aberrant cellular conditions.
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Affiliation(s)
- Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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40
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Sun B, Luo J, Li Z, Chen D, Wang Q, Si W. Muscone alleviates neuronal injury via increasing stress granules formation and reducing apoptosis in acute ischemic stroke. Exp Neurol 2024; 373:114678. [PMID: 38185313 DOI: 10.1016/j.expneurol.2024.114678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
As the main bioactive component of musk, muscone has been reported to have marked protective effects in treating acute ischemic stroke (AIS). However, the specific anti-stroke mechanism of muscone still needs further research. In the current investigation, the PC12 cells OGD/R and the rat transient MCAO/R models were utilized as the AIS models. Serum hepatic and renal functional indexes (ALT, AST, BUN, and Cr) and cell viability were determined to select the appropriate muscone concentrations for in vitro and in vivo experiments. TTC, Hematoxylin and eosin (H&E), and Live/Dead staining were utilized to evaluate the protective effects of muscone in injured tissues and cells. Western blotting analysis, TUNEL staining, propidium iodide, and annexin V staining were applied to detect the anti-apoptotic effect of muscone. Double-label immunofluorescence staining of T-cell intracellular antigen-1 (TIA1) and Ras-GAP SH3 domain-binding protein 1 (G3BP1) was performed to observe whether muscone regulated the SG formation level. Molecular docking, TIA1 silencing and TIA1 overexpression experiments were employed to investigate the molecular mechanism underlying the regulation of SG formation by muscone. The 2, 3, 5-Triphenyl-tetrazolium chloride (TTC) staining and live/dead staining showed the AIS injury level of MCAO/R rat and the OGD/R PC12 cells were attenuated by muscone administration. The muscone significantly minimized the apoptosis rate in MCAO/R rats and OGD/R PC12 cells following flow cytometry analysis, western blotting analysis, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. The double-label immunofluorescence staining data revealed that muscone promoted the SG formation level in OGD/R PC12 cells and the cortex MCAO/R rats. The results of molecular docking, TIA1 silencing and TIA1 overexpression experiments revealed that muscone could bind to TIA1 protein and regulate its expression level, thereby promoting the formation of stress granules and exerting a protective effect against AIS injury. This study indicated that the significant protective effect of muscone in reducing apoptosis levels might be via promoting SG formation under AIS conditions. This study further explores the therapeutic effect and anti-apoptosis mechanism of muscone in AIS, which may provide a potential candidate drug for the clinical treatment of AIS injury.
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Affiliation(s)
- Bin Sun
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, PR China
| | - Jing Luo
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, PR China
| | - Zhen Li
- Department of Neurology, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, Guangdong 518104, PR China
| | - Dongfeng Chen
- Department of Anatomy, The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| | - Qizhang Wang
- Department of Neurology, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, Guangdong 518104, PR China
| | - Wenwen Si
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, PR China.
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41
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Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [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: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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42
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Wang X, Fan X, Zhang J, Wang F, Chen J, Wen Y, Wang L, Li T, Li H, Gu H, Zhang Y, Yuan S. hnRNPA2B1 represses the disassembly of arsenite-induced stress granules and is essential for male fertility. Cell Rep 2024; 43:113769. [PMID: 38363675 DOI: 10.1016/j.celrep.2024.113769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/19/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Although the composition and assembly of stress granules (SGs) are well understood, the molecular mechanisms underlying SG disassembly remain unclear. Here, we identify that heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1) is associated with SGs and that its absence specifically enhances the disassembly of arsenite-induced SGs depending on the ubiquitination-proteasome system but not the autophagy pathway. hnRNPA2B1 interacts with many core SG proteins, including G3BP1, G3BP2, USP10, and Caprin-1; USP10 can deubiquitinate G3BP1; and hnRNPA2B1 depletion attenuates the G3BP1-USP10/Caprin-1 interaction but elevates the G3BP1 ubiquitination level under arsenite treatment. Moreover, the disease-causing mutation FUSR521C also disassembles faster from SGs in HNRNPA2B1 mutant cells. Furthermore, knockout of hnRNPA2B1 in mice leads to Sertoli cell-only syndrome (SCOS), causing complete male infertility. Consistent with this, arsenite-induced SGs disassemble faster in Hnrnpa2b1 knockout (KO) mouse Sertoli cells as well. These findings reveal the essential roles of hnRNPA2B1 in regulating SG disassembly and male mouse fertility.
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Affiliation(s)
- Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xu Fan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fengli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingshou Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lingjuan Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huaibiao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Heng Gu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou 510600, China
| | - Youzhi Zhang
- School of Pharmacy, Hubei University of Science and Technology, Xianning 437100, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Laboratory of the Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518057, China.
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43
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Zhang Q, Xian W, Li Z, Lu Q, Chen X, Ge J, Tang Z, Liu B, Chen Z, Gao X, Hottiger MO, Zhang P, Qiu J, Shao F, Liu X. Shigella induces stress granule formation by ADP-riboxanation of the eIF3 complex. Cell Rep 2024; 43:113789. [PMID: 38368608 DOI: 10.1016/j.celrep.2024.113789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 01/09/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Under stress conditions, translationally stalled mRNA and associated proteins undergo liquid-liquid phase separation and condense into cytoplasmic foci called stress granules (SGs). Many viruses hijack SGs for their pathogenesis; however, whether pathogenic bacteria also exploit this pathway remains unknown. Here, we report that members of the OspC family of Shigella flexneri induce SG formation in infected cells. Mechanistically, the OspC effectors target multiple subunits of the host translation initiation factor 3 complex by ADP-riboxanation. The modification of eIF3 leads to translational arrest and thus the formation of SGs. Furthermore, OspC-mediated SGs are beneficial for S. flexneri replication within infected host cells, and bacterial strains unable to induce SGs are attenuated for virulence in a murine model of infection. Our findings reveal a mechanism by which bacterial pathogens induce SG assembly by inactivating host translational machinery and promote bacterial proliferation in host cells.
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Affiliation(s)
- Qinxin Zhang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zilin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qian Lu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xindi Chen
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bohao Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhe Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao 266000, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of Life Science, Shandong University, Qingdao 266000, China
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Peipei Zhang
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Department of Biochemistry, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Feng Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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44
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Pernin F, Cui QL, Mohammadnia A, Fernandes MGF, Hall JA, Srour M, Dudley RWR, Zandee SEJ, Klement W, Prat A, Salapa HE, Levin MC, Moore GRW, Kennedy TE, Vande Velde C, Antel JP. Regulation of stress granule formation in human oligodendrocytes. Nat Commun 2024; 15:1524. [PMID: 38374028 PMCID: PMC10876533 DOI: 10.1038/s41467-024-45746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Oligodendrocyte (OL) injury and subsequent loss is a pathologic hallmark of multiple sclerosis (MS). Stress granules (SGs) are membrane-less organelles containing mRNAs stalled in translation and considered as participants of the cellular response to stress. Here we show SGs in OLs in active and inactive areas of MS lesions as well as in normal-appearing white matter. In cultures of primary human adult brain derived OLs, metabolic stress conditions induce transient SG formation in these cells. Combining pro-inflammatory cytokines, which alone do not induce SG formation, with metabolic stress results in persistence of SGs. Unlike sodium arsenite, metabolic stress induced SG formation is not blocked by the integrated stress response inhibitor. Glycolytic inhibition also induces persistent SGs indicating the dependence of SG formation and disassembly on the energetic glycolytic properties of human OLs. We conclude that SG persistence in OLs in MS reflects their response to a combination of metabolic stress and pro-inflammatory conditions.
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Affiliation(s)
- Florian Pernin
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Qiao-Ling Cui
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Milton G F Fernandes
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Jeffery A Hall
- Department of Neurosurgery, McGill University Health Centre, Montreal, QC, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Montreal Children's Hospital, Montreal, QC, Canada
| | - Roy W R Dudley
- Department of Pediatric Neurosurgery, Montreal Children's Hospital, Montreal, QC, Canada
| | - Stephanie E J Zandee
- Centre de Recherche Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Wendy Klement
- Centre de Recherche Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Alexandre Prat
- Centre de Recherche Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Hannah E Salapa
- Cameco Multiple Sclerosis Neuroscience Research Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael C Levin
- Cameco Multiple Sclerosis Neuroscience Research Center, University of Saskatchewan, Saskatoon, SK, Canada
| | - G R Wayne Moore
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Timothy E Kennedy
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
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45
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Cho HS, Park YH, Moon S, Park C, Jung HS, Namkoong S. Targeting the NTF2-like domain of G3BP1: Novel modulators of intracellular granule dynamics. Biochem Biophys Res Commun 2024; 697:149497. [PMID: 38262290 DOI: 10.1016/j.bbrc.2024.149497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Stress granule (SG) is a temporary cellular structure that plays a crucial role in the regulation of mRNA and protein sequestration during various cellular stress conditions. SG enables cells to cope with stress more effectively, conserving vital energy and resources. Focusing on the NTF2-like domain of G3BP1, a key protein in SG dynamics, we explore to identify and characterize novel small molecules involved in SG modulation without external stressors. Through in silico molecular docking approach to simulate the interaction between various compounds and the NTF2-like domain of G3BP1, we identified three compounds as potential candidates that could bind to the NTF2-like domain of G3BP1. Subsequent immunofluorescence experiments demonstrated that these compounds induce the formation of SG-like, G3BP1-positive granules. Importantly, the granule formation by these compounds occurs independent from the phosphorylation of eIF2α, a common mechanism in SG formation, suggesting that it might offer a new strategy for influencing SG dynamics implicated in various diseases.
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Affiliation(s)
- Hyun Suh Cho
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Yoon Ho Park
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Chihyun Park
- Department of Computer Science and Engineering, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Hyun Suk Jung
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Sim Namkoong
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Yeganeh Markid T, Hosseinpour Feizi MA, Talebi M, Rezazadeh M, Khalaj-Kondori M. Gene expression investigation of four key regulators of polyadenylation and alternative adenylation in the periphery of late-onset Alzheimer's disease patients. Gene 2024; 895:148013. [PMID: 37981081 DOI: 10.1016/j.gene.2023.148013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/11/2023] [Accepted: 11/15/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a genetic and sporadic neurodegenerative disease considered by an archetypal cognitive impairment and a decrease in less common cognitive impairment. Notably, the discovery of goals in this paradigm is still a challenge, and understanding basic mechanisms is an important step toward improving disease management. Polyadenylation (PA) and alternative polyadenylation (APA) are two of the most critical RNA processing stages in 3'UTRs that influence various AD-related genes. METHODS In this study, we assessed Cleavage and polyadenylation specificity factors 1 and 6 (CPSF1 and CPSF6), cleavage stimulation factor 1 (CSTF1), and WD Repeat Domain 33 (WDR33) genes expression in the periphery of 50 AD patients and 50 healthy individuals with age and gender-matched by quantitative real-time PCR. RESULTS Comparing AD patients with healthy people using expression analysis revealed a substantial increase in CSTF1 (posterior beta = 0.773, adjusted P-value = 0.042). Significant positive correlations were found between CSTF1 and CPSF1 (r = 0.365, P < 0.001), WDR33 (r = 0.506, P < 0.001), and CPSF6 (r = 0.446, P < 0.001) expression levels. CONCLUSION Although further research is required to determine their potential contribution to AD, our findings offer a fresh perspective on molecular regulatory pathways associated with AD pathogenic mechanisms associated with PA and APA.
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Affiliation(s)
- Tarlan Yeganeh Markid
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Iran; Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | - Mahnaz Talebi
- Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Iran; Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Khalaj-Kondori
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
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47
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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48
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Vural A, Lanier SM. Properties of biomolecular condensates defined by Activator of G-protein Signaling 3. J Cell Sci 2024; 137:jcs261326. [PMID: 38264908 PMCID: PMC10911133 DOI: 10.1242/jcs.261326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024] Open
Abstract
Activator of G-protein signaling 3 (AGS3; also known as GPSM1), a receptor-independent activator of G-protein signaling, oscillates among defined subcellular compartments and biomolecular condensates (BMCs) in a regulated manner that is likely related to the functional diversity of the protein. We determined the influence of cell stress on the cellular distribution of AGS3 and core material properties of AGS3 BMCs. Cellular stress (oxidative, pHi and thermal) induced the formation of AGS3 BMCs in HeLa and COS-7 cells, as determined by fluorescent microscopy. Oxidative stress-induced AGS3 BMCs were distinct from G3BP1 stress granules and from RNA processing BMCs defined by the P-body protein Dcp1a. Immunoblots indicated that cellular stress shifted AGS3, but not the stress granule protein G3BP1 to a membrane pellet fraction following cell lysis. The stress-induced generation of AGS3 BMCs was reduced by co-expression of the signaling protein Gαi3, but not the AGS3-binding partner DVL2. Fluorescent recovery following photobleaching of individual AGS3 BMCs indicated that there are distinct diffusion kinetics and restricted fluidity for AGS3 BMCs. These data suggest that AGS3 BMCs represent a distinct class of stress granules that serve as a previously unrecognized signal processing node.
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Affiliation(s)
- Ali Vural
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Stephen M. Lanier
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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49
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Lee YJ, Rio DC. A mutation in the low-complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks. Genes Dev 2024; 38:11-30. [PMID: 38182429 PMCID: PMC10903937 DOI: 10.1101/gad.351104.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/14/2023] [Indexed: 01/07/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease characterized by loss of motor neurons. Human genetic studies have linked mutations in RNA-binding proteins as causative for this disease. The hnRNPA1 protein, a known pre-mRNA splicing factor, is mutated in some ALS patients. Here, two human cell models were generated to investigate how a mutation in the C-terminal low-complexity domain (LCD) of hnRNPA1 can cause splicing changes of thousands of transcripts that collectively are linked to the DNA damage response, cilium organization, and translation. We show that the hnRNPA1 D262V mutant protein binds to new binding sites on differentially spliced transcripts from genes that are linked to ALS. We demonstrate that this ALS-linked hnRNPA1 mutation alters normal RNA-dependent protein-protein interactions. Furthermore, cells expressing this hnRNPA1 mutant exhibit a cell aggregation phenotype, markedly reduced growth rates, changes in stress granule kinetics, and aberrant growth of neuronal processes. This study provides insight into how a single amino acid mutation in a splicing factor can alter RNA splicing networks of genes linked to ALS.
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Affiliation(s)
- Yeon J Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, USA
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50
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Kharel P, Ivanov P. RNA G-quadruplexes and stress: emerging mechanisms and functions. Trends Cell Biol 2024:S0962-8924(24)00005-9. [PMID: 38341346 DOI: 10.1016/j.tcb.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
RNA G-quadruplexes (rG4s) are noncanonical secondary structures formed by guanine-rich sequences that are found in different regions of RNA molecules. These structures have been implicated in diverse biological processes, including translation, splicing, and RNA stability. Recent studies have suggested that rG4s play a role in the cellular response to stress. This review summarizes the current knowledge on rG4s under stress, focusing on their formation, regulation, and potential functions in stress response pathways. We discuss the molecular mechanisms that regulate the formation of rG4 under different stress conditions and the impact of these structures on RNA metabolism, gene expression, and cell survival. Finally, we highlight the potential therapeutic implications of targeting rG4s for the treatment of stress-related diseases through modulating cell survival.
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Affiliation(s)
- Prakash Kharel
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; HMS Initiative for RNA Medicine, Boston, MA 02115, USA.
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