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Huang WP, Ellis BCS, Hodgson RE, Sanchez Avila A, Kumar V, Rayment J, Moll T, Shelkovnikova TA. Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion. Cell Rep 2024; 43:114421. [PMID: 38941189 DOI: 10.1016/j.celrep.2024.114421] [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: 01/10/2024] [Revised: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024] Open
Abstract
TDP-43 protein is dysregulated in several neurodegenerative diseases, which often have a multifactorial nature and may have extrinsic stressors as a "second hit." TDP-43 undergoes reversible nuclear condensation in stressed cells including neurons. Here, we demonstrate that stress-inducible nuclear TDP-43 condensates are RNA-depleted, non-liquid assemblies distinct from the known nuclear bodies. Their formation requires TDP-43 oligomerization and ATP and is inhibited by RNA. Using a confocal nanoscanning assay, we find that amyotrophic lateral sclerosis (ALS)-linked mutations alter stress-induced TDP-43 condensation by changing its affinity to liquid-like ribonucleoprotein assemblies. Stress-induced nuclear condensation transiently inactivates TDP-43, leading to loss of interaction with its protein binding partners and loss of function in splicing. Splicing changes are especially prominent and persisting for STMN2 RNA, and STMN2 protein becomes rapidly depleted early during stress. Our results point to early pathological changes to TDP-43 in the nucleus and support therapeutic modulation of stress response in ALS.
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Affiliation(s)
- Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Brittany C S Ellis
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Anna Sanchez Avila
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Vedanth Kumar
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Jessica Rayment
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK.
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2
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Westover KR, Jin P, Yao B. Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics 2024; 16:589-608. [PMID: 38530068 PMCID: PMC11160457 DOI: 10.2217/epi-2023-0379] [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: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.
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Affiliation(s)
- Katherine R Westover
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
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3
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De Marchi F, Venkatesan S, Saraceno M, Mazzini L, Grossini E. Acetyl-L-carnitine and Amyotrophic Lateral Sclerosis: Current Evidence and Potential use. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2024; 23:588-601. [PMID: 36998125 DOI: 10.2174/1871527322666230330083757] [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] [Received: 10/11/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND The management of neurodegenerative diseases can be frustrating for clinicians, given the limited progress of conventional medicine in this context. AIM For this reason, a more comprehensive, integrative approach is urgently needed. Among various emerging focuses for intervention, the modulation of central nervous system energetics, oxidative stress, and inflammation is becoming more and more promising. METHODS In particular, electrons leakage involved in the mitochondrial energetics can generate reactive oxygen-free radical-related mitochondrial dysfunction that would contribute to the etiopathology of many disorders, such as Alzheimer's and other dementias, Parkinson's disease, multiple sclerosis, stroke, and amyotrophic lateral sclerosis (ALS). RESULTS In this context, using agents, like acetyl L-carnitine (ALCAR), provides mitochondrial support, reduces oxidative stress, and improves synaptic transmission. CONCLUSION This narrative review aims to update the existing literature on ALCAR molecular profile, tolerability, and translational clinical potential use in neurodegeneration, focusing on ALS.
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Affiliation(s)
- Fabiola De Marchi
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale 28100 Novara, Italy
| | - Sakthipriyan Venkatesan
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale 28100, Novara, Italy
| | - Massimo Saraceno
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale 28100 Novara, Italy
| | - Letizia Mazzini
- ALS Center, Neurology Unit, Department of Translational Medicine, University of Piemonte Orientale 28100 Novara, Italy
| | - Elena Grossini
- Laboratory of Physiology, Department of Translational Medicine, University of Piemonte Orientale 28100, Novara, Italy
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4
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Peggion C, Massimino ML, Pereira D, Granuzzo S, Righetto F, Bortolotto R, Agostini J, Sartori G, Bertoli A, Lopreiato R. Structural Integrity of Nucleolin Is Required to Suppress TDP-43-Mediated Cytotoxicity in Yeast and Human Cell Models. Int J Mol Sci 2023; 24:17466. [PMID: 38139294 PMCID: PMC10744044 DOI: 10.3390/ijms242417466] [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: 10/03/2023] [Revised: 11/28/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Transactivating response (TAR) element DNA-binding of 43 kDa (TDP-43) is mainly implicated in the regulation of gene expression, playing multiple roles in RNA metabolism. Pathologically, it is implicated in amyotrophic lateral sclerosis and in a class of neurodegenerative diseases broadly going under the name of frontotemporal lobar degeneration (FTLD). A common hallmark of most forms of such diseases is the presence of TDP-43 insoluble inclusions in the cell cytosol. The molecular mechanisms of TDP-43-related cell toxicity are still unclear, and the contribution to cell damage from either loss of normal TDP-43 function or acquired toxic properties of protein aggregates is yet to be established. Here, we investigate the effects on cell viability of FTLD-related TDP-43 mutations in both yeast and mammalian cell models. Moreover, we focus on nucleolin (NCL) gene, recently identified as a genetic suppressor of TDP-43 toxicity, through a thorough structure/function characterization aimed at understanding the role of NCL domains in rescuing TDP-43-induced cytotoxicity. Using functional and biochemical assays, our data demonstrate that the N-terminus of NCL is necessary, but not sufficient, to exert its antagonizing effects on TDP-43, and further support the relevance of the DNA/RNA binding central region of the protein. Concurrently, data suggest the importance of the NCL nuclear localization for TDP-43 trafficking, possibly related to both TDP-43 physiology and toxicity.
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Affiliation(s)
- Caterina Peggion
- Department of Biology, University of Padova, 35131 Padova, Italy
| | | | - Daniel Pereira
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Department of Bioengineering, iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
| | - Sara Granuzzo
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesca Righetto
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Raissa Bortolotto
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Jessica Agostini
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Alessandro Bertoli
- Neuroscience Institute, Consiglio Nazionale Delle Ricerche, 35131 Padova, Italy
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
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5
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Wilkins OG, Chien MZ, Wlaschin JJ, Pisliakova M, Thompson D, Digby H, Simkin RL, Diaz JA, Mehta PR, Keuss MJ, Zanovello M, Brown AL, Harley P, Darbey A, Karda R, Fisher EM, Cunningham TJ, Le Pichon CE, Ule J, Fratta P. Creation of de novo cryptic splicing for ALS/FTD precision medicine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.565967. [PMID: 38014203 PMCID: PMC10680699 DOI: 10.1101/2023.11.15.565967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
A system enabling the expression of therapeutic proteins specifically in diseased cells would be transformative, providing greatly increased safety and the possibility of pre-emptive treatment. Here we describe "TDP-REG", a precision medicine approach primarily for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which exploits the cryptic splicing events that occur in cells with TDP-43 loss-of-function (TDP-LOF) in order to drive expression specifically in diseased cells. In addition to modifying existing cryptic exons for this purpose, we develop a deep-learning-powered algorithm for generating customisable cryptic splicing events, which can be embedded within virtually any coding sequence. By placing part of a coding sequence within a novel cryptic exon, we tightly couple protein expression to TDP-LOF. Protein expression is activated by TDP-LOF in vitro and in vivo, including TDP-LOF induced by cytoplasmic TDP-43 aggregation. In addition to generating a variety of fluorescent and luminescent reporters, we use this system to perform TDP-LOF-dependent genomic prime editing to ablate the UNC13A cryptic donor splice site. Furthermore, we design a panel of tightly gated, autoregulating vectors encoding a TDP-43/Raver1 fusion protein, which rescue key pathological cryptic splicing events. In summary, we combine deep-learning and rational design to create sophisticated splicing sensors, resulting in a platform that provides far safer therapeutics for neurodegeneration, potentially even enabling preemptive treatment of at-risk individuals.
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Affiliation(s)
- Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Max Z.Y.J. Chien
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Josette J. Wlaschin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Maria Pisliakova
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - David Thompson
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Holly Digby
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Rebecca L. Simkin
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Juan Antinao Diaz
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Anna-Leigh Brown
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Annalucia Darbey
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Rajvinder Karda
- EGA-Institute for Women’s Health, University College London; London, WC1E 6HX, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
| | - Tom J. Cunningham
- Mammalian Genetics Unit, MRC Harwell Institute; Oxfordshire, OX11 0RD, UK
| | - Claire E. Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892, USA
| | - Jernej Ule
- The Francis Crick Institute; London, NW1 1AT, UK
- UK Dementia Research Institute at King’s College London, Maurice Wohl Clinical Neuroscience Institute; London, SE5 9RX, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
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6
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Rajaratnam S, Soman AP, Phalguna KS, Pradhan SS, Manjunath M, Rao RK, Dandamudi RB, Bhagavatham SKS, Pulukool SK, Rathnakumar S, Kocherlakota S, Pargaonkar A, Veeranna RP, Arumugam N, Almansour AI, Choudhary B, Sivaramakrishnan V. Integrated Omic Analysis Delineates Pathways Modulating Toxic TDP-43 Protein Aggregates in Amyotrophic Lateral Sclerosis. Cells 2023; 12:cells12091228. [PMID: 37174628 PMCID: PMC10177613 DOI: 10.3390/cells12091228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multi-systemic, incurable, amyloid disease affecting the motor neurons, resulting in the death of patients. The disease is either sporadic or familial with SOD1, C9orf72, FUS, and TDP-43 constituting the majority of familial ALS. Multi-omics studies on patients and model systems like mice and yeast have helped in understanding the association of various signaling and metabolic pathways with the disease. The yeast model system has played a pivotal role in elucidating the gene amyloid interactions. We carried out an integrated transcriptomic and metabolomic analysis of the TDP-43 expressing yeast model to elucidate deregulated pathways associated with the disease. The analysis shows the deregulation of the TCA cycle, single carbon metabolism, glutathione metabolism, and fatty acid metabolism. Transcriptomic analysis of GEO datasets of TDP-43 expressing motor neurons from mice models of ALS and ALS patients shows considerable overlap with experimental results. Furthermore, a yeast model was used to validate the obtained results using metabolite addition and gene knock-out experiments. Taken together, our result shows a potential role for the TCA cycle, cellular redox pathway, NAD metabolism, and fatty acid metabolism in disease. Supplementation of reduced glutathione, nicotinate, and the keto diet might help to manage the disease.
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Affiliation(s)
- Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Akhil P Soman
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
- Central Water and Power Research Station, Khadakwasla, Pune 411024, Maharashtra, India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India
| | - Raksha Kanthavara Rao
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India
| | | | - Sai Krishna Srimadh Bhagavatham
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sujith Kumar Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru 560066, Karnataka, India
| | - Ravindra P Veeranna
- Department of Biochemistry, Council of Scientific & Industrial Research (CSIR)-Central Food Technological Research Institute (CFTRI), Mysuru 570020, Karnataka, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
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7
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Doke AA, Jha SK. Shapeshifter TDP-43: Molecular mechanism of structural polymorphism, aggregation, phase separation and their modulators. Biophys Chem 2023; 295:106972. [PMID: 36812677 DOI: 10.1016/j.bpc.2023.106972] [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: 12/28/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
TDP-43 is a nucleic acid-binding protein that performs physiologically essential functions and is known to undergo phase separation and aggregation during stress. Initial observations have shown that TDP-43 forms heterogeneous assemblies, including monomer, dimer, oligomers, aggregates, phase-separated assemblies, etc. However, the significance of each assembly of TDP-43 concerning its function, phase separation, and aggregation is poorly known. Furthermore, how different assemblies of TDP-43 are related to each other is unclear. In this review, we focus on the various assemblies of TDP-43 and discuss the plausible origin of the structural heterogeneity of TDP-43. TDP-43 is involved in multiple physiological processes like phase separation, aggregation, prion-like seeding, and performing physiological functions. However, the molecular mechanism behind the physiological process performed by TDP-43 is not well understood. The current review discusses the plausible molecular mechanism of phase separation, aggregation, and prion-like propagation of TDP-43.
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Affiliation(s)
- Abhilasha A Doke
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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8
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Shenoy J, Lends A, Berbon M, Bilal M, El Mammeri N, Bertoni M, Saad A, Morvan E, Grélard A, Lecomte S, Theillet FX, Buell AK, Kauffmann B, Habenstein B, Loquet A. Structural polymorphism of the low-complexity C-terminal domain of TDP-43 amyloid aggregates revealed by solid-state NMR. Front Mol Biosci 2023; 10:1148302. [PMID: 37065450 PMCID: PMC10095165 DOI: 10.3389/fmolb.2023.1148302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Aberrant aggregation of the transactive response DNA-binding protein (TDP-43) is associated with several lethal neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. Cytoplasmic neuronal inclusions of TDP-43 are enriched in various fragments of the low-complexity C-terminal domain and are associated with different neurotoxicity. Here we dissect the structural basis of TDP-43 polymorphism using magic-angle spinning solid-state NMR spectroscopy in combination with electron microscopy and Fourier-transform infrared spectroscopy. We demonstrate that various low-complexity C-terminal fragments, namely TDP-13 (TDP-43300–414), TDP-11 (TDP-43300–399), and TDP-10 (TDP-43314–414), adopt distinct polymorphic structures in their amyloid fibrillar state. Our work demonstrates that the removal of less than 10% of the low-complexity sequence at N- and C-termini generates amyloid fibrils with comparable macroscopic features but different local structural arrangement. It highlights that the assembly mechanism of TDP-43, in addition to the aggregation of the hydrophobic region, is also driven by complex interactions involving low-complexity aggregation-prone segments that are a potential source of structural polymorphism.
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Affiliation(s)
- Jayakrishna Shenoy
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Alons Lends
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Muhammed Bilal
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Nadia El Mammeri
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mathilde Bertoni
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Ahmad Saad
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Axelle Grélard
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sophie Lecomte
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - François-Xavier Theillet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-surYvette Cedex, France
| | - Alexander K. Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Brice Kauffmann
- University Bordeaux, CNRS, INSERM, IECB, UAR 3033, Pessac, France
| | - Birgit Habenstein
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
| | - Antoine Loquet
- University Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
- *Correspondence: Birgit Habenstein, ; Antoine Loquet,
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9
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Cooper‐Knock J, Julian TH, Feneberg E, Highley JR, Sidra M, Turner MR, Talbot K, Ansorge O, Allen SP, Moll T, Shelkovnikova T, Castelli L, Hautbergue GM, Hewitt C, Kirby J, Wharton SB, Mead RJ, Shaw PJ. Atypical TDP-43 protein expression in an ALS pedigree carrying a p.Y374X truncation mutation in TARDBP. Brain Pathol 2023; 33:e13104. [PMID: 35871544 PMCID: PMC9836368 DOI: 10.1111/bpa.13104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/30/2022] [Indexed: 01/25/2023] Open
Abstract
We describe an autosomal dominant, multi-generational, amyotrophic lateral sclerosis (ALS) pedigree in which disease co-segregates with a heterozygous p.Y374X nonsense mutation within TDP-43. Mislocalization of TDP-43 and formation of insoluble TDP-43-positive neuronal cytoplasmic inclusions is the hallmark pathology in >95% of ALS patients. Neuropathological examination of the single case for which CNS tissue was available indicated typical TDP-43 pathology within lower motor neurons, but classical TDP-43-positive inclusions were absent from motor cortex. The mutated allele is transcribed and translated in patient fibroblasts and motor cortex tissue, but overall TDP-43 protein expression is reduced compared to wild-type controls. Despite absence of TDP-43-positive inclusions we confirmed deficient TDP-43 splicing function within motor cortex tissue. Furthermore, urea fractionation and mass spectrometry of motor cortex tissue carrying the mutation revealed atypical TDP-43 protein species but not typical C-terminal fragments. We conclude that the p.Y374X mutation underpins a monogenic, fully penetrant form of ALS. Reduced expression of TDP-43 combined with atypical TDP-43 protein species and absent C-terminal fragments extends the molecular phenotypes associated with TDP-43 mutations and with ALS more broadly. Future work will need to include the findings from this pedigree in dissecting the mechanisms of TDP-43-mediated toxicity.
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Affiliation(s)
- Johnathan Cooper‐Knock
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Thomas H. Julian
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Emily Feneberg
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Neurology Department, Klinikum Rechts der IsarTechnical University of MunichMunichGermany
| | - J. Robin Highley
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Maurice Sidra
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Martin R. Turner
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Kevin Talbot
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Olaf Ansorge
- Academic Unit of NeuropathologyUniversity of OxfordOxfordUK
| | - Scott P. Allen
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Tatyana Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Lydia Castelli
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Guillaume M. Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Christopher Hewitt
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
- Amarin UK LimitedAmarin CorporationLondonUK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Stephen B. Wharton
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Richard J. Mead
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
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10
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Ng W, Ng SY. Remodeling of astrocyte secretome in amyotrophic lateral sclerosis: uncovering novel targets to combat astrocyte-mediated toxicity. Transl Neurodegener 2022; 11:54. [PMID: 36567359 PMCID: PMC9791755 DOI: 10.1186/s40035-022-00332-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/05/2022] [Indexed: 12/27/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset paralytic disease characterized by progressive degeneration of upper and lower motor neurons in the motor cortex, brainstem and spinal cord. Motor neuron degeneration is typically caused by a combination of intrinsic neuronal (cell autonomous) defects as well as extrinsic (non-cell autonomous) factors such as astrocyte-mediated toxicity. Astrocytes are highly plastic cells that react to their microenvironment to mediate relevant responses. In neurodegeneration, astrocytes often turn reactive and in turn secrete a slew of factors to exert pro-inflammatory and neurotoxic effects. Various efforts have been carried out to characterize the diseased astrocyte secretome over the years, revealing that pro-inflammatory chemokines, cytokines and microRNAs are the main players in mediating neuronal death. As metabolomic technologies mature, these studies begin to shed light on neurotoxic metabolites such as secreted lipids. In this focused review, we will discuss changes in the astrocyte secretome during ALS. In particular, we will discuss the components of the reactive astrocyte secretome that contribute to neuronal death in ALS.
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Affiliation(s)
- Winanto Ng
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673 Singapore
| | - Shi-Yan Ng
- grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673 Singapore
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11
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Doll SG, Cingolani G. Importin α/β and the tug of war to keep TDP-43 in solution: quo vadis? Bioessays 2022; 44:e2200181. [PMID: 36253101 PMCID: PMC9969346 DOI: 10.1002/bies.202200181] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/29/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022]
Abstract
The transactivation response-DNA binding protein of 43 kDa (TDP-43) is an aggregation-prone nucleic acid-binding protein linked to the etiology of Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD). These conditions feature the accumulation of insoluble TDP-43 aggregates in the neuronal cytoplasm that lead to cell death. The dynamics between cytoplasmic and nuclear TDP-43 are altered in the disease state where TDP-43 mislocalizes to the cytoplasm, disrupting Nuclear Pore Complexes (NPCs), and ultimately forming large fibrils stabilized by the C-terminal prion-like domain. Here, we review three emerging and poorly understood aspects of TDP-43 biology linked to its aggregation. First, how post-translational modifications in the proximity of TDP-43 N-terminal domain (NTD) promote aggregation. Second, how TDP-43 engages FG-nucleoporins in the NPC, disrupting the pore permeability and function. Third, how the importin α/β heterodimer prevents TDP-43 aggregation, serving both as a nuclear import transporter and a cytoplasmic chaperone.
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Affiliation(s)
- Steven G. Doll
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Gino Cingolani
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA,Corresponding author: Gino Cingolani,
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12
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Šušnjar U, Škrabar N, Brown AL, Abbassi Y, Phatnani H, Cortese A, Cereda C, Bugiardini E, Cardani R, Meola G, Ripolone M, Moggio M, Romano M, Secrier M, Fratta P, Buratti E. Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. Commun Biol 2022; 5:314. [PMID: 35383280 PMCID: PMC8983780 DOI: 10.1038/s42003-022-03253-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/11/2022] [Indexed: 12/26/2022] Open
Abstract
TDP-43 (TAR DNA-binding protein 43) aggregation and redistribution are recognised as a hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. As TDP-43 inclusions have recently been described in the muscle of inclusion body myositis patients, this highlights the need to understand the role of TDP-43 beyond the central nervous system. Using RNA-seq, we directly compare TDP-43-mediated RNA processing in muscle (C2C12) and neuronal (NSC34) mouse cells. TDP-43 displays a cell-type-characteristic behaviour targeting unique transcripts in each cell-type, which is due to characteristic expression of RNA-binding proteins, that influence TDP-43's performance and define cell-type specific splicing. Among splicing events commonly dysregulated in both cell lines, we identify some that are TDP-43-dependent also in human cells. Inclusion levels of these alternative exons are altered in tissues of patients suffering from FTLD and IBM. We therefore propose that TDP-43 dysfunction contributes to disease development either in a common or a tissue-specific manner.
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Affiliation(s)
- Urša Šušnjar
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Neva Škrabar
- Tumour Virology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
- Generatio GmbH, Center for Animal, Genetics, Tübingen, Germany
| | - Anna-Leigh Brown
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Yasmine Abbassi
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, USA
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- Department of Brain and Behaviour Sciences, University of Pavia, Pavia, Italy
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Rosanna Cardani
- BioCor Biobank, UOC SMEL-1 of Clinical Pathology, IRCCS-Policlinico San Donato, San Donato Milanese, Italy
| | - Giovanni Meola
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- Department of Neurorehabilitation Sciences, Casa di Cura del Policlinico, Milan, Italy
| | - Michela Ripolone
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maurizio Moggio
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Emanuele Buratti
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.
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13
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Gilodi M, Lisi S, F. Dudás E, Fantini M, Puglisi R, Louka A, Marcatili P, Cattaneo A, Pastore A. Selection and Modelling of a New Single-Domain Intrabody Against TDP-43. Front Mol Biosci 2022; 8:773234. [PMID: 35237655 PMCID: PMC8884700 DOI: 10.3389/fmolb.2021.773234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder associated to deteriorating motor and cognitive functions, and short survival. The disease is caused by neuronal death which results in progressive muscle wasting and weakness, ultimately leading to lethal respiratory failure. The misbehaviour of a specific protein, TDP-43, which aggregates and becomes toxic in ALS patient’s neurons, is supposed to be one of the causes. TDP-43 is a DNA/RNA-binding protein involved in several functions related to nucleic acid metabolism. Sequestration of TDP-43 aggregates is a possible therapeutic strategy that could alleviate or block pathology. Here, we describe the selection and characterization of a new intracellular antibody (intrabody) against TDP-43 from a llama nanobody library. The structure of the selected intrabody was predicted in silico and the model was used to suggest mutations that enabled to improve its expression yield, facilitating its experimental validation. We showed how coupling experimental methodologies with in silico design may allow us to obtain an antibody able to recognize the RNA binding regions of TDP-43. Our findings illustrate a strategy for the mitigation of TDP-43 proteinopathy in ALS and provide a potential new tool for diagnostics.
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Affiliation(s)
- Martina Gilodi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Erika F. Dudás
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Rita Puglisi
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Alexandra Louka
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
| | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
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14
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TDP-43 Pathology and Prionic Behavior in Human Cellular Models of Alzheimer’s Disease Patients. Biomedicines 2022; 10:biomedicines10020385. [PMID: 35203594 PMCID: PMC8962248 DOI: 10.3390/biomedicines10020385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder for which there is currently no effective treatment. Despite advances in the molecular pathology of the characteristic histopathological markers of the disease (tau protein and β-amyloid), their translation to the clinic has not provided the expected results. Increasing evidences have demonstrated the presence of aggregates of TDP-43 (TAR DNA binding protein 43) in the postmortem brains of patients diagnosed with AD. The present research is focused on of the study of the pathological role of TDP-43 in AD. For this purpose, immortalized lymphocytes samples from patients diagnosed with different severity of sporadic AD were used and the TDP-43 pathology was analyzed against controls, looking for differences in their fragmentation, phosphorylation and cellular location using Western blot and immunocytochemical techniques. The results revealed an increase in TDP-43 fragmentation, as well as increased phosphorylation and aberrant localization of TDP-43 in the cytosolic compartment of lymphocytes of patients diagnosed with severe AD. Moreover, a fragment of approximately 25 KD was found in the extracellular medium of cells derived from severe AD individuals that seem to have prion-like characteristics. We conclude that TDP-43 plays a key role in AD pathogenesis and its cell to cell propagation.
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15
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TDP-43 pathology: from noxious assembly to therapeutic removal. Prog Neurobiol 2022; 211:102229. [DOI: 10.1016/j.pneurobio.2022.102229] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 02/08/2023]
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16
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Unzipping the Secrets of Amyloid Disassembly by the Human Disaggregase. Cells 2021; 10:cells10102745. [PMID: 34685723 PMCID: PMC8534776 DOI: 10.3390/cells10102745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 01/08/2023] Open
Abstract
Neurodegenerative diseases (NDs) are increasingly positioned as leading causes of global deaths. The accelerated aging of the population and its strong relationship with neurodegeneration forecast these pathologies as a huge global health problem in the upcoming years. In this scenario, there is an urgent need for understanding the basic molecular mechanisms associated with such diseases. A major molecular hallmark of most NDs is the accumulation of insoluble and toxic protein aggregates, known as amyloids, in extracellular or intracellular deposits. Here, we review the current knowledge on how molecular chaperones, and more specifically a ternary protein complex referred to as the human disaggregase, deals with amyloids. This machinery, composed of the constitutive Hsp70 (Hsc70), the class B J-protein DnaJB1 and the nucleotide exchange factor Apg2 (Hsp110), disassembles amyloids of α-synuclein implicated in Parkinson’s disease as well as of other disease-associated proteins such as tau and huntingtin. We highlight recent studies that have led to the dissection of the mechanism used by this chaperone system to perform its disaggregase activity. We also discuss whether this chaperone-mediated disassembly mechanism could be used to solubilize other amyloidogenic substrates. Finally, we evaluate the implications of the chaperone system in amyloid clearance and associated toxicity, which could be critical for the development of new therapies.
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17
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Cragnaz L, Spinelli G, De Conti L, Bureau EA, Brownlees J, Feiguin F, Romano V, Skoko N, Klima R, Kettleborough CA, Baralle FE, Baralle M. Thioridazine reverts the phenotype in cellular and Drosophila models of amyotrophic lateral sclerosis by enhancing TDP-43 aggregate clearance. Neurobiol Dis 2021; 160:105515. [PMID: 34571136 DOI: 10.1016/j.nbd.2021.105515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 01/22/2023] Open
Abstract
Brain inclusions mainly composed of misfolded and aggregated TAR DNA binding protein 43 (TDP-43), are characteristic hallmarks of amyotrophic lateral sclerosis (ALS). Irrespective of the role played by the inclusions, their reduction represents an important therapeutic pathway that is worth exploring. Their removal can either lead to the recovery of TDP-43 function by removing the self-templating conformers that sequester the protein in the inclusions, and/or eliminate any potential intrinsic toxicity of the aggregates. The search for curative therapies has been hampered by the lack of ALS models for use in high-throughput screening. We adapted, optimised, and extensively characterised our previous ALS cellular model for such use. The model demonstrated efficient aggregation of endogenous TDP-43, and concomitant loss of its splicing regulation function. We provided a proof-of-principle for its eventual use in high-throughput screening using compounds of the tricyclic family and showed that recovery of TDP-43 function can be achieved by the enhanced removal of TDP-43 aggregates by these compounds. We observed that the degradation of the aggregates occurs independent of the autophagy pathway beyond autophagosome-lysosome fusion, but requires a functional proteasome pathway. The in vivo translational effect of the cellular model was tested with two of these compounds in a Drosophila model expressing a construct analogous to the cellular model, where thioridazine significantly improved the locomotive defect. Our findings have important implications as thioridazine cleared TDP-43 aggregates and recovered TDP-43 functionality. This study also highlights the importance of a two-stage, in vitro and in vivo model system to cross-check the search for small molecules that can clear TDP-43 aggregates in TDP-43 proteinopathies.
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Affiliation(s)
- Lucia Cragnaz
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Greta Spinelli
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Laura De Conti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Emilie A Bureau
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage SG1 2FX, United Kingdom
| | - Janet Brownlees
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage SG1 2FX, United Kingdom
| | - Fabian Feiguin
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy; Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Cagliari, Italy
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Natasa Skoko
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Raffaella Klima
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | | | - Francisco E Baralle
- Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, ss14, Km 163.5, Basovizza, 34149 Trieste, Italy
| | - Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.
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18
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Baralle M, Romano M. Characterization of the human TARDBP gene promoter. Sci Rep 2021; 11:10438. [PMID: 34002018 PMCID: PMC8129075 DOI: 10.1038/s41598-021-89973-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/04/2021] [Indexed: 02/03/2023] Open
Abstract
The expression of TDP-43, the main component of neuronal intracellular inclusions across a broad spectrum of ALS and FTD disorders, is developmentally regulated and studies in vivo have shown that TDP-43 overexpression can be toxic, even before observation of pathological aggregates. Starting from these observations, the regulation of its expression at transcriptional level might represent a further key element for the pathogenesis of neurodegenerative diseases. Therefore, we have characterized the human TARDBP promoter, in order to study the transcriptional mechanisms of expression. Mapping of cis-acting elements by luciferase assays in different cell outlined that the activity of the promoter seems to be higher in SH-SY5Y, Neuro2A, and HeLa than in HEK293. In addition, we tested effects of two SNPs found in the promoter region of ALS patients and observed no significant effect on transcription levels in all tested cell lines. Lastly, while TDP-43 overexpression did not affect significantly the activity of its promoter (suggesting that TDP-43 does not influence its own transcription), the presence of the 5'UTR sequence and of intron-1 splicing seem to impact positively on TDP-43 expression without affecting transcript stability. In conclusion, we have identified the region spanning nucleotides 451-230 upstream from the transcription start site as the minimal region with a significant transcription activity. These results lay an important foundation for exploring the regulation of the TARDBP gene transcription by exogenous and endogenous stimuli and the implication of transcriptional mechanisms in the pathogenesis of TDP-43 proteinopathies.
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Affiliation(s)
- Marco Baralle
- grid.425196.d0000 0004 1759 4810International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Padriciano, Trieste, Italy
| | - Maurizio Romano
- grid.5133.40000 0001 1941 4308Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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19
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Smeltzer S, Quadri Z, Miller A, Zamudio F, Hunter J, Stewart NJF, Saji S, Lee DC, Chaput D, Selenica MLB. Hypusination of Eif5a regulates cytoplasmic TDP-43 aggregation and accumulation in a stress-induced cellular model. Biochim Biophys Acta Mol Basis Dis 2021; 1867:165939. [PMID: 32882370 DOI: 10.1016/j.bbadis.2020.165939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/27/2020] [Accepted: 08/17/2020] [Indexed: 11/23/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is a nuclear RNA/DNA binding protein involved in mRNA metabolism. Aberrant mislocalization to the cytoplasm and formation of phosphorylated/aggregated TDP-43 inclusions remains the hallmark pathology in a spectrum of neurodegenerative diseases, including frontotemporal disorders and Alzheimer's disease. Eukaryotic Translation Initiation Factor 5A undergoes a unique post-translation modification of lysine to hypusine (K50), which determines eIF5A binding partners. We used a sodium arsenite-induced cellular stress model to investigate the role of hypusinated eIF5A (eIF5AHypK50) in governing TDP-43 cytoplasmic mislocalization and accumulation in stress granule. Our proteomics and functional data provide evidence that eIF5A interacts with TDP-43 in a hypusine-dependent manner. Additionally, we showed that following stress TDP-43 interactions with eIF5AHypK50 were induced both in the cytoplasm and stress granules. Pharmacological reduction of hypusination or mutations of lysine residues within the hypusine loop decreased phosphorylated and insoluble TDP-43 levels. The proteomic and biochemical analysis also identified nuclear pore complex importins KPNA1/2, KPNB1, and RanGTP as interacting partners of eIF5AHypK50. These findings are the first to provide a novel pathway and potential therapeutic targets that require further investigation in models of TDP-43 proteinopathies.
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Affiliation(s)
- Shayna Smeltzer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Zainuddin Quadri
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA; Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY, USA
| | - Abraian Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Frank Zamudio
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Jordan Hunter
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Nicholas J F Stewart
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Sheba Saji
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA
| | - Daniel C Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA; Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY, USA
| | - Dale Chaput
- Proteomics and Mass Spectrometry Core Facility, Florida Center of Excellence for Drug Discovery and Innovation (CDDI), University of South Florida, 3720 Spectrum Blvd, Suite 303, Tampa, FL 33612, USA
| | - Maj-Linda B Selenica
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612, USA; Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, KY, USA.
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20
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Huang C, Yan S, Zhang Z. Maintaining the balance of TDP-43, mitochondria, and autophagy: a promising therapeutic strategy for neurodegenerative diseases. Transl Neurodegener 2020; 9:40. [PMID: 33126923 PMCID: PMC7597011 DOI: 10.1186/s40035-020-00219-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are the energy center of cell operations and are involved in physiological functions and maintenance of metabolic balance and homeostasis in the body. Alterations of mitochondrial function are associated with a variety of degenerative and acute diseases. As mitochondria age in cells, they gradually become inefficient and potentially toxic. Acute injury can trigger the permeability of mitochondrial membranes, which can lead to apoptosis or necrosis. Transactive response DNA-binding protein 43 kDa (TDP-43) is a protein widely present in cells. It can bind to RNA, regulate a variety of RNA processes, and play a role in the formation of multi-protein/RNA complexes. Thus, the normal physiological functions of TDP-43 are particularly important for cell survival. Normal TDP-43 is located in various subcellular structures including mitochondria, mitochondrial-associated membrane, RNA particles and stress granules to regulate the endoplasmic reticulum–mitochondrial binding, mitochondrial protein translation, and mRNA transport and translation. Importantly, TDP-43 is associated with a variety of neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal dementia and Alzheimer's disease, which are characterized by abnormal phosphorylation, ubiquitination, lysis or nuclear depletion of TDP-43 in neurons and glial cells. Although the pathogenesis of TDP-43 proteinopathy remains unknown, the presence of pathological TDP-43 inside or outside of mitochondria and the functional involvement of TDP-43 in the regulation of mitochondrial morphology, transport, and function suggest that mitochondria are associated with TDP-43-related diseases. Autophagy is a basic physiological process that maintains the homeostasis of cells, including targeted clearance of abnormally aggregated proteins and damaged organelles in the cytoplasm; therefore, it is considered protective against neurodegenerative diseases. However, the combination of abnormal TDP-43 aggregation, mitochondrial dysfunction, and insufficient autophagy can lead to a variety of aging-related pathologies. In this review, we describe the current knowledge on the associations of mitochondria with TDP-43 and the role of autophagy in the clearance of abnormally aggregated TDP-43 and dysfunctional mitochondria. Finally, we discuss a novel approach for neurodegenerative treatment based on the knowledge.
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Affiliation(s)
- Chunhui Huang
- Institute of New Drug Research, Guangdong Province Key Laboratory of Pharmacodynamic, Constituents of Traditional Chinese Medicine and New Drug Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Sen Yan
- Ministry of Education CNS Regeneration Collaborative Joint Laboratory, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
| | - Zaijun Zhang
- Institute of New Drug Research, Guangdong Province Key Laboratory of Pharmacodynamic, Constituents of Traditional Chinese Medicine and New Drug Research, College of Pharmacy, Jinan University, Guangzhou, 510632, China.
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21
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Flores BN, Li X, Malik AM, Martinez J, Beg AA, Barmada SJ. An Intramolecular Salt Bridge Linking TDP43 RNA Binding, Protein Stability, and TDP43-Dependent Neurodegeneration. Cell Rep 2020; 27:1133-1150.e8. [PMID: 31018129 PMCID: PMC6499398 DOI: 10.1016/j.celrep.2019.03.093] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/28/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022] Open
Abstract
The majority of individuals with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) exhibit neuronal cytoplasmic inclusions rich in the RNA binding protein TDP43. Even so, the relation between the RNA binding properties of TDP43 and neurodegeneration remains obscure. Here, we show that engineered mutations disrupting a salt bridge between the RNA recognition motifs of TDP43 interfere with RNA binding and eliminate the recognition of native TDP43 substrates. The same mutations dramatically destabilize TDP43, alter its subcellular localization, and abrogate TDP43-dependent neuro-degeneration. Worms harboring homologous TDP-1 mutations phenocopy knockout strains, confirming the necessity of salt bridge residues for TDP43 function. Moreover, the accumulation of functional TDP43, but not RNA binding-deficient variants, disproportionately affects transcripts encoding ribo-some and oxidative phosphorylation components. These studies demonstrate the significance of the salt bridge in sustaining TDP43 stability and RNA binding properties, factors that are crucial for neurodegeneration arising from TDP43 deposition in ALS and FTD. Flores et al. uncover essential roles for an intramolecular salt bridge in the function of TDP43, an RNA binding protein implicated in neurodegenerative diseases. Salt bridge interruption attenuates TDP43 RNA binding affinity and specificity, destabilizes the protein, and prevents TDP43-mediated neurotoxicity arising from misprocessing of ribosomal and mitochondrial transcripts.
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Affiliation(s)
- Brittany N Flores
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48104, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Ahmed M Malik
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48104, USA; Neuroscience Graduate Program, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Jose Martinez
- Neuroscience Graduate Program, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Asim A Beg
- Neuroscience Graduate Program, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Sami J Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48104, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48104, USA; Neuroscience Graduate Program, Department of Pharmacology, University of Michigan, Ann Arbor, MI 48104, USA.
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22
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Weskamp K, Tank EM, Miguez R, McBride JP, Gómez NB, White M, Lin Z, Gonzalez CM, Serio A, Sreedharan J, Barmada SJ. Shortened TDP43 isoforms upregulated by neuronal hyperactivity drive TDP43 pathology in ALS. J Clin Invest 2020; 130:1139-1155. [PMID: 31714900 PMCID: PMC7269575 DOI: 10.1172/jci130988] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Cortical hyperexcitability and mislocalization of the RNA-binding protein TDP43 are highly conserved features in amyotrophic lateral sclerosis (ALS). Nevertheless, the relationship between these phenomena remains poorly defined. Here, we showed that hyperexcitability recapitulates TDP43 pathology by upregulating shortened TDP43 (sTDP43) splice isoforms. These truncated isoforms accumulated in the cytoplasm and formed insoluble inclusions that sequestered full-length TDP43 via preserved N-terminal interactions. Consistent with these findings, sTDP43 overexpression was toxic to mammalian neurons, suggesting neurodegeneration arising from complementary gain- and loss-of-function mechanisms. In humans and mice, sTDP43 transcripts were enriched in vulnerable motor neurons, and we observed a striking accumulation of sTDP43 within neurons and glia of ALS patients. Collectively, these studies uncover a pathogenic role for alternative TDP43 isoforms in ALS, and implicate sTDP43 as a key contributor to the susceptibility of motor neurons in this disorder.
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Affiliation(s)
| | | | | | - Jonathon P. McBride
- Department of Neurology
- Cellular and Molecular Biology Program, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicolás B. Gómez
- Department of Neurology
- Cellular and Molecular Biology Program, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Ziqiang Lin
- Department of Basic and Clinical Neuroscience and
| | - Carmen Moreno Gonzalez
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
| | - Andrea Serio
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, United Kingdom
| | | | - Sami J. Barmada
- Department of Neurology
- Neuroscience Graduate Program, and
- Cellular and Molecular Biology Program, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
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23
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Ormeño F, Hormazabal J, Moreno J, Riquelme F, Rios J, Criollo A, Albornoz A, Alfaro IE, Budini M. Chaperone Mediated Autophagy Degrades TDP-43 Protein and Is Affected by TDP-43 Aggregation. Front Mol Neurosci 2020; 13:19. [PMID: 32132902 PMCID: PMC7040037 DOI: 10.3389/fnmol.2020.00019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
TAR DNA binding protein 43 kDa (TDP-43) is a ribonuclear protein regulating many aspects of RNA metabolism. Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD) are fatal neurodegenerative diseases with the presence of TDP-43 aggregates in neuronal cells. Chaperone Mediated Autophagy (CMA) is a lysosomal degradation pathway participating in the proteostasis of several cytosolic proteins including neurodegenerative associated proteins. In addition, protein oligomers or aggregates can affect the status of CMA. In this work, we studied the relationship between CMA and the physiological and pathological forms of TDP-43. First, we found that recombinant TDP-43 was specifically degraded by rat liver’s CMA+ lysosomes and that endogenous TDP-43 is localized in rat brain’s CMA+ lysosomes, indicating that TDP-43 can be a CMA substrate in vivo. Next, by using a previously reported TDP-43 aggregation model, we have shown that wild-type and an aggregate-prone form of TDP-43 are detected in CMA+ lysosomes isolated from cell cultures. In addition, their protein levels increased in cells displaying CMA down-regulation, indicating that these two TDP-43 forms are CMA substrates in vitro. Finally, we observed that the aggregate-prone form of TDP-43 is able to interact with Hsc70, to co-localize with Lamp2A, and to up-regulate the levels of these molecular components of CMA. The latter was followed by an up-regulation of the CMA activity and lysosomal damage. Altogether our data shows that: (i) TDP-43 is a CMA substrate; (ii) CMA can contribute to control the turnover of physiological and pathological forms of TDP-43; and (iii) TDP-43 aggregation can affect CMA performance. Overall, this work contributes to understanding how a dysregulation between CMA and TDP-43 would participate in neuropathological mechanisms associated with TDP-43 aggregation.
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Affiliation(s)
- Fernando Ormeño
- Dentistry Faculty, Molecular and Cellular Pathology Laboratory, Institute in Dentistry Sciences, University of Chile, Santiago, Chile.,Autophagy Research Center (ARC), University of Chile, Santiago, Chile
| | - Juan Hormazabal
- Lysosome Biology Research Laboratory, Fundación Ciencia y Vida, Santiago, Chile
| | - José Moreno
- Dentistry Faculty, Molecular and Cellular Pathology Laboratory, Institute in Dentistry Sciences, University of Chile, Santiago, Chile
| | - Felipe Riquelme
- Dentistry Faculty, Molecular and Cellular Pathology Laboratory, Institute in Dentistry Sciences, University of Chile, Santiago, Chile
| | - Javiera Rios
- Dentistry Faculty, Molecular and Cellular Pathology Laboratory, Institute in Dentistry Sciences, University of Chile, Santiago, Chile.,Autophagy Research Center (ARC), University of Chile, Santiago, Chile
| | - Alfredo Criollo
- Cellular Biology Laboratory, Dentistry Faculty, Institute in Dentistry Sciences, University of Chile, Santiago, Chile
| | | | - Iván E Alfaro
- Lysosome Biology Research Laboratory, Fundación Ciencia y Vida, Santiago, Chile.,Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Mauricio Budini
- Dentistry Faculty, Molecular and Cellular Pathology Laboratory, Institute in Dentistry Sciences, University of Chile, Santiago, Chile.,Autophagy Research Center (ARC), University of Chile, Santiago, Chile
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24
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Shenoy J, El Mammeri N, Dutour A, Berbon M, Saad A, Lends A, Morvan E, Grélard A, Lecomte S, Kauffmann B, Theillet FX, Habenstein B, Loquet A. Structural dissection of amyloid aggregates of TDP-43 and its C-terminal fragments TDP-35 and TDP-16. FEBS J 2019; 287:2449-2467. [PMID: 31782904 DOI: 10.1111/febs.15159] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 10/17/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
The TAR DNA-binding protein (TDP-43) self-assembles into prion-like aggregates considered to be the structural hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. Here, we use a combination of electron microscopy, X-ray fiber diffraction, Fourier-transform infrared spectroscopy analysis, and solid-state NMR spectroscopy to investigate the molecular organization of different TDP constructs, namely the full-length TDP-43 (1-414), two C-terminal fragments [TDP-35 (90-414) and TDP-16 (267-414)], and a C-terminal truncated fragment (TDP-43 ∆GaroS2), in their fibrillar state. Although the different protein constructs exhibit similar fibril morphology and a typical cross-β signature by X-ray diffraction, solid-state NMR indicates that TDP-43 and TDP-35 share the same polymorphic molecular structure, while TDP-16 encompasses a well-ordered amyloid core. We identified several residues in the so-called C-terminal GaroS2 (368-414) domain that participates in the rigid core of TDP-16 fibrils, underlining its importance during the aggregation process. Our findings demonstrate that C-terminal fragments can adopt a different molecular conformation in isolation or in the context of the full-length assembly, suggesting that the N-terminal domain and RRM domains play an important role in the TDP-43 amyloid transition.
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Affiliation(s)
- Jayakrishna Shenoy
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Nadia El Mammeri
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Dutour
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Mélanie Berbon
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Ahmad Saad
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Alons Lends
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Estelle Morvan
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - Axelle Grélard
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Sophie Lecomte
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - François-Xavier Theillet
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Birgit Habenstein
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Loquet
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
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25
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Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Mol Cell 2019; 74:951-965.e13. [PMID: 31047794 PMCID: PMC6561722 DOI: 10.1016/j.molcel.2019.03.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 02/12/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
RNA-binding proteins (RBPs) and long non-coding RNAs (lncRNAs) are key regulators of gene expression, but their joint functions in coordinating cell fate decisions are poorly understood. Here we show that the expression and activity of the RBP TDP-43 and the long isoform of the lncRNA Neat1, the scaffold of the nuclear compartment "paraspeckles," are reciprocal in pluripotent and differentiated cells because of their cross-regulation. In pluripotent cells, TDP-43 represses the formation of paraspeckles by enhancing the polyadenylated short isoform of Neat1. TDP-43 also promotes pluripotency by regulating alternative polyadenylation of transcripts encoding pluripotency factors, including Sox2, which partially protects its 3' UTR from miR-21-mediated degradation. Conversely, paraspeckles sequester TDP-43 and other RBPs from mRNAs and promote exit from pluripotency and embryonic patterning in the mouse. We demonstrate that cross-regulation between TDP-43 and Neat1 is essential for their efficient regulation of a broad network of genes and, therefore, of pluripotency and differentiation.
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Affiliation(s)
- Miha Modic
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Markus Grosch
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Gregor Rot
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Silvia Schirge
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tjasa Lepko
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Flora C Y Lee
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ejona Rusha
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael Palo
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Davide Cacchiarelli
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Telethon Institute of Genetics and Medicine (TIGEM), NA 80078 Pozzuoli, Italy
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; Biomedical Research Institute BRIS, 1000 Ljubljana, Slovenia
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland
| | - Alexander Meissner
- Broad Institute of Harvard University/MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Heiko Lickert
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Comprehensive Pneumology Center (CPC-M), Ludwig-Maximilians-Universität München, Asklepios Fachkliniken München-Gauting und Helmholtz Zentrum München, Max-Lebsche-Platz 31, 81377 Munich, Germany.
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26
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Izumikawa K, Nobe Y, Ishikawa H, Yamauchi Y, Taoka M, Sato K, Nakayama H, Simpson RJ, Isobe T, Takahashi N. TDP-43 regulates site-specific 2'-O-methylation of U1 and U2 snRNAs via controlling the Cajal body localization of a subset of C/D scaRNAs. Nucleic Acids Res 2019; 47:2487-2505. [PMID: 30759234 PMCID: PMC6412121 DOI: 10.1093/nar/gkz086] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
TDP-43 regulates cellular levels of Cajal bodies (CBs) that provide platforms for the assembly and RNA modifications of small nuclear ribonucleoproteins (snRNPs) involved in pre-mRNA splicing. Alterations in these snRNPs may be linked to pathogenesis of amyotrophic lateral sclerosis. However, specific roles for TDP-43 in CBs remain unknown. Here, we demonstrate that TDP-43 regulates the CB localization of four UG-rich motif-bearing C/D-box-containing small Cajal body-specific RNAs (C/D scaRNAs; i.e. scaRNA2, 7, 9 and 28) through the direct binding to these scaRNAs. TDP-43 enhances binding of a CB-localizing protein, WD40-repeat protein 79 (WDR79), to a subpopulation of scaRNA2 and scaRNA28; the remaining population of the four C/D scaRNAs was localized to CB-like structures even with WDR79 depletion. Depletion of TDP-43, in contrast, shifted the localization of these C/D scaRNAs, mainly into the nucleolus, as well as destabilizing scaRNA2, and reduced the site-specific 2'-O-methylation of U1 and U2 snRNAs, including at 70A in U1 snRNA and, 19G, 25G, 47U and 61C in U2 snRNA. Collectively, we suggest that TDP-43 and WDR79 have separate roles in determining CB localization of subsets of C/D and H/ACA scaRNAs.
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Affiliation(s)
- Keiichi Izumikawa
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Hideaki Ishikawa
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Ko Sato
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Richard J Simpson
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
- La Trobe Institute for Molecular Science (LIMS), LIMS Building 1, Room 412 La Trobe University, Melbourne Victoria 3086, Australia
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
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27
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Tann JY, Wong LW, Sajikumar S, Ibáñez CF. Abnormal TDP-43 function impairs activity-dependent BDNF secretion, synaptic plasticity, and cognitive behavior through altered Sortilin splicing. EMBO J 2019; 38:embj.2018100989. [PMID: 30692134 DOI: 10.15252/embj.2018100989] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
Aberrant function of the RNA-binding protein TDP-43 has been causally linked to multiple neurodegenerative diseases. Due to its large number of targets, the mechanisms through which TDP-43 malfunction cause disease are unclear. Here, we report that knockdown, aggregation, or disease-associated mutation of TDP-43 all impair intracellular sorting and activity-dependent secretion of the neurotrophin brain-derived neurotrophic factor (BDNF) through altered splicing of the trafficking receptor Sortilin. Adult mice lacking TDP-43 specifically in hippocampal CA1 show memory impairment and synaptic plasticity defects that can be rescued by restoring Sortilin splicing or extracellular BDNF. Human neurons derived from patient iPSCs carrying mutated TDP-43 also show altered Sortilin splicing and reduced levels of activity-dependent BDNF secretion, which can be restored by correcting the mutation. We propose that major disease phenotypes caused by aberrant TDP-43 activity may be explained by the abnormal function of a handful of critical proteins, such as BDNF.
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Affiliation(s)
- Jason Y Tann
- Department of Physiology, National University of Singapore, Singapore City, Singapore.,Life Sciences Institute, National University of Singapore, Singapore City, Singapore
| | - Lik-Wei Wong
- Department of Physiology, National University of Singapore, Singapore City, Singapore.,Life Sciences Institute, National University of Singapore, Singapore City, Singapore
| | - Sreedharan Sajikumar
- Department of Physiology, National University of Singapore, Singapore City, Singapore.,Life Sciences Institute, National University of Singapore, Singapore City, Singapore
| | - Carlos F Ibáñez
- Department of Physiology, National University of Singapore, Singapore City, Singapore .,Life Sciences Institute, National University of Singapore, Singapore City, Singapore.,Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
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28
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Abstract
Trans activation response DNA/RNA-binding protein 43 kDa (TDP-43) regulates RNA splicing and stability. TDP-43 is a component of ubiquitin-positive inclusion bodies of motor neurons from patients with amyotrophic lateral sclerosis, suggesting a role in disease pathogenesis. Toxic intracellular TDP-43 aggregation may cause neuronal cell death. The loss of TDP-43 in animal models causes lethality in early development. Furthermore, TDP-43 knockdown in adult animals and cells increases aberrant splicing. Uridine-rich small nuclear RNA (U snRNA) regulation is disrupted in cultured neuroblastoma cells with TDP-43 knockdown and in motor neurons in amyotrophic lateral sclerosis. Aberrant mRNA splicing and U snRNA expression are likely key processes in neuronal cell death. We review the research history and future perspectives of aberrant splicing by TDP-43 loss.
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Affiliation(s)
- Akira Kitamura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan 001-0021
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29
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Jeon GS, Shim YM, Lee DY, Kim JS, Kang M, Ahn SH, Shin JY, Geum D, Hong YH, Sung JJ. Pathological Modification of TDP-43 in Amyotrophic Lateral Sclerosis with SOD1 Mutations. Mol Neurobiol 2018; 56:2007-2021. [PMID: 29982983 PMCID: PMC6394608 DOI: 10.1007/s12035-018-1218-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/29/2018] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, adult-onset, progressive neurodegenerative disorder with no known cure. Cu/Zn-superoxide dismutase (SOD1) was the first identified protein associated with familial ALS (fALS). Recently, TAR DNA-binding protein 43 (TDP-43) has been found to be a principal component of ubiquitinated cytoplasmic inclusions in neurons and glia in ALS. However, it remains unclear whether these ALS-linked proteins partly have a shared pathogenesis. Here, we determine the association between mutant SOD1 and the modification of TDP-43 and the relationship of pathologic TDP-43 to neuronal cytotoxicity in SOD1 ALS. In this work, using animal model, human tissue, and cell models, we provide the evidence that the association between the TDP-43 modification and the pathogenesis of SOD1 fALS. We demonstrated an age-dependent increase in TDP-43 C-terminal fragments and phosphorylation in motor neurons and glia of SOD1 mice and SOD1G85S ALS patient. Cytoplasmic TDP-43 was also observed in iPSC-derived motor neurons from SOD1G17S ALS patient. Moreover, we observed that mutant SOD1 interacts with TDP-43 in co-immunoprecipitation assays with G93A hSOD1-transfected cell lines. Mutant SOD1 overexpression led to an increase in TDP-43 modification in the detergent-insoluble fraction in the spinal cord of SOD1 mice and fALS patient. Additionally, we showed cellular apoptosis in response to the interaction of mutant SOD1 and fragment forms of TDP-43. These findings suggest that mutant SOD1 could affect the solubility/insolubility of TDP-43 through physical interactions and the resulting pathological modifications of TDP-43 may be involved in motor neuron death in SOD1 fALS.
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Affiliation(s)
- Gye Sun Jeon
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Yu-Mi Shim
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Do-Yeon Lee
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Jun-Soon Kim
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - MinJin Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - So Hyun Ahn
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Je-Young Shin
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Dongho Geum
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Yoon Ho Hong
- Department of Neurology, Seoul National University Seoul Metropolitan Government Boramae Medical Center, Seoul, South Korea
| | - Jung-Joon Sung
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea. .,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
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30
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Prakash A, Kumar V, Meena NK, Lynn AM. Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43. RSC Adv 2018; 8:19835-19845. [PMID: 35548664 PMCID: PMC9088055 DOI: 10.1039/c8ra03368d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
The N-terminal domain of the RNA binding protein TDP-43 (NTD) is essential to both physiology and proteinopathy; however, elucidation of its folding/unfolding still remains a major quest. In this study, we have investigated the biophysical behavior of intermediate ensembles employing all-atom molecular dynamics simulations in 8 M urea accelerated with high temperatures to achieve unfolded states in a confined computation time. The cumulative results of the 2.75 μs simulations show that unfolding of the NTD at 350 K evolves through different stable and meta-stable intermediate states. The free-energy landscape reveals two meta-stable intermediates (IN and IU) stabilized by non-native interactions, which are largely hydrophilic and highly energetically frustrated. A single buried tryptophan residue, W80, undergoes solvent exposure to different extents during unfolding; this suggests a structurally heterogeneous population of intermediate ensembles. Furthermore, the structure properties of the IN state show a resemblance to the molten globule (MG) state with most of the secondary structures intact. The unfolding of the NTD is initiated by the loss of β-strands, and the unfolded (U) states exhibit a population of non-native α-helices. These non-native unfolded intermediate ensembles may mediate protein oligomerization, leading to the formation of pathological, irreversible aggregates, characteristics of disease pathogenesis.
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Affiliation(s)
- Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia Jamia Nagar New Delhi-110025 India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University New Delhi-110067 India
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31
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Zhang K, Coyne AN, Lloyd TE. Drosophila models of amyotrophic lateral sclerosis with defects in RNA metabolism. Brain Res 2018; 1693:109-120. [PMID: 29752901 DOI: 10.1016/j.brainres.2018.04.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022]
Abstract
The fruit fly Drosophila Melanogaster has been widely used to study neurodegenerative diseases. The conservation of nervous system biology coupled with the rapid life cycle and powerful genetic tools in the fly have enabled the identification of novel therapeutic targets that have been validated in vertebrate model systems and human patients. A recent example is in the study of the devastating motor neuron degenerative disease amyotrophic lateral sclerosis (ALS). Mutations in genes that regulate RNA metabolism are a major cause of inherited ALS, and functional analysis of these genes in the fly nervous system has shed light on how mutations cause disease. Importantly, unbiased genetic screens have identified key pathways that contribute to ALS pathogenesis such as nucleocytoplasmic transport and stress granule assembly. In this review, we will discuss the utilization of Drosophila models of ALS with defects in RNA metabolism.
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Affiliation(s)
- Ke Zhang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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32
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Langellotti S, Romano G, Feiguin F, Baralle FE, Romano M. RhoGAPp190: A potential player in tbph-mediated neurodegeneration in Drosophila. PLoS One 2018; 13:e0195845. [PMID: 29652933 PMCID: PMC5898758 DOI: 10.1371/journal.pone.0195845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/01/2018] [Indexed: 12/13/2022] Open
Abstract
TDP-43 is an ubiquitous and highly conserved ribonucleoprotein involved in several cellular processes including pre-mRNA splicing, transcription, mRNA stability and transport. Notwithstanding the evidence of TDP-43 involvement in the pathogenesis of different neurodegenerative disorders (i.e. ALS and FTLD), the underlying mechanisms are still unclear. Given the high degree of functional similarity between the human and fly orthologs of TDP-43, Drosophila melanogaster is a simple and useful model to study the pathophysiological role of this protein in vivo. It has been demonstrated that the depletion of the TDP-43 fly ortholog (tbph) induces deficient locomotive behaviors and reduces life span and anatomical defects at the neuromuscular junction. In this study, using the known binding specificity of TDP-43/tbph for (UG) repeated sequences, we performed a bioinformatic screening for fly genes with at least 6 (TG) repeats in a row within the 3'-UTR regions in order to identify the genes that might be regulated by this factor. Among these genes, we were able to identify RhoGAPp190 as a potential target of the tbph-mediated neurodegeneration. RhoGAPp190 is a negative regulator of Drosophila RhoA, a GTPase protein implicated in the fine modulation of critical cellular processes including axon branch stability and motor axon defasciculation at muscle level and cognitive processes. We were able to demonstrate that the RhoGAPp190 expression is upregulated in a tbph-null fly model, providing evidence that this deregulation is associated to tbph silencing. Our results introduce RhoGAPp190 as a novel potential mediator in the complex scenario of events resulting from in vivo tbph loss-of-function.
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Affiliation(s)
- Simona Langellotti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giulia Romano
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
- * E-mail:
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33
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Shenouda M, Zhang AB, Weichert A, Robertson J. Mechanisms Associated with TDP-43 Neurotoxicity in ALS/FTLD. ADVANCES IN NEUROBIOLOGY 2018; 20:239-263. [PMID: 29916022 DOI: 10.1007/978-3-319-89689-2_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of TDP-43 as a major disease protein in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) was first made in 2006. Prior to 2006 there were only 11 publications related to TDP-43, now there are over 2000, indicating the importance of TDP-43 to unraveling the complex molecular mechanisms that underpin the pathogenesis of ALS/FTLD. Subsequent to this discovery, TDP-43 pathology was also found in other neurodegenerative diseases, including Alzheimer's disease, the significance of which is still in the early stages of exploration. TDP-43 is a predominantly nuclear DNA/RNA-binding protein, one of a number of RNA-binding proteins that are now known to be linked with ALS/FTLD, including Fused in Sarcoma (FUS), heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), and heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1). However, what sets TDP-43 apart is the vast number of cases in which TDP-43 pathology is present, providing a point of convergence, the understanding of which could lead to broadly applicable therapeutics. Here we will focus on TDP-43 in ALS/FTLD, its nuclear and cytoplasmic functions, and consequences should these functions go awry.
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Affiliation(s)
- Marc Shenouda
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada
| | - Ashley B Zhang
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada
| | - Anna Weichert
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 2S8, Canada.
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Abstract
In this issue of Structure, Conicella et al. (2016) present evidence that the low complexity C-terminal region of TDP-43 undergoes liquid-liquid phase separation. ALS-associated mutations alter this phase separation process, providing a possible mechanism for the pathology caused by these TDP-43 mutations. The work is strongly supportive of toxic loss of RNA processing function in ALS.
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Affiliation(s)
- P Andrew Chong
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Julie D Forman-Kay
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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35
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Appocher C, Mohagheghi F, Cappelli S, Stuani C, Romano M, Feiguin F, Buratti E. Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells. Nucleic Acids Res 2017; 45:8026-8045. [PMID: 28575377 PMCID: PMC5570092 DOI: 10.1093/nar/gkx477] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 05/16/2017] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor TDP-43 is known to play an important role in several neurodegenerative pathologies. In general, TDP-43 is an abundant protein within the eukaryotic nucleus that binds to many coding and non-coding RNAs and influence their processing. Using Drosophila, we have performed a functional screening to establish the ability of major hnRNP proteins to affect TDP-43 overexpression/depletion phenotypes. Interestingly, we observed that lowering hnRNP and TDP-43 expression has a generally harmful effect on flies locomotor abilities. In parallel, our study has also identified a distinct set of hnRNPs that is capable of powerfully rescuing TDP-43 toxicity in the fly eye (Hrb27c, CG42458, Glo and Syp). Most importantly, removing the human orthologs of Hrb27c (DAZAP1) in human neuronal cell lines can correct several pre-mRNA splicing events altered by TDP-43 depletion. Moreover, using RNA sequencing analysis we show that DAZAP1 and TDP-43 can co-regulate an extensive number of biological processes and molecular functions potentially important for the neuron/motor neuron pathophysiology. Our results suggest that changes in hnRNP expression levels can significantly modulate TDP-43 functions and affect pathological outcomes.
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Affiliation(s)
- Chiara Appocher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Fatemeh Mohagheghi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Sara Cappelli
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
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36
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Tsoi PS, Choi K, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N‐Terminal Domain of ALS‐Linked TDP‐43 Assembles without Misfolding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Phoebe S. Tsoi
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Kyoung‐Jae Choi
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Paul G. Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function University of Texas MD Anderson Cancer Center Houston TX USA
| | - Antons Sizovs
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Kevin R. MacKenzie
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
- Department of Pathology and Immunology Baylor College of Medicine Houston TX USA
| | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
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37
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Tsoi PS, Choi KJ, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N-Terminal Domain of ALS-Linked TDP-43 Assembles without Misfolding. Angew Chem Int Ed Engl 2017; 56:12590-12593. [PMID: 28833982 DOI: 10.1002/anie.201706769] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/08/2017] [Indexed: 12/28/2022]
Abstract
Transactivation response element (TAR) DNA-binding protein 43 (TDP-43) misfolding is implicated in several neurodegenerative diseases characterized by aggregated protein inclusions. Misfolding is believed to be mediated by both the N- and C-terminus of TDP-43; however, the mechanistic basis of the contribution of individual domains in the process remained elusive. Here, using single-molecule fluorescence and ensemble biophysical techniques, and a wide range of pH and temperature conditions, we show that TDP-43NTD is thermodynamically stable, well-folded and undergoes reversible oligomerization. We propose that, in full-length TDP-43, association between folded N-terminal domains enhances the propensity of the intrinsically unfolded C-terminal domains to drive pathological aggregation.
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Affiliation(s)
- Phoebe S Tsoi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kyoung-Jae Choi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Paul G Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Antons Sizovs
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin R MacKenzie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
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38
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Biology and Pathobiology of TDP-43 and Emergent Therapeutic Strategies. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a024554. [PMID: 27920024 DOI: 10.1101/cshperspect.a024554] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytoplasmic TDP-43 mislocalization and aggregation is a pathological hallmark of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 is an RNA-binding protein (RBP) with a prion-like domain (PrLD) that promotes TDP-43 misfolding. PrLDs possess compositional similarity to canonical prion domains of various yeast proteins, including Sup35. Strikingly, disease-causing TDP-43 mutations reside almost exclusively in the PrLD and can enhance TDP-43 misfolding and toxicity. Another ∼70 human RBPs harbor PrLDs, including FUS, TAF15, EWSR1, hnRNPA1, and hnRNPA2, which have surfaced in the etiology of neurodegenerative diseases. Importantly, PrLDs enable RBP function and mediate phase transitions that partition functional ribonucleoprotein compartments. This PrLD activity, however, renders RBPs prone to populating deleterious oligomers or self-templating fibrils that might spread disease, and disease-linked PrLD mutations can exacerbate this risk. Several strategies have emerged to counter TDP-43 proteinopathies, including engineering enhanced protein disaggregases based on Hsp104.
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39
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Garnier C, Devred F, Byrne D, Puppo R, Roman AY, Malesinski S, Golovin AV, Lebrun R, Ninkina NN, Tsvetkov PO. Zinc binding to RNA recognition motif of TDP-43 induces the formation of amyloid-like aggregates. Sci Rep 2017; 7:6812. [PMID: 28754988 PMCID: PMC5533730 DOI: 10.1038/s41598-017-07215-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Aggregation of TDP-43 (transactive response DNA binding protein 43 kDa) is a hallmark of certain forms of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Moreover, intracellular TDP-43-positive inclusions are often found in other neurodegenerative diseases. Recently it was shown that zinc ions can provoke the aggregation of endogenous TDP-43 in cells, allowing to assume a direct interaction of TDP-43 with zinc ions. In this work, we investigated zinc binding to the 102-269 TDP-43 fragment, which comprise the two RNA recognition motifs. Using isothermal titration calorimetry, mass spectrometry, and differential scanning fluorimetry, we showed that zinc binds to this TDP-43 domain with a dissociation constant in the micromolar range and modifies its tertiary structure leading to a decrease of its thermostability. Moreover, the study by dynamic light scattering and negative stain electron microscopy demonstrated that zinc ions induce auto-association process of this TDP-43 fragment into rope-like structures. These structures are thioflavin-T-positive allowing to hypothesize the direct implication of zinc ions in pathological aggregation of TDP-43.
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Affiliation(s)
- Cyrille Garnier
- Mécanismes Moléculaires dans les Démences Neurodégénératives, Université de Montpellier, EPHE, INSERM, U1198, F-34095, Montpellier, France
- Université de Rennes 1, Campus de Beaulieu, 35042, Rennes cedex, France
| | - François Devred
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Deborah Byrne
- Institut de Microbiologie de la Méditerranée, CNRS, FR3479, Aix-Marseille Université, Marseille, France
| | - Rémy Puppo
- Institut de Microbiologie de la Méditerranée, CNRS, FR3479, Aix-Marseille Université, Marseille, France
| | - Andrei Yu Roman
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
- Institute of Physiologically Active Compounds, RAS, 142432, Chernogolovka, Russian Federation
| | - Soazig Malesinski
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Andrey V Golovin
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Régine Lebrun
- Institut de Microbiologie de la Méditerranée, CNRS, FR3479, Aix-Marseille Université, Marseille, France
| | - Natalia N Ninkina
- Institute of Physiologically Active Compounds, RAS, 142432, Chernogolovka, Russian Federation.
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Philipp O Tsvetkov
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France.
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Borroni B, Stanic J, Verpelli C, Mellone M, Bonomi E, Alberici A, Bernasconi P, Culotta L, Zianni E, Archetti S, Manes M, Gazzina S, Ghidoni R, Benussi L, Stuani C, Di Luca M, Sala C, Buratti E, Padovani A, Gardoni F. Anti-AMPA GluA3 antibodies in Frontotemporal dementia: a new molecular target. Sci Rep 2017; 7:6723. [PMID: 28751743 PMCID: PMC5532270 DOI: 10.1038/s41598-017-06117-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/07/2017] [Indexed: 12/12/2022] Open
Abstract
Frontotemporal Dementia (FTD) is a neurodegenerative disorder mainly characterised by Tau or TDP43 inclusions. A co-autoimmune aetiology has been hypothesised. In this study, we aimed at defining the pathogenetic role of anti-AMPA GluA3 antibodies in FTD. Serum and cerebrospinal fluid (CSF) anti-GluA3 antibody dosage was carried out and the effect of CSF with and without anti-GluA3 antibodies was tested in rat hippocampal neuronal primary cultures and in differentiated neurons from human induced pluripotent stem cells (hiPSCs). TDP43 and Tau expression in hiPSCs exposed to CSF was assayed. Forty-one out of 175 screened FTD sera were positive for the presence of anti-GluA3 antibodies (23.4%). FTD patients with anti-GluA3 antibodies more often presented presenile onset, behavioural variant FTD with bitemporal atrophy. Incubation of rat hippocampal neuronal primary cultures with CSF with anti-GluA3 antibodies led to a decrease of GluA3 subunit synaptic localization of the AMPA receptor (AMPAR) and loss of dendritic spines. These results were confirmed in differentiated neurons from hiPSCs, with a significant reduction of the GluA3 subunit in the postsynaptic fraction along with increased levels of neuronal Tau. In conclusion, autoimmune mechanism might represent a new potentially treatable target in FTD and might open new lights in the disease underpinnings.
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Affiliation(s)
- B Borroni
- Neurology Unit, Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy.
| | - J Stanic
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - C Verpelli
- CNR Institute of Neuroscience and Department of Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - M Mellone
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - E Bonomi
- Neurology Unit, Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - A Alberici
- Neurology Unit, Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | | | - L Culotta
- CNR Institute of Neuroscience and Department of Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - E Zianni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - S Archetti
- III Laboratory of Analyses, Biotechnology Laboratory, Brescia Hospital, Brescia, Italy
| | - M Manes
- Neurology Unit, Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - S Gazzina
- Neurology Unit, Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - R Ghidoni
- Molecular Markers Laboratory, IRCCS Fatebenefratelli S. Giovanni di Dio, Brescia, Italy
| | - L Benussi
- Molecular Markers Laboratory, IRCCS Fatebenefratelli S. Giovanni di Dio, Brescia, Italy
| | - C Stuani
- International Centre for Genetic Engineering and Biotechnology-ICGEB, Trieste, Italy
| | - M Di Luca
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - C Sala
- CNR Institute of Neuroscience and Department of Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - E Buratti
- International Centre for Genetic Engineering and Biotechnology-ICGEB, Trieste, Italy
| | - A Padovani
- Neurology Unit, Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - F Gardoni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy.
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41
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Jiang LL, Xue W, Hong JY, Zhang JT, Li MJ, Yu SN, He JH, Hu HY. The N-terminal dimerization is required for TDP-43 splicing activity. Sci Rep 2017; 7:6196. [PMID: 28733604 PMCID: PMC5522446 DOI: 10.1038/s41598-017-06263-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/08/2017] [Indexed: 12/12/2022] Open
Abstract
TDP-43 is a nuclear factor that functions in promoting pre-mRNA splicing. Deletion of the N-terminal domain (NTD) and nuclear localization signal (NLS) (i.e., TDP-35) results in mislocalization to cytoplasm and formation of inclusions. However, how the NTD functions in TDP-43 activity and proteinopathy remains largely unknown. Here, we studied the structure and function of the NTD in inclusion formation and pre-mRNA splicing of TDP-43 by using biochemical and biophysical approaches. We found that TDP-43 NTD forms a homodimer in solution in a concentration-dependent manner, and formation of intermolecular disulfide results in further tetramerization. Based on the NMR structure of TDP-43 NTD, the dimerization interface centered on Leu71 and Val72 around the β7-strand was defined by mutagenesis and size-exclusion chromatography. Cell experiments revealed that the N-terminal dimerization plays roles in protecting TDP-43 against formation of cytoplasmic inclusions and enhancing pre-mRNA splicing activity of TDP-43 in nucleus. This study may provide mechanistic insights into the physiological function of TDP-43 and its related proteinopathies.
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Affiliation(s)
- Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China
| | - Wei Xue
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China
| | - Jun-Ye Hong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China
| | - Jun-Ting Zhang
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Min-Jun Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai, 201204, P.R. China
| | - Shao-Ning Yu
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai, 201204, P.R. China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China.
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Mompeán M, Romano V, Pantoja-Uceda D, Stuani C, Baralle FE, Buratti E, Laurents DV. Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions. J Biol Chem 2017; 292:11992-12006. [PMID: 28566288 PMCID: PMC5512090 DOI: 10.1074/jbc.m117.775965] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) performs multiple tasks in mRNA processing, transport, and translational regulation, but it also forms aggregates implicated in amyotrophic lateral sclerosis. TDP-43's N-terminal domain (NTD) is important for these activities and dysfunctions; however, there is an open debate about whether or not it adopts a specifically folded, stable structure. Here, we studied NTD mutations designed to destabilize its structure utilizing NMR and fluorescence spectroscopies, analytical ultracentrifugation, splicing assays, and cell microscopy. The substitutions V31R and T32R abolished TDP-43 activity in splicing and aggregation processes, and even the rather mild L28A mutation severely destabilized the NTD, drastically reducing TDP-43's in vitro splicing activity and inducing aberrant localization and aggregation in cells. These findings strongly support the idea that a stably folded NTD is essential for correct TDP-43 function. The stably folded NTD also promotes dimerization, which is pertinent to the protein's activities and pathological aggregation, and we present an atomic-level structural model for the TDP-43 dimer based on NMR data. Leu-27 is evolutionarily well conserved even though it is exposed in the monomeric NTD. We found here that Leu-27 is buried in the dimer and that the L27A mutation promotes monomerization. In conclusion, our study sheds light on the structural and biological properties of the TDP-43 NTD, indicating that the NTD must be stably folded for TDP-43's physiological functions, and has implications for understanding the mechanisms promoting the pathological aggregation of this protein.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - David Pantoja-Uceda
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain.
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43
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De Conti L, Borroni B, Baralle M. New routes in frontotemporal dementia drug discovery. Expert Opin Drug Discov 2017; 12:659-671. [DOI: 10.1080/17460441.2017.1329294] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Laura De Conti
- Biotechnology Development Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Barbara Borroni
- Centre for Neurodegenerative Disorders - Neurology Unit, University of Brescia, Brescia, Italy
| | - Marco Baralle
- Biotechnology Development Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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44
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Budini M, Buratti E, Morselli E, Criollo A. Autophagy and Its Impact on Neurodegenerative Diseases: New Roles for TDP-43 and C9orf72. Front Mol Neurosci 2017; 10:170. [PMID: 28611593 PMCID: PMC5447761 DOI: 10.3389/fnmol.2017.00170] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a catabolic mechanism where intracellular material is degraded by vesicular structures called autophagolysosomes. Autophagy is necessary to maintain the normal function of the central nervous system (CNS), avoiding the accumulation of misfolded and aggregated proteins. Consistently, impaired autophagy has been associated with the pathogenesis of various neurodegenerative diseases. The proteins TAR DNA-binding protein-43 (TDP-43), which regulates RNA processing at different levels, and chromosome 9 open reading frame 72 (C9orf72), probably involved in membrane trafficking, are crucial in the development of neurodegenerative diseases such as Amyotrophic lateral sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD). Additionally, recent studies have identified a role for these proteins in the control of autophagy. In this manuscript, we review what is known regarding the autophagic mechanism and discuss the involvement of TDP-43 and C9orf72 in autophagy and their impact on neurodegenerative diseases.
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Affiliation(s)
- Mauricio Budini
- Dentistry Faculty, Institute in Dentistry Sciences, University of ChileSantiago, Chile
| | - Emanuele Buratti
- International Centre for Genetic Engineering and BiotechnologyTrieste, Italy
| | - Eugenia Morselli
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Alfredo Criollo
- Dentistry Faculty, Institute in Dentistry Sciences, University of ChileSantiago, Chile.,Advanced Center for Chronic DiseasesSantiago, Chile
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45
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Webster CP, Smith EF, Shaw PJ, De Vos KJ. Protein Homeostasis in Amyotrophic Lateral Sclerosis: Therapeutic Opportunities? Front Mol Neurosci 2017; 10:123. [PMID: 28512398 PMCID: PMC5411428 DOI: 10.3389/fnmol.2017.00123] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis (proteostasis), the correct balance between production and degradation of proteins, is essential for the health and survival of cells. Proteostasis requires an intricate network of protein quality control pathways (the proteostasis network) that work to prevent protein aggregation and maintain proteome health throughout the lifespan of the cell. Collapse of proteostasis has been implicated in the etiology of a number of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), the most common adult onset motor neuron disorder. Here, we review the evidence linking dysfunctional proteostasis to the etiology of ALS and discuss how ALS-associated insults affect the proteostasis network. Finally, we discuss the potential therapeutic benefit of proteostasis network modulation in ALS.
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Affiliation(s)
- Christopher P Webster
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - Emma F Smith
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
| | - Kurt J De Vos
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of SheffieldSheffield, UK
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46
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Oberstadt M, Claßen J, Arendt T, Holzer M. TDP-43 and Cytoskeletal Proteins in ALS. Mol Neurobiol 2017; 55:3143-3151. [PMID: 28466273 DOI: 10.1007/s12035-017-0543-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/07/2017] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) represents a rapidly progressing neurodegenerative disease and is characterized by a degeneration of motor neurons. Motor neurons are particularly susceptible to selective and early degeneration because of their extended axon length and their dependency on the cytoskeleton for its stability, signaling, and axonal transport. The motor neuron cytoskeleton comprises actin filaments, neurofilaments like peripherin, and microtubules. The Transactivating Response Region (TAR) DNA Binding Protein (TDP-43) forms characteristic cytoplasmic aggregates in motor neurons of ALS patients, and at least in part, the pathogenesis of ALS seems to be driven by toxic pTDP-43 aggregates in cytoplasm, which lead to a diminished axon formation and reduced axon length. Diminished axon formation and reduced axon length suggest an interaction of TDP-43 with the cytoskeleton of motor neurons. TDP-43 interacts with several cytoskeletal components, e.g., the microtubule-associated protein 1B (MAP1B) or the neurofilament light chain (NFL) through direct binding to its RNA. From a clinical perspective, cytoskeletal biomarkers like phosphorylated neurofilament heavy chain (pNFH) and NFL are already clinically used in ALS patients to predict survival, disease progression, and duration. Thus, in this review, we focus on the interaction of TDP-43 with the different cytoskeleton components such as actin filaments, neurofilaments, and microtubules as well as their associated proteins as one aspect in the complex pathogenesis of ALS.
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Affiliation(s)
- Moritz Oberstadt
- Department of Neurology, University of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany.
| | - Joseph Claßen
- Department of Neurology, University of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Thomas Arendt
- Department for Molecular and Cellular Mechanisms of Neurodegeneration, Paul Flechsig Institute for Brain Research, University of Leipzig, Liebigstraße 19, 04103, Leipzig, Germany
| | - Max Holzer
- Department for Molecular and Cellular Mechanisms of Neurodegeneration, Paul Flechsig Institute for Brain Research, University of Leipzig, Liebigstraße 19, 04103, Leipzig, Germany
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Abstract
TDP-43 is a dimeric nuclear protein that plays a central role in RNA metabolism. In recent years, this protein has become a focal point of research in the amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) disease spectrum, as pathognomonic inclusions within affected neurons contain post-translationally modified TDP-43. A key question in TDP-43 research involves determining the mechanisms and triggers that cause TDP-43 to form pathological aggregates. This review gives a brief overview of the physiological and pathological roles of TDP-43 and focuses on the structural features of its protein domains and how they may contribute to normal protein function and to disease. A special emphasis is placed on the C-terminal prion-like region thought to be implicated in pathology, as it is where nearly all ALS/FTD-associated mutations reside. Recent structural studies of this domain revealed its crucial role in the formation of phase-separated liquid droplets through a partially populated α-helix. This new discovery provides further support for the theory that liquid droplets such as stress granules may be precursors to pathological aggregates, linking environmental effects such as stress to the potential etiology of the disease. The transition of TDP-43 among soluble, droplet, and aggregate phases and the implications of these transitions for pathological aggregation are summarized and discussed.
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Affiliation(s)
- Yulong Sun
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada
| | - Avijit Chakrabartty
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada.,Department of Biochemistry, University of Toronto , Toronto, Ontario M5G1L7, Canada
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Lee JM, Tan V, Lovejoy D, Braidy N, Rowe DB, Brew BJ, Guillemin GJ. Involvement of quinolinic acid in the neuropathogenesis of amyotrophic lateral sclerosis. Neuropharmacology 2017; 112:346-364. [DOI: 10.1016/j.neuropharm.2016.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
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49
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Bozzo F, Mirra A, Carrì M. Oxidative stress and mitochondrial damage in the pathogenesis of ALS: New perspectives. Neurosci Lett 2017; 636:3-8. [DOI: 10.1016/j.neulet.2016.04.065] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/05/2016] [Accepted: 04/29/2016] [Indexed: 02/07/2023]
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50
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Rossi S, Cozzolino M, Carrì MT. Old versus New Mechanisms in the Pathogenesis of ALS. Brain Pathol 2016; 26:276-86. [PMID: 26779612 DOI: 10.1111/bpa.12355] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is recognized as a very complex disease. As we have learned in the past 20 years from studies in patients and in models based on the expression of mutant SOD1, ALS is not a purely motor neuron disease as previously thought. While undoubtedly motor neurons are lost in patients, a number of alterations in those cell-types that interact functionally with motor neurons (astrocytes, microglia, muscle fibers, oligodendrocytes) take place even long before onset of symptoms. At the same time, disturbance of several, only partly inter-related physiological functions play some role in the onset and progression of the disease. Traditionally, mitochondrial damage and oxidative stress, excitotoxicity, neuroinflammation, altered axonal transport, ER stress, protein aggregation and defective removal of toxic proteins have been considered as key factors in the pathogenesis of ALS, with the relatively recent addition of disturbances in RNA metabolism. This complexity makes the search for an effective treatment extremely difficult and prompts further studies to reveal other possible, previously unappreciated aspects of the pathogenesis of ALS. In this review, we focus on previous knowledge on ALS mechanisms as well as new facets emerging from studies on genetic ALS patients and models that may both provide precious information for a novel therapeutic approach.
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Affiliation(s)
- Simona Rossi
- Institute of Translational Pharmacology, National Research Council (CNR), Rome, Italy
| | - Mauro Cozzolino
- Institute of Translational Pharmacology, National Research Council (CNR), Rome, Italy.,Lab of Neurochemistry, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Maria Teresa Carrì
- Lab of Neurochemistry, Fondazione Santa Lucia IRCCS, Rome, Italy.,Department of Biology, University of Rome Tor Vergata
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