1
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Lang R, Hodgson RE, Shelkovnikova TA. TDP-43 in nuclear condensates: where, how, and why. Biochem Soc Trans 2024:BST20231447. [PMID: 38958608 DOI: 10.1042/bst20231447] [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: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
TDP-43 is an abundant and ubiquitously expressed nuclear protein that becomes dysfunctional in a spectrum of neurodegenerative diseases. TDP-43's ability to phase separate and form/enter biomolecular condensates of varying size and composition is critical for its functionality. Despite the high density of phase-separated assemblies in the nucleus and the nuclear abundance of TDP-43, our understanding of the condensate-TDP-43 relationship in this cellular compartment is only emerging. Recent studies have also suggested that misregulation of nuclear TDP-43 condensation is an early event in the neurodegenerative disease amyotrophic lateral sclerosis. This review aims to draw attention to the nuclear facet of functional and aberrant TDP-43 condensation. We will summarise the current knowledge on how TDP-43 containing nuclear condensates form and function and how their homeostasis is affected in disease.
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Affiliation(s)
- Ruaridh Lang
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
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2
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Kitamura A, Fujimoto A, Kawashima R, Lyu Y, Sasaki K, Hamada Y, Moriya K, Kurata A, Takahashi K, Brielmann R, Bott LC, Morimoto RI, Kinjo M. Hetero-oligomerization of TDP-43 carboxy-terminal fragments with cellular proteins contributes to proteotoxicity. Commun Biol 2024; 7:743. [PMID: 38902525 PMCID: PMC11190292 DOI: 10.1038/s42003-024-06410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
Carboxy terminal fragments (CTFs) of TDP-43 contain an intrinsically disordered region (IDR) and form cytoplasmic condensates containing amyloid fibrils. Such condensates are toxic and associated with pathogenicity in amyotrophic lateral sclerosis. However, the molecular details of how the domain of TDP-43 CTFs leads to condensation and cytotoxicity remain elusive. Here, we show that truncated RNA/DNA-recognition motif (RRM) at the N-terminus of TDP-43 CTFs leads to the structural transition of the IDR, whereas the IDR itself of TDP-43 CTFs is difficult to assemble even if they are proximate intermolecularly. Hetero-oligomers of TDP-43 CTFs that have recruited other proteins are more toxic than homo-oligomers, implicating loss-of-function of the endogenous proteins by such oligomers is associated with cytotoxicity. Furthermore, such toxicity of TDP-43 CTFs was cell-nonautonomously affected in the nematodes. Therefore, misfolding and oligomeric characteristics of the truncated RRM at the N-terminus of TDP-43 CTFs define their condensation properties and toxicity.
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Affiliation(s)
- Akira Kitamura
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan.
- PRIME, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan.
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan.
| | - Ai Fujimoto
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Rei Kawashima
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Yidan Lyu
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kotetsu Sasaki
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Yuta Hamada
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kanami Moriya
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Ayumi Kurata
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kazuho Takahashi
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Reneé Brielmann
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Laura C Bott
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Richard I Morimoto
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
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3
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Ke H, Liu K, Jiao B, Zhao L. Implications of TDP-43 in non-neuronal systems. Cell Commun Signal 2023; 21:338. [PMID: 37996849 PMCID: PMC10666381 DOI: 10.1186/s12964-023-01336-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/26/2023] [Indexed: 11/25/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a versatile RNA/DNA-binding protein with multifaceted processes. While TDP-43 has been extensively studied in the context of degenerative diseases, recent evidence has also highlighted its crucial involvement in diverse life processes beyond neurodegeneration. Here, we mainly reviewed the function of TDP-43 in non-neurodegenerative physiological and pathological processes, including spermatogenesis, embryonic development, mammary gland development, tumor formation, and viral infection, highlighting its importance as a key regulatory factor for the maintenance of normal functions throughout life. TDP-43 exhibits diverse and sometimes opposite functionality across different cell types through various mechanisms, and its roles can shift at distinct stages within the same biological system. Consequently, TDP-43 operates in both a context-dependent and a stage-specific manner in response to a variety of internal and external stimuli. Video Abstract.
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Affiliation(s)
- Hao Ke
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China
| | - Kang Liu
- Ganzhou People's Hospital, Ganzhou, 341000, China
| | - Baowei Jiao
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Limin Zhao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China.
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4
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Nag S, Schneider JA. Limbic-predominant age-related TDP43 encephalopathy (LATE) neuropathological change in neurodegenerative diseases. Nat Rev Neurol 2023; 19:525-541. [PMID: 37563264 PMCID: PMC10964248 DOI: 10.1038/s41582-023-00846-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 08/12/2023]
Abstract
TAR DNA-binding protein 43 (TDP43) is a focus of research in late-onset dementias. TDP43 pathology in the brain was initially identified in amyotrophic lateral sclerosis and frontotemporal lobar degeneration, and later in Alzheimer disease (AD), other neurodegenerative diseases and ageing. Limbic-predominant age-related TDP43 encephalopathy (LATE), recognized as a clinical entity in 2019, is characterized by amnestic dementia resembling AD dementia and occurring most commonly in adults over 80 years of age. Neuropathological findings in LATE, referred to as LATE neuropathological change (LATE-NC), consist of neuronal and glial cytoplasmic TDP43 localized predominantly in limbic areas with or without coexisting hippocampal sclerosis and/or AD neuropathological change and without frontotemporal lobar degeneration or amyotrophic lateral sclerosis pathology. LATE-NC is frequently associated with one or more coexisting pathologies, mainly AD neuropathological change. The focus of this Review is the pathology, genetic risk factors and nature of the cognitive impairments and dementia in pure LATE-NC and in LATE-NC associated with coexisting pathologies. As the clinical and cognitive profile of LATE is currently not easily distinguishable from AD dementia, it is important to develop biomarkers to aid in the diagnosis of this condition in the clinic. The pathogenesis of LATE-NC should be a focus of future research to form the basis for the development of preventive and therapeutic strategies.
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Affiliation(s)
- Sukriti Nag
- Rush Alzheimer's Disease Center, Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL, USA.
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL, USA.
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5
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Clarke JP, Thibault PA, Fatima S, Salapa HE, Kalyaanamoorthy S, Ganesan A, Levin MC. Sequence- and structure-specific RNA oligonucleotide binding attenuates heterogeneous nuclear ribonucleoprotein A1 dysfunction. Front Mol Biosci 2023; 10:1178439. [PMID: 37426420 PMCID: PMC10325567 DOI: 10.3389/fmolb.2023.1178439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023] Open
Abstract
The RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (A1) regulates RNA metabolism, which is crucial to maintaining cellular homeostasis. A1 dysfunction mechanistically contributes to reduced cell viability and loss, but molecular mechanisms of how A1 dysfunction affects cell viability and loss, and methodologies to attenuate its dysfunction, are lacking. Utilizing in silico molecular modeling and an in vitro optogenetic system, this study examined the consequences of RNA oligonucleotide (RNAO) treatment on attenuating A1 dysfunction and its downstream cellular effects. In silico and thermal shift experiments revealed that binding of RNAOs to the RNA Recognition Motif 1 of A1 is stabilized by sequence- and structure-specific RNAO-A1 interactions. Using optogenetics to model A1 cellular dysfunction, we show that sequence- and structure-specific RNAOs significantly attenuated abnormal cytoplasmic A1 self-association kinetics and A1 cytoplasmic clustering. Downstream of A1 dysfunction, we demonstrate that A1 clustering affects the formation of stress granules, activates cell stress, and inhibits protein translation. With RNAO treatment, we show that stress granule formation is attenuated, cell stress is inhibited, and protein translation is restored. This study provides evidence that sequence- and structure-specific RNAO treatment attenuates A1 dysfunction and its downstream effects, thus allowing for the development of A1-specific therapies that attenuate A1 dysfunction and restore cellular homeostasis.
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Affiliation(s)
- Joseph P. Clarke
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
| | - Patricia A. Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sakina Fatima
- ArGan’s Lab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, ON, Canada
| | - Hannah E. Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK, Canada
| | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, Waterloo, ON, Canada
| | - Aravindhan Ganesan
- ArGan’s Lab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, ON, Canada
| | - Michael C. Levin
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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6
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Horio T, Ishikura Y, Ohashi R, Shiina N. Regulation of RNG105/caprin1 dynamics by pathogenic cytoplasmic FUS and TDP-43 in neuronal RNA granules modulates synaptic loss. Heliyon 2023; 9:e17065. [PMID: 37484309 PMCID: PMC10361247 DOI: 10.1016/j.heliyon.2023.e17065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
In neurodegenerative diseases, the condensation of FUS and TDP-43 with RNA granules in neurons is linked to pathology, including synaptic disorders. However, the effects of FUS and TDP-43 on RNA granule factors remain unclear. Here, using primary cultured neurons from the mouse cerebral cortex, we show that excess cytoplasmic FUS and TDP-43 accumulated in dendritic RNA granules, where they increased the dynamics of a scaffold protein RNG105/caprin1 and dissociated it from the granules. This coincided with reduced levels of mRNA and translation around the granules and synaptic loss in dendrites. These defects were suppressed by non-dissociable RNG105, suggesting that RNG105 dissociation mediated the defects. In contrast to the model where FUS and TDP-43 co-aggregate with RNA granule factors to repress their activity, our findings provide a novel pathogenic mechanism whereby FUS and TDP-43 dissociate RNA scaffold proteins from RNA granules which are required for local translation that regulates synapse formation.
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Affiliation(s)
- Tomoyo Horio
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
| | - Yui Ishikura
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
| | - Rie Ohashi
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Life Science Research Center, University of Toyama, Toyama, Toyama 930-0194, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8585, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
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7
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Merjane J, Chung R, Patani R, Lisowski L. Molecular mechanisms of amyotrophic lateral sclerosis as broad therapeutic targets for gene therapy applications utilizing adeno-associated viral vectors. Med Res Rev 2023. [PMID: 36786126 DOI: 10.1002/med.21937] [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: 11/13/2021] [Revised: 08/19/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Despite the devastating clinical outcome of the neurodegenerative disease, amyotrophic lateral sclerosis (ALS), its etiology remains mysterious. Approximately 90% of ALS is characterized as sporadic, signifying that the patient has no family history of the disease. The development of an impactful disease modifying therapy across the ALS spectrum has remained out of grasp, largely due to the poorly understood mechanisms of disease onset and progression. Currently, ALS is invariably fatal and rapidly progressive. It is hypothesized that multiple factors can lead to the development of ALS, however, treatments are often focused on targeting specific familial forms of the disease (10% of total cases). There is a strong need to develop disease modifying treatments for ALS that can be effective across the full ALS spectrum of familial and sporadic cases. Although the onset of disease varies significantly between patients, there are general disease mechanisms and progressions that can be seen broadly across ALS patients. Therefore, this review explores the targeting of these widespread disease mechanisms as possible areas for therapeutic intervention to treat ALS broadly. In particular, this review will focus on targeting mechanisms of defective protein homeostasis and RNA processing, which are both increasingly recognized as design principles of ALS pathogenesis. Additionally, this review will explore the benefits of gene therapy as an approach to treating ALS, specifically focusing on the use of adeno-associated virus (AAV) as a vector for gene delivery to the CNS and recent advances in the field.
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Affiliation(s)
- Jessica Merjane
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Roger Chung
- Department of Biomedical Sciences, Centre for Motor Neuron Disease Research, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Rickie Patani
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK.,The Francis Crick Institute, London, UK
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia.,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
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8
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Gelon PA, Dutchak PA, Sephton CF. Synaptic dysfunction in ALS and FTD: anatomical and molecular changes provide insights into mechanisms of disease. Front Mol Neurosci 2022; 15:1000183. [PMID: 36263379 PMCID: PMC9575515 DOI: 10.3389/fnmol.2022.1000183] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022] Open
Abstract
Synaptic loss is a pathological feature of all neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS is a disease of the cortical and spinal motor neurons resulting in fatal paralysis due to denervation of muscles. FTD is a form of dementia that primarily affects brain regions controlling cognition, language and behavior. Once classified as two distinct diseases, ALS and FTD are now considered as part of a common disease spectrum based on overlapping clinical, pathological and genetic evidence. At the cellular level, aggregation of common proteins and overlapping gene susceptibilities are shared in both ALS and FTD. Despite the convergence of these two fields of research, the underlying disease mechanisms remain elusive. However, recent discovers from ALS and FTD patient studies and models of ALS/FTD strongly suggests that synaptic dysfunction is an early event in the disease process and a unifying hallmark of these diseases. This review provides a summary of the reported anatomical and cellular changes that occur in cortical and spinal motor neurons in ALS and FTD tissues and models of disease. We also highlight studies that identify changes in the proteome and transcriptome of ALS and FTD models and provide a conceptual overview of the processes that contribute to synaptic dysfunction in these diseases. Due to space limitations and the vast number of publications in the ALS and FTD fields, many articles have not been discussed in this review. As such, this review focuses on the three most common shared mutations in ALS and FTD, the hexanucleuotide repeat expansion within intron 1 of chromosome 9 open reading frame 72 (C9ORF72), transactive response DNA binding protein 43 (TARDBP or TDP-43) and fused in sarcoma (FUS), with the intention of highlighting common pathways that promote synaptic dysfunction in the ALS-FTD disease spectrum.
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9
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Gosset P, Camu W, Raoul C, Mezghrani A. Prionoids in amyotrophic lateral sclerosis. Brain Commun 2022; 4:fcac145. [PMID: 35783556 PMCID: PMC9242622 DOI: 10.1093/braincomms/fcac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/16/2022] [Accepted: 06/01/2022] [Indexed: 12/20/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the third most frequent neurodegenerative disease after Alzheimer’s and Parkinson’s disease. ALS is characterized by the selective and progressive loss of motoneurons in the spinal cord, brainstem and cerebral cortex. Clinical manifestations typically occur in midlife and start with focal muscle weakness, followed by the rapid and progressive wasting of muscles and subsequent paralysis. As with other neurodegenerative diseases, the condition typically begins at an initial point and then spreads along neuroanatomical tracts. This feature of disease progression suggests the spreading of prion-like proteins called prionoids in the affected tissues, which is similar to the spread of prion observed in Creutzfeldt-Jakob disease. Intensive research over the last decade has proposed the ALS-causing gene products Cu/Zn superoxide dismutase 1, TAR DNA-binding protein of 43 kDa, and fused in sarcoma as very plausible prionoids contributing to the spread of the pathology. In this review, we will discuss the molecular and cellular mechanisms leading to the propagation of these prionoids in ALS.
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Affiliation(s)
- Philippe Gosset
- INM, Univ Montpellier, INSERM, CNRS, Montpellier 34095, France
| | - William Camu
- INM, Univ Montpellier, INSERM, CNRS, Montpellier 34095, France
| | - Cedric Raoul
- INM, Univ Montpellier, INSERM, CNRS, Montpellier 34095, France
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10
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Wang Y, Yasmin L, Li L, Gao P, Xu X, Sun X, Godbout R. DDX1 vesicles control calcium-dependent mitochondrial activity in mouse embryos. Nat Commun 2022; 13:3794. [PMID: 35778392 PMCID: PMC9249788 DOI: 10.1038/s41467-022-31497-9] [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: 04/14/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
The DEAD box protein DDX1, previously associated with 3'-end RNA processing and DNA repair, forms large aggregates in the cytoplasm of early mouse embryos. Ddx1 knockout causes stalling of embryos at the 2-4 cell stages. Here, we identify a DDX1-containing membrane-bound calcium-containing organelle with a nucleic acid core. We show that aggregates of these organelles form ring-like structures in early-stage embryos which we have named Membrane Associated RNA-containing Vesicles. We present evidence that DDX1 is required for the formation of Membrane Associated RNA-containing Vesicles which in turn regulate the spatial distribution of calcium in embryos. We find that Ddx1 knockout in early embryos disrupts calcium distribution, and increases mitochondria membrane potential, mitochondrial activity, and reactive oxygen species. Sequencing analysis of embryos from Ddx1 heterozygote crosses reveals downregulation of a subset of RNAs involved in developmental and mitochondrial processes in the embryos with low Ddx1 RNA. We propose a role for Membrane Associated RNA-containing Vesicles in calcium-controlled mitochondrial functions that are essential for embryonic development.
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Affiliation(s)
- Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Lubna Yasmin
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Lei Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Pinzhang Gao
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Xia Xu
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Xuejun Sun
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, T6G 1Z2, Canada.
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11
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Louka A, Bagnoli S, Rupert J, Esapa B, Tartaglia GG, Cellerino A, Pastore A, Terzibasi Tozzini E. New lessons on TDP-43 from old N. furzeri killifish. Aging Cell 2022; 21:e13517. [PMID: 34939315 PMCID: PMC8761016 DOI: 10.1111/acel.13517] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/26/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are fatal and incurable neurodegenerative diseases linked to the pathological aggregation of the TDP-43 protein. This is an essential DNA/RNA-binding protein involved in transcription regulation, pre-RNA processing, and RNA transport. Having suitable animal models to study the mechanisms of TDP-43 aggregation is crucial to develop treatments against disease. We have previously demonstrated that the killifish Nothobranchius furzeri offers the advantage of being the shortest-lived vertebrate with a clear aging phenotype. Here, we show that the two N. furzeri paralogs of TDP-43 share high sequence homology with the human protein and recapitulate its cellular and biophysical behavior. During aging, N. furzeri TDP-43 spontaneously forms insoluble intracellular aggregates with amyloid characteristics and colocalizes with stress granules. Our results propose this organism as a valuable new model of TDP-43-related pathologies making it a powerful tool for the study of disease mechanism.
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Affiliation(s)
- Alexandra Louka
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
| | | | - Jakob Rupert
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
- Universita' di Roma “La Sapienza” Rome Italy
| | - Benjamin Esapa
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
| | | | - Alessandro Cellerino
- Bio@SNS Scuola Normale Superiore Pisa Italy
- Leibniz Institute on Aging Fritz Lipmann Institute Jena Germany
| | - Annalisa Pastore
- Department of Clinical and Basic Neuroscience King's College London UK‐DRI Centre at the Maurice Wohl Institute London UK
- European Synchrotron Radiation Facility Grenoble France
| | - Eva Terzibasi Tozzini
- Bio@SNS Scuola Normale Superiore Pisa Italy
- Stazione Zoologica Anton Dohrn (SZN) Naples Italy
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12
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Strategies in the design and development of (TAR) DNA-binding protein 43 (TDP-43) binding ligands. Eur J Med Chem 2021; 225:113753. [PMID: 34388383 DOI: 10.1016/j.ejmech.2021.113753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 01/09/2023]
Abstract
The human transactive responsive (TAR) DNA-binding protein 43 (TDP-43) is involved in a number of physiological processes in the body. Its primary function involves RNA regulation. The TDP-43 protein is also involved in many diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), Parkinson's disease (PD) and even cancers. These TDP-43 mediated diseases are collectively called as TDP-43 proteinopathies. Intense research in the last decade has increased our understanding on TDP-43 structure and function in biology. The three-dimensional structures of TDP-43 domains such as N-terminal domain (NTD), RNA-recognition motif-1 (RRM1), RNA-recognition motif-2 (RRM2) and the C-terminal domain (CTD) or low-complexity domain (LCD) have been solved. These structures have yielded insights into novel binding sites and pockets at various TDP-43 domains, which can be targeted by designing a diverse library of ligands including small molecules, peptides and oligonucleotides as molecular tools to (i) study TDP-43 function, (ii) develop novel diagnostic agents and (iii) discover disease-modifying therapies to treat TDP-43 proteinopathies. This review provides a summary on recent progress in the development of TDP-43 binding ligands and uses the solved structures of various TDP-43 domains to investigate putative ligand binding regions that can be exploited to discover novel molecular probes to modulate TDP-43 structure and function.
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Mechanisms of TDP-43 Proteinopathy Onset and Propagation. Int J Mol Sci 2021; 22:ijms22116004. [PMID: 34199367 PMCID: PMC8199531 DOI: 10.3390/ijms22116004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 01/21/2023] Open
Abstract
TDP-43 is an RNA-binding protein that has been robustly linked to the pathogenesis of a number of neurodegenerative disorders, including amyotrophic lateral sclerosis and frontotemporal dementia. While mutations in the TARDBP gene that codes for the protein have been identified as causing disease in a small subset of patients, TDP-43 proteinopathy is present in the majority of cases regardless of mutation status. This raises key questions regarding the mechanisms by which TDP-43 proteinopathy arises and spreads throughout the central nervous system. Numerous studies have explored the role of a variety of cellular functions on the disease process, and nucleocytoplasmic transport, protein homeostasis, RNA interactions and cellular stress have all risen to the forefront as possible contributors to the initiation of TDP-43 pathogenesis. There is also a small but growing body of evidence suggesting that aggregation-prone TDP-43 can recruit physiological TDP-43, and be transmitted intercellularly, providing a mechanism whereby small-scale proteinopathy spreads from cell to cell, reflecting the spread of clinical symptoms observed in patients. This review will discuss the potential role of the aforementioned cellular functions in TDP-43 pathogenesis, and explore how aberrant pathology may spread, and result in a feed-forward cascade effect, leading to robust TDP-43 proteinopathy and disease.
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Russo K, Wharton KA. BMP/TGF-β signaling as a modulator of neurodegeneration in ALS. Dev Dyn 2021; 251:10-25. [PMID: 33745185 DOI: 10.1002/dvdy.333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
This commentary focuses on the emerging intersection between BMP/TGF-β signaling roles in nervous system function and the amyotrophic lateral sclerosis (ALS) disease state. Future research is critical to elucidate the molecular underpinnings of this intersection of the cellular processes disrupted in ALS and those influenced by BMP/TGF-β signaling, including synapse structure, neurotransmission, plasticity, and neuroinflammation. Such knowledge promises to inform us of ideal entry points for the targeted modulation of dysfunctional cellular processes in an effort to abrogate ALS pathologies. It is likely that different interventions are required, either at discrete points in disease progression, or across multiple dysfunctional processes which together lead to motor neuron degeneration and death. We discuss the challenging, but intriguing idea that modulation of the pleiotropic nature of BMP/TGF-β signaling could be advantageous, as a way to simultaneously treat defects in more than one cell process across different forms of ALS.
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Affiliation(s)
- Kathryn Russo
- Department of Neuroscience, Brown University, Providence, Rhode Island, USA.,Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, Rhode Island, USA
| | - Kristi A Wharton
- Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, Rhode Island, USA.,Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
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Vuocolo B, Holder JL. Unwind and Relax: DDX3X RNA Helicase as a Critical Mediator of Cortical Neurogenesis. Neuron 2020; 106:357-358. [PMID: 32380046 DOI: 10.1016/j.neuron.2020.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this issue of Neuron, Lennox et al. (2020) report the largest cohort of patients to date with DDX3X syndrome, discovering unique genotype-phenotype relationships that inform molecular pathogenesis. They then uncover unique roles of DDX3X in cortical neuron development and ribonucleoprotein granule formation.
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Affiliation(s)
- Blake Vuocolo
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - J Lloyd Holder
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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Watabe K, Kato Y, Sakuma M, Murata M, Niida-Kawaguchi M, Takemura T, Hanagata N, Tada M, Kakita A, Shibata N. Praja1 RING-finger E3 ubiquitin ligase suppresses neuronal cytoplasmic TDP-43 aggregate formation. Neuropathology 2020; 40:570-586. [PMID: 32686212 PMCID: PMC7818255 DOI: 10.1111/neup.12694] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 01/07/2023]
Abstract
Transactivation response DNA-binding protein of 43 kDa (TDP-43) is a major constituent of cytoplasmic aggregates in neuronal and glial cells in cases of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). We have previously shown neuronal cytoplasmic aggregate formation induced by recombinant adenoviruses expressing human wild-type and C-terminal fragment (CTF) TDP-43 under the condition of proteasome inhibition in vitro and in vivo. In the present study, we demonstrated that the formation of the adenoviral TDP-43 aggregates was markedly suppressed in rat neural stem cell-derived neuronal cells by co-infection of an adenovirus expressing heat shock transcription factor 1 (HSF1), a master regulator of heat shock response. We performed DNA microarray analysis and searched several candidate molecules, located downstream of HSF1, which counteract TDP-43 aggregate formation. Among these, we identified Praja 1 RING-finger E3 ubiquitin ligase (PJA1) as a suppressor of phosphorylation and aggregate formation of TDP-43. Co-immunoprecipitation assay revealed that PJA1 binds to CTF TDP-43 and the E2-conjugating enzyme UBE2E3. PJA1 also suppressed formation of cytoplasmic phosphorylated TDP-43 aggregates in mouse facial motor neurons in vivo. Furthermore, phosphorylated TDP-43 aggregates were detected in PJA1-immunoreactive human ALS motor neurons. These results indicate that PJA1 is one of the principal E3 ubiquitin ligases for TDP-43 to counteract its aggregation propensity and could be a potential therapeutic target for ALS and FTLD.
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Affiliation(s)
- Kazuhiko Watabe
- Department of Medical Technology (Neuropathology), Kyorin University, Tokyo, Japan.,Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoichiro Kato
- Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan
| | - Miho Sakuma
- School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Makiko Murata
- Department of Medical Technology (Neuropathology), Kyorin University, Tokyo, Japan
| | | | - Taro Takemura
- Research Network and Facility Services Division, National Institute for Materials Science, Tsukuba, Japan
| | - Nobutaka Hanagata
- Research Network and Facility Services Division, National Institute for Materials Science, Tsukuba, Japan
| | - Mari Tada
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Noriyuki Shibata
- Department of Pathology, Tokyo Women's Medical University, Tokyo, Japan
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