1
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Bartolomé-Nafría A, García-Pardo J, Ventura S. Mutations in human prion-like domains: pathogenic but not always amyloidogenic. Prion 2024; 18:28-39. [PMID: 38512820 PMCID: PMC10962614 DOI: 10.1080/19336896.2024.2329186] [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: 01/08/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are multifunctional proteins with integral roles in RNA metabolism and the regulation of alternative splicing. These proteins typically contain prion-like domains of low complexity (PrLDs or LCDs) that govern their assembly into either functional or pathological amyloid fibrils. To date, over 60 mutations targeting the LCDs of hnRNPs have been identified and associated with a spectrum of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease (AD). The cryo-EM structures of pathological and functional fibrils formed by different hnRNPs have been recently elucidated, including those of hnRNPA1, hnRNPA2, hnRNPDL-2, TDP-43, and FUS. In this review, we discuss the structural features of these amyloid assemblies, placing particular emphasis on scrutinizing the impact of prevalent disease-associated mutations mapping within their LCDs. By performing systematic energy calculations, we reveal a prevailing trend of destabilizing effects induced by these mutations in the amyloid structure, challenging the traditionally assumed correlation between pathogenicity and amyloidogenic propensity. Understanding the molecular basis of this discrepancy might provide insights for developing targeted therapeutic strategies to combat hnRNP-associated diseases.
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Affiliation(s)
- Andrea Bartolomé-Nafría
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier García-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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2
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Ko YH, Lokareddy RK, Doll SG, Yeggoni DP, Girdhar A, Mawn I, Klim JR, Rizvi NF, Meyers R, Gillilan RE, Guo L, Cingolani G. Single Acetylation-mimetic Mutation in TDP-43 Nuclear Localization Signal Disrupts Importin α1/β Signaling. J Mol Biol 2024; 436:168751. [PMID: 39181183 PMCID: PMC11443512 DOI: 10.1016/j.jmb.2024.168751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/19/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Cytoplasmic aggregation of the TAR-DNA binding protein of 43 kDa (TDP-43) is the hallmark of sporadic amyotrophic lateral sclerosis (ALS). Most ALS patients with TDP-43 aggregates in neurons and glia do not have mutations in the TDP-43 gene but contain aberrantly post-translationally modified TDP-43. Here, we found that a single acetylation-mimetic mutation (K82Q) near the TDP-43 minor Nuclear Localization Signal (NLS) box, which mimics a post-translational modification identified in an ALS patient, can lead to TDP-43 mislocalization to the cytoplasm and irreversible aggregation. We demonstrate that the acetylation mimetic disrupts binding to importins, halting nuclear import and preventing importin α1/β anti-aggregation activity. We propose that perturbations near the NLS are an additional mechanism by which a cellular insult other than a genetically inherited mutation leads to TDP-43 aggregation and loss of function. Our findings are relevant to deciphering the molecular etiology of sporadic ALS.
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Affiliation(s)
- Ying-Hui Ko
- Dept. of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Ravi K Lokareddy
- Dept. of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Steven G Doll
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; Dept. of Neurology, Johns Hopkins University School of Medicine, 1800 Orleans St Baltimore, Baltimore, MD 21287, USA
| | - Daniel P Yeggoni
- Dept. of Cell Biology, UConn Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Amandeep Girdhar
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ian Mawn
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | | | | | | | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Lin Guo
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
| | - Gino Cingolani
- Dept. of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA.
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3
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Barmaki H, Nourazarian A, Shademan B, Khaki-Khatibi F. The autophagy paradox: A new hypothesis in neurodegenerative disorders. Neurochem Int 2024; 179:105827. [PMID: 39111406 DOI: 10.1016/j.neuint.2024.105827] [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: 05/22/2024] [Revised: 07/20/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
A recent study showed that while autophagy is usually tied to protein and organelle turnover, it can also play dual roles in neurodegenerative diseases. Traditionally, autophagy was seen as protective since it removes damaged proteins and organelles. but new data suggests autophagy can sometimes promote neuron death. and This review tackles autophagy's seemingly contradictory effects in neurodegeneration, or the "autophagy paradox. " It offers a framework for understanding autophagy in neurodegenerative research and the cellular processes involved. In short, our data uncovers a harmful autophagy role in certain situations, conflicting the view that it's always beneficial. We describe the distinct, disease-specific autophagy pathways functioning in various neurodegenerative diseases. Part two concerns potential therapeutic implications of manipulating autophagy and current strategies targeting the autophagic system, suggesting interesting areas for future research into tailored modulators. This could eventually enable activating or controlling specific autophagy pathways and aid in developing more effective treatments. Researchers believe more molecular-level research is needed so patient-tailored autophagy-modulating therapeutics can be developed given this dilemma. Moreover, research must translate faster into effective neurodegenerative disease treatment options. This article aims to provide a wholly new perspective on autophagy's classically described role in these severe diseases, challenging current dogma and opening new therapeutic avenue options.
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Affiliation(s)
- Haleh Barmaki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran; Student Research Committee, Khoy University of Medical Sciences, Khoy, Iran.
| | - Behrouz Shademan
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Khaki-Khatibi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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4
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Haider R, Shipley B, Surewicz K, Hinczewski M, Surewicz WK. Pathological C-terminal phosphomimetic substitutions alter the mechanism of liquid-liquid phase separation of TDP-43 low complexity domain. Protein Sci 2024; 33:e5179. [PMID: 39302099 PMCID: PMC11413918 DOI: 10.1002/pro.5179] [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: 03/11/2024] [Revised: 08/20/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024]
Abstract
C-terminally phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) marks the proteinaceous inclusions that characterize a number of age-related neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal lobar degeneration and Alzheimer's disease. TDP-43 phosphorylation at S403/S404 and (especially) at S409/S410 is, in fact, accepted as a biomarker of proteinopathy. These residues are located within the low complexity domain (LCD), which also drives the protein's liquid-liquid phase separation (LLPS). The impact of phosphorylation at these LCD sites on phase separation of the protein is a topic of great interest, as these post-translational modifications and LLPS are both implicated in proteinopathies. Here, we employed a combination of experimental and simulation-based approaches to explore this question on a phosphomimetic model of the TDP-43 LCD. Our turbidity and fluorescence microscopy data show that phosphomimetic Ser-to-Asp substitutions at residues S403, S404, S409 and S410 alter the LLPS behavior of TDP-43 LCD. In particular, unlike the LLPS of unmodified protein, LLPS of the phosphomimetic variants displays a biphasic dependence on salt concentration. Through coarse-grained modeling, we find that this biphasic salt dependence is derived from an altered mechanism of phase separation, in which LLPS-driving short-range intermolecular hydrophobic interactions are modulated by long-range attractive electrostatic interactions. Overall, this in vitro and in silico study provides a physiochemical foundation for understanding the impact of pathologically relevant C-terminal phosphorylation on the LLPS of TDP-43 in a more complex cellular environment.
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Affiliation(s)
- Raza Haider
- Department of Physiology and Biophysics and the Case Western Reserve UniversityClevelandOhioUSA
| | - Brandon Shipley
- Department of PhysicsCase Western Reserve UniversityClevelandOhioUSA
| | - Krystyna Surewicz
- Department of Physiology and Biophysics and the Case Western Reserve UniversityClevelandOhioUSA
| | | | - Witold K. Surewicz
- Department of Physiology and Biophysics and the Case Western Reserve UniversityClevelandOhioUSA
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5
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He Q, Wang Y, Zhao F, Wei S, Li X, Zeng G. APE1: A critical focus in neurodegenerative conditions. Biomed Pharmacother 2024; 179:117332. [PMID: 39191031 DOI: 10.1016/j.biopha.2024.117332] [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: 06/18/2024] [Revised: 08/04/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
The global growth of the aging population has resulted in an increased prevalence of neurodegenerative diseases, characterized by the progressive loss of central nervous system (CNS) structure and function. Given the high incidence and debilitating nature of neurodegenerative diseases, there is an urgent need to identify potential biomarkers and novel therapeutic targets thereof. Apurinic/apyrimidinic endonuclease 1 (APE1), has been implicated in several neurodegenerative diseases, as having a significant role. Abnormal APE1 expression has been observed in conditions including Alzheimer's disease, stroke, amyotrophic lateral sclerosis, Parkinson's disease, Huntington's disease, and epilepsy. However, whether this dysregulation is protective or harmful remains unclear. This review aims to comprehensively review the current understanding of the involvement of APE1 in neurodegenerative diseases.
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Affiliation(s)
- Qianxiong He
- Department of Ophthalmology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China; School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yi Wang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Feng Zhao
- Department of Health Laboratory Technology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Shigang Wei
- Department of Clinical Laboratory, People's Hospital of Pengzhou city, Pengzhou, Sichuan province 611930, China
| | - Xingfu Li
- Department of Clinical Laboratory, The Honghe Autonomous Prefecture 3rd Hospital, Honghe 661021, China
| | - Guangqun Zeng
- Department of Clinical Laboratory, People's Hospital of Pengzhou city, Pengzhou, Sichuan province 611930, China.
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6
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Song J. Molecular Mechanisms of Phase Separation and Amyloidosis of ALS/FTD-linked FUS and TDP-43. Aging Dis 2024; 15:2084-2112. [PMID: 38029395 PMCID: PMC11346406 DOI: 10.14336/ad.2023.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023] Open
Abstract
FUS and TDP-43, two RNA-binding proteins from the heterogeneous nuclear ribonucleoprotein family, have gained significant attention in the field of neurodegenerative diseases due to their association with amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). They possess folded domains for binding ATP and various nucleic acids including DNA and RNA, as well as substantial intrinsically disordered regions (IDRs) including prion-like domains (PLDs) and RG-/RGG-rich regions. They play vital roles in various cellular processes, including transcription, splicing, microRNA maturation, RNA stability and transport and DNA repair. In particular, they are key components for forming ribonucleoprotein granules and stress granules (SGs) through homotypic or heterotypic liquid-liquid phase separation (LLPS). Strikingly, liquid-like droplets formed by FUS and TDP-43 may undergo aging to transform into less dynamic assemblies such as hydrogels, inclusions, and amyloid fibrils, which are the pathological hallmarks of ALS and FTD. This review aims to synthesize and consolidate the biophysical knowledge of the sequences, structures, stability, dynamics, and inter-domain interactions of FUS and TDP-43 domains, so as to shed light on the molecular mechanisms underlying their liquid-liquid phase separation (LLPS) and amyloidosis. The review further delves into the mechanisms through which ALS-causing mutants of the well-folded hPFN1 disrupt the dynamics of LLPS of FUS prion-like domain, providing key insights into a potential mechanism for misfolding/aggregation-prone proteins to cause neurodegenerative diseases and aging by gain of functions. With better understanding of different biophysical aspects of FUS and TDP-43, the ultimate goal is to develop drugs targeting LLPS and amyloidosis, which could mediate protein homeostasis within cells and lead to new treatments for currently intractable diseases, particularly neurodegenerative diseases such as ALS, FTD and aging. However, the study of membrane-less organelles and condensates is still in its infancy and therefore the review also highlights key questions that require future investigation.
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7
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Cheung SW, Willis EF, Simmons DG, Bellingham MC, Noakes PG. Phagocytosis of aggrecan-positive perineuronal nets surrounding motor neurons by reactive microglia expressing MMP-9 in TDP-43 Q331K ALS model mice. Neurobiol Dis 2024; 200:106614. [PMID: 39067491 DOI: 10.1016/j.nbd.2024.106614] [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: 01/16/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024] Open
Abstract
Perineuronal nets (PNNs) are extracellular matrix structures that surround excitable neurons and their proximal dendrites. PNNs play an important role in neuroprotection against oxidative stress. Oxidative stress within motor neurons can act as a trigger for neuronal death, and this has been implicated in motor neuron degeneration in amyotrophic lateral sclerosis (ALS). We therefore characterised PNNs around alpha motor neurons and the possible contributing cellular factors in the mutant TDP-43Q331K transgenic mouse, a slow onset ALS mouse model. PNNs around alpha motor neurons showed significant loss at mid-stage disease in TDP-43Q331K mice compared to wild type strain control mice. PNN loss coincided with an increased expression of matrix metallopeptidase-9 (MMP-9), an endopeptidase known to cleave PNNs, within the ventral horn. During mid-stage disease, increased numbers of microglia and astrocytes expressing MMP-9 were present in the ventral horn of TDP-43Q331K mice. In addition, TDP-43Q331K mice showed increased levels of aggrecan, a PNN component, in the ventral horn by microglia and astrocytes during this period. Elevated aggrecan levels within glia were accompanied by an increase in fractalkine expression, a chemotaxic protein responsible for the recruitment of microglia, in alpha motor neurons of onset and mid-stage TDP-43Q331K mice. Following PNN loss, alpha motor neurons in mid-stage TDP-43Q331K mice showed increased 3-nitrotyrosine expression, an indicator of protein oxidation. Together, our observations along with previous PNN research provide suggests a possible model whereby microglia and astrocytes expressing MMP-9 degrade PNNs surrounding alpha motor neurons in the TDP-43Q331K mouse. This loss of nets may expose alpha-motor neurons to oxidative damage leading to degeneration of the alpha motor neurons in the TDP-43Q331K ALS mouse model.
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Affiliation(s)
- Sang Won Cheung
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Emily F Willis
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - David G Simmons
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mark C Bellingham
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Peter G Noakes
- School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Queensland Brain Institute, The University of Queensland, St. Lucia, QLD 4072, Australia.
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8
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Tang H, Sun Y, Wang L, Ke PC, Ding F. Uncovering Intermolecular Interactions Driving the Liquid-Liquid Phase Separation of the TDP-43 Low-Complexity Domain via Atomistic Dimerization Simulations. J Chem Inf Model 2024. [PMID: 39342654 DOI: 10.1021/acs.jcim.4c00943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Liquid-liquid phase separation (LLPS) of transactive response DNA-binding protein of 43 kDa (TDP-43), which exerts multiple functions in the splicing, trafficking, and stabilization of RNA, mediates the formation of membraneless condensates with crucial physiological roles, while its aberrant LLPS is linked to multiple neurodegenerative diseases. However, due to the heterogeneous and dynamic nature of LLPS, major gaps remain in understanding the precise intermolecular interactions driving LLPS and how specific mutations alter LLPS dynamics. Here, we investigated the molecular mechanisms underlying the LLPS of the TDP-43 low-complexity domain (LCD) by simulating the dimerization process using all-atom discrete molecular dynamics with microsecond-long simulations. Our results showed that the TDP-43 LCD was intrinsically disordered, with helical structures consistent with prior nuclear magnetic resonance studies. Phase separation propensity was assessed by simulating the dimerization of the TDP-43 LCD and four mutants, showing that A321G, W334G, and M337V inhibited self-association, while G335D promoted it, fully consistent with experimental reports. During the dimerization process, two peptides experienced both elastic and nonelastic collisions, and the self-associated dimer featured both high- and low-contact states. These results suggested that the dimerization process of the TDP-43 LCD was accordingly dynamic and heterogeneous. Additionally, we identified crucial regions containing hydrophobic clusters and aromatic residues in the N-terminus, central region, and C-terminus that were essential for the self-association of the TDP-43 LCD. These residues with high binding affinities can act as stickers to form peptide networks in LLPS. Together, our simulation provides a comprehensive picture of the intermolecular interactions driving the phase separation of the TDP-43 LCD, offering insights into both physiological functions and pathological mechanisms.
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Affiliation(s)
- Huayuan Tang
- Department of Engineering Mechanics, Hohai University, Nanjing 210098, China
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Lei Wang
- Department of Engineering Mechanics, Hohai University, Nanjing 210098, China
| | - Pu Chun Ke
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
- Nanomedicine Centre, the Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou 510700, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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9
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Xu Z, Tang J, Gong Y, Zhang J, Zou Y. Atomistic Insights into the Stabilization of TDP-43 Protofibrils by ATP. J Chem Inf Model 2024. [PMID: 39292611 DOI: 10.1021/acs.jcim.4c01140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
The aberrant accumulation of the transactive response deoxyribonucleic acid (DNA)-binding protein of 43 kDa (TDP-43) aggregates in the cytoplasm of motor neurons is the main pathological hallmark of amyotrophic lateral sclerosis (ALS). Previous experiments reported that adenosine triphosphate (ATP), the universal energy currency for all living cells, could induce aggregation and enhance the folding of TDP-43 fibrillar aggregates. However, the significance of ATP on TDP-43 fibrillation and the mechanism behind it remain elusive. In this work, we conducted multiple atomistic molecular dynamics (MD) simulations totaling 20 μs to search the critical nucleus size of TDP-43282-360 and investigate the impact of ATP molecules on preformed protofibrils. The results reveal that the trimer is the critical nucleus for TDP-43282-360 fibril formation and the tetramer is the minimal stable nucleus. When ATP molecules bind to the TDP-43282-360 trimer and tetramer, they can consolidate the TDP-43282-360 protofibrils by increasing the content of the β-sheet structure and promoting the formation of hydrogen bonds (H-bonds). Binding site analyses show that the N-terminus of TDP-43282-360 protofibrils is the main binding site of ATP, and R293 dominates the direct binding of ATP. Further analyses reveal that the π-π, cation-π, salt bridge, and H-bonding interactions together contribute to the binding of ATP to TDP-43282-360 protofibrils. This study decoded the detailed stabilization mechanism of protofibrillar TDP-43282-360 oligomers by ATP, and may provide new avenues for the development of drug design against ALS.
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Affiliation(s)
- Zhengdong Xu
- Department of Physical Education, Shanghai University of Engineering Science, 333 Long Teng Road, Shanghai 201620, People's Republic of China
| | - Jiaxing Tang
- College of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Yehong Gong
- General Education Center, Westlake University, 600 Dunyu Road, Hangzhou 310030, People's Republic of China
| | - Jianxin Zhang
- Department of Physical Education, Shanghai University of Engineering Science, 333 Long Teng Road, Shanghai 201620, People's Republic of China
| | - Yu Zou
- Department Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310007, People's Republic of China
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10
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Luthi-Carter R, Cappelli S, Le Roux-Bourdieu M, Tentillier N, Quinn JP, Petrozziello T, Gopalakrishnan L, Sethi P, Choudhary H, Bartolini G, Gebara E, Stuani C, Font L, An J, Ortega V, Sage J, Kosa E, Trombetta BA, Simeone R, Seredenina T, Afroz T, Berry JD, Arnold SE, Carlyle BC, Adolfsson O, Sadri-Vakili G, Buratti E, Bowser R, Agbas A. Location and function of TDP-43 in platelets, alterations in neurodegenerative diseases and arising considerations for current plasma biobank protocols. Sci Rep 2024; 14:21837. [PMID: 39294194 PMCID: PMC11410945 DOI: 10.1038/s41598-024-70822-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
The TAR DNA Binding Protein 43 (TDP-43) has been implicated in the pathogenesis of human neurodegenerative diseases and exhibits hallmark neuropathology in amyotrophic lateral sclerosis (ALS). Here, we explore its tractability as a plasma biomarker of disease and describe its localization and possible functions in the cytosol of platelets. Novel TDP-43 immunoassays were developed on three different technical platforms and qualified for specificity, signal-to-noise ratio, detection range, variation, spike recovery and dilution linearity in human plasma samples. Surprisingly, implementation of these assays demonstrated that biobank-archived plasma samples yielded considerable heterogeneity in TDP-43 levels. Importantly, subsequent investigation attributed these differences to variable platelet recovery. Fractionations of fresh blood revealed that ≥ 95% of the TDP-43 in platelet-containing plasma was compartmentalized within the platelet cytosol. We reasoned that this highly concentrated source of TDP-43 comprised an interesting substrate for biochemical analyses. Additional characterization of platelets revealed the presence of the disease-associated phosphoserine 409/410 TDP-43 proteoform and many neuron- and astrocyte-expressed TDP-43 mRNA targets. Considering these striking similarities, we propose that TDP-43 may serve analogous functional roles in platelets and synapses, and that the study of platelet TDP-43 might provide a window into disease-related TDP-43 dyshomeostasis in the central nervous system.
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Affiliation(s)
- Ruth Luthi-Carter
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland.
| | - Sara Cappelli
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | | | - Noemie Tentillier
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - James P Quinn
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
- MassGeneral Institute for Neurodegenerative Disease, 114 16th Street, Charlestown, MA, 02129, USA
- Eisai US, 35 Cambridgepark Drive, Cambridge, MA, 02140, USA
| | - Tiziana Petrozziello
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Lathika Gopalakrishnan
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Purva Sethi
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
| | - Himanshi Choudhary
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | - Giorgia Bartolini
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Elias Gebara
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | - Laure Font
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Jiyan An
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Vanessa Ortega
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Jessica Sage
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
- Boehringer Ingelheim Vetmedica, St Joseph, MO, 64503, USA
| | - Edina Kosa
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
| | - Bianca A Trombetta
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
| | - Roberto Simeone
- Dipartimento di Medicina Trasfusionale Giuliano-Isontina, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), Trieste, Italy
| | - Tamara Seredenina
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Tariq Afroz
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - James D Berry
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
- Neurological Clinical Research Institute, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Steven E Arnold
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
- MassGeneral Institute for Neurodegenerative Disease, 114 16th Street, Charlestown, MA, 02129, USA
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Becky C Carlyle
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- Massachusetts Alzheimer's Disease Research Center (ADRC), 114 16th Street, Charlestown, MA, 02129, USA
- Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX13QU, UK
| | - Oskar Adolfsson
- AC Immune, SA (ACIU), EPFL Innovation Park Building B, 1015, Lausanne, Switzerland
| | - Ghazaleh Sadri-Vakili
- Massachusetts General Hospital Department of Neurology, 114 16th Street, Charlestown, MA, 02129, USA
- MassGeneral Institute for Neurodegenerative Disease, 114 16th Street, Charlestown, MA, 02129, USA
- Sean M. Healey and AMG Center for ALS at MassGeneral, Massachusetts General Hospital, 165 Cambridge Street, Boston, MA, 02114, USA
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
| | - Robert Bowser
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W. Thomas Road, Phoenix, AZ, 85013, USA
| | - Abdulbaki Agbas
- Kansas City University, 1750 Independence Ave, Kansas City, MO, 64106, USA
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11
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Dow CT, Pierce ES, Sechi LA. Mycobacterium paratuberculosis: A HERV Turn-On for Autoimmunity, Neurodegeneration, and Cancer? Microorganisms 2024; 12:1890. [PMID: 39338563 PMCID: PMC11434025 DOI: 10.3390/microorganisms12091890] [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: 06/28/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that, over millions of years, became integrated into the human genome. While normally inactive, environmental stimuli such as infections have contributed to the transcriptional reactivation of HERV-promoting pathological conditions, including the development of autoimmunity, neurodegenerative disease and cancer. What infections trigger HERV activation? Mycobacterium avium subspecies paratuberculosis (MAP) is a pluripotent driver of human disease. Aside from granulomatous diseases, Crohn's disease, sarcoidosis and Blau syndrome, MAP is associated with autoimmune disease: type one diabetes (T1D), multiple sclerosis (MS), rheumatoid arthritis (RA) and autoimmune thyroiditis. MAP is also associated with Alzheimer's disease (AD) and Parkinson's disease (PD). Autoimmune diabetes, MS and RA are the diseases with the strongest MAP/HERV association. There are several other diseases associated with HERV activation, including diseases whose epidemiology and/or pathology would prompt speculation for a causal role of MAP. These include non-solar uveal melanoma, colon cancer, glioblastoma and amyotrophic lateral sclerosis (ALS). This article further points to MAP infection as a contributor to autoimmunity, neurodegenerative disease and cancer via the un-silencing of HERV. We examine the link between the ever-increasing number of MAP-associated diseases and the MAP/HERV intersection with these diverse medical conditions, and propose treatment opportunities based upon this association.
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Affiliation(s)
- Coad Thomas Dow
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Leonardo A. Sechi
- Department of Biomedical Science, University of Sassari, 07100 Sassari, Italy;
- Azienda Ospedaliera Universitaria di Sassari, Viale San Pietro, 07100 Sassari, Italy
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12
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Duranti E, Villa C. From Brain to Muscle: The Role of Muscle Tissue in Neurodegenerative Disorders. BIOLOGY 2024; 13:719. [PMID: 39336146 PMCID: PMC11428675 DOI: 10.3390/biology13090719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/02/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024]
Abstract
Neurodegenerative diseases (NDs), like amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), and Parkinson's disease (PD), primarily affect the central nervous system, leading to progressive neuronal loss and motor and cognitive dysfunction. However, recent studies have revealed that muscle tissue also plays a significant role in these diseases. ALS is characterized by severe muscle wasting as a result of motor neuron degeneration, as well as alterations in gene expression, protein aggregation, and oxidative stress. Muscle atrophy and mitochondrial dysfunction are also observed in AD, which may exacerbate cognitive decline due to systemic metabolic dysregulation. PD patients exhibit muscle fiber atrophy, altered muscle composition, and α-synuclein aggregation within muscle cells, contributing to motor symptoms and disease progression. Systemic inflammation and impaired protein degradation pathways are common among these disorders, highlighting muscle tissue as a key player in disease progression. Understanding these muscle-related changes offers potential therapeutic avenues, such as targeting mitochondrial function, reducing inflammation, and promoting muscle regeneration with exercise and pharmacological interventions. This review emphasizes the importance of considering an integrative approach to neurodegenerative disease research, considering both central and peripheral pathological mechanisms, in order to develop more effective treatments and improve patient outcomes.
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Affiliation(s)
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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13
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Santiago J, Pocevičiūtė D, Wennström M. Perivascular phosphorylated TDP-43 inclusions are associated with Alzheimer's disease pathology and loss of CD146 and Aquaporin-4. Brain Pathol 2024:e13304. [PMID: 39251230 DOI: 10.1111/bpa.13304] [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: 06/01/2024] [Accepted: 08/16/2024] [Indexed: 09/11/2024] Open
Abstract
The majority of patients with Alzheimer's disease (AD) exhibit aggregates of Trans-active response DNA binding protein 43 (TDP-43) in their hippocampus, which is associated with a more aggressive disease progression. The TDP-43 inclusions are commonly found in neurons, but also in astrocytes. The impact of the inclusions in astrocytes is less known. In the current study, we investigate the presence of phosphorylated TDP-43 (pTDP-43) inclusions in astrocytic endfeet and their potential association with blood-brain barrier (BBB) damage, glymphatic system dysfunction, and AD pathology. By staining postmortem hippocampal sections from AD patients and non-demented controls against TDP-43 and pTDP-43 together with the astrocytic markers glial fibrillary acidic protein (GFAP), astrocytic endfeet marker Aquaporin-4 (AQP4), and markers for BBB alterations (CD146) and leakiness (Immunoglobulin A), we demonstrate a close association between perivascular pTDP-43 or TDP-43 inclusions and GFAP or AQP4. These perivascular inclusions were more prominent in AD and correlated with the disease severity and loss of CD146 and AQP4. The findings indicate a relationship between pTDP-43 accumulation in astrocytic endfeet and BBB and glymphatic system dysfunction, which may contribute to the downstream pathological events seen in AD patients and the aggressive disease progression.
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Affiliation(s)
- Jessica Santiago
- Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Dovilė Pocevičiūtė
- Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Malin Wennström
- Cognitive Disorder Research Unit, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
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14
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Bedwell L, Mavrotas M, Demchenko N, Yaa RM, Willis B, Demianova Z, Syed N, Whitwell HJ, Nott A. FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei. J Proteome Res 2024; 23:3847-3857. [PMID: 39056441 PMCID: PMC11385383 DOI: 10.1021/acs.jproteome.4c00161] [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] [Indexed: 07/28/2024]
Abstract
Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programs, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localized to the nucleus; however, nuclear-localized proteins are often underrepresented in gene expression studies and have been understudied in the context of the brain. To address this challenge, we have optimized an approach for nuclei isolation that is compatible with proteomic analysis. This was coupled to a mass spectrometry protocol for detecting proteins in low-concentration samples. We have generated nuclear proteomes for neurons, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclear proteins associated with chromatin structure and organization, chromatin modifiers such as transcription factors, and RNA-binding proteins, among others. Our nuclear proteomics platform paves the way for assessing brain cell type changes in the nuclear proteome across health and disease, such as neurodevelopmental, aging, neurodegenerative, and neuroinflammatory conditions. Data are available via ProteomeXchange with the identifier PXD053515.
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Affiliation(s)
- Lucy Bedwell
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
| | - Myrto Mavrotas
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
| | - Nikita Demchenko
- MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0NN, U.K
| | - Reuben M Yaa
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
| | - Brittannie Willis
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
| | | | - Nelofer Syed
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
| | - Harry J Whitwell
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
| | - Alexi Nott
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
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15
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Yang J, Li Y, Li H, Zhang H, Guo H, Zheng X, Yu XF, Wei W. HIV-1 Vpu induces neurotoxicity by promoting Caspase 3-dependent cleavage of TDP-43. EMBO Rep 2024:10.1038/s44319-024-00238-y. [PMID: 39242776 DOI: 10.1038/s44319-024-00238-y] [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: 03/05/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/09/2024] Open
Abstract
Despite the efficacy of highly active antiretroviral therapy in controlling the incidence and mortality of AIDS, effective interventions for HIV-1-induced neurological damage and cognitive impairment remain elusive. In this study, we found that HIV-1 infection can induce proteolytic cleavage and aberrant aggregation of TAR DNA-binding protein 43 (TDP-43), a pathological protein associated with various severe neurological disorders. The HIV-1 accessory protein Vpu was found to be responsible for the cleavage of TDP-43, as ectopic expression of Vpu alone was sufficient to induce TDP-43 cleavage, whereas HIV-1 lacking Vpu failed to cleave TDP-43. Mechanistically, the cleavage of TDP-43 at Asp89 by HIV-1 relies on Vpu-mediated activation of Caspase 3, and pharmacological inhibition of Caspase 3 activity effectively suppressed the HIV-1-induced aggregation and neurotoxicity of TDP-43. Overall, these results suggest that TDP-43 is a conserved host target of HIV-1 Vpu and provide evidence for the involvement of TDP-43 dysregulation in the neural pathogenesis of HIV-1.
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Affiliation(s)
- Jiaxin Yang
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Yan Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Huili Li
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Haichen Zhang
- Department of Neurology and Neuroscience Center, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Haoran Guo
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Xiangyu Zheng
- Department of Neurology and Neuroscience Center, First Hospital, Jilin University, 130021, Changchun, Jilin, China
| | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wei Wei
- Institute of Virology and AIDS Research, First Hospital, Jilin University, 130021, Changchun, Jilin, China.
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, 130021, Changchun, Jilin, China.
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16
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Mohan M, Mannan A, Nauriyal A, Singh TG. Emerging targets in amyotrophic lateral sclerosis (ALS): The promise of ATP-binding cassette (ABC) transporter modulation. Behav Brain Res 2024; 476:115242. [PMID: 39243983 DOI: 10.1016/j.bbr.2024.115242] [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: 08/13/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative primarily affecting motor neurons, leading to disability and neuronal death, and ATP-Binding Cassette (ABC) transporter due to their role in drug efflux and modulation of various cellular pathways contributes to the pathogenesis of ALS. In this article, we extensively investigated various molecular and mechanistic pathways linking ALS transporter to the pathogenesis of ALS; this involves inflammatory pathways such as Mitogen-Activated Protein Kinase (MAPK), Phosphatidylinositol-3-Kinase/Protein Kinase B (PI3K/Akt), Toll-Like Receptor (TLR), Glycogen Synthase Kinase 3β (GSK-3β), Nuclear Factor Kappa-B (NF-κB), and Cyclooxygenase (COX). Oxidative pathways such as Astrocytes, Glutamate, Nuclear factor (erythroid-derived 2)-like 2 (Nrf2), Sirtuin 1 (SIRT-1), Forkhead box protein O (FOXO), Extracellular signal-regulated kinase (ERK). Additionally, we delve into the role of autophagic pathways like TAR DNA-binding protein 43 (TDP-43), AMP-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), and lastly, the apoptotic pathways. Furthermore, by understanding these intricate interactions, we aim to develop novel therapeutic strategies targeting ABC transporters, improving drug delivery, and ultimately offering a promising avenue for treating ALS.
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Affiliation(s)
- Maneesh Mohan
- Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India
| | - Ashi Mannan
- Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India
| | - Aayush Nauriyal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India
| | - Thakur Gurjeet Singh
- Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India.
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17
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Noches V, Campos-Melo D, Droppelmann CA, Strong MJ. Epigenetics in the formation of pathological aggregates in amyotrophic lateral sclerosis. Front Mol Neurosci 2024; 17:1417961. [PMID: 39290830 PMCID: PMC11405384 DOI: 10.3389/fnmol.2024.1417961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
The progressive degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) is accompanied by the formation of a broad array of cytoplasmic and nuclear neuronal inclusions (protein aggregates) largely containing RNA-binding proteins such as TAR DNA-binding protein 43 (TDP-43) or fused in sarcoma/translocated in liposarcoma (FUS/TLS). This process is driven by a liquid-to-solid phase separation generally from proteins in membrane-less organelles giving rise to pathological biomolecular condensates. The formation of these protein aggregates suggests a fundamental alteration in the mRNA expression or the levels of the proteins involved. Considering the role of the epigenome in gene expression, alterations in DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA modifications become highly relevant to understanding how this pathological process takes effect. In this review, we explore the evidence that links epigenetic mechanisms with the formation of protein aggregates in ALS. We propose that a greater understanding of the role of the epigenome and how this inter-relates with the formation of pathological LLPS in ALS will provide an attractive therapeutic target.
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Affiliation(s)
- Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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18
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Tam S, Wear D, Morrone CD, Yu WH. The complexity of extracellular vesicles: Bridging the gap between cellular communication and neuropathology. J Neurochem 2024; 168:2391-2422. [PMID: 38650384 DOI: 10.1111/jnc.16108] [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: 01/14/2024] [Revised: 03/12/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024]
Abstract
Brain-derived extracellular vesicles (EVs) serve a prominent role in maintaining homeostasis and contributing to pathology in health and disease. This review establishes a crucial link between physiological processes leading to EV biogenesis and their impacts on disease. EVs are involved in the clearance and transport of proteins and nucleic acids, responding to changes in cellular processes associated with neurodegeneration, including autophagic disruption, organellar dysfunction, aging, and other cell stresses. In neurodegenerative disorders (e.g., Alzheimer's disease, Parkinson's disease, etc.), EVs contribute to the spread of pathological proteins like amyloid β, tau, ɑ-synuclein, prions, and TDP-43, exacerbating neurodegeneration and accelerating disease progression. Despite evidence for both neuropathological and neuroprotective effects of EVs, the mechanistic switch between their physiological and pathological functions remains elusive, warranting further research into their involvement in neurodegenerative disease. Moreover, owing to their innate ability to traverse the blood-brain barrier and their ubiquitous nature, EVs emerge as promising candidates for novel diagnostic and therapeutic strategies. The review uniquely positions itself at the intersection of EV cell biology, neurophysiology, and neuropathology, offering insights into the diverse biological roles of EVs in health and disease.
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Affiliation(s)
- Stephanie Tam
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Darcy Wear
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Christopher D Morrone
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Wai Haung Yu
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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19
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Samuel Olajide T, Oyerinde TO, Omotosho OI, Okeowo OM, Olajide OJ, Ijomone OM. Microglial senescence in neurodegeneration: Insights, implications, and therapeutic opportunities. NEUROPROTECTION 2024; 2:182-195. [PMID: 39364217 PMCID: PMC11449118 DOI: 10.1002/nep3.56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/03/2024] [Indexed: 10/05/2024]
Abstract
The existing literature on neurodegenerative diseases (NDDs) reveals a common pathological feature: the accumulation of misfolded proteins. However, the heterogeneity in disease onset mechanisms and the specific brain regions affected complicates the understanding of the diverse clinical manifestations of individual NDDs. Dementia, a hallmark symptom across various NDDs, serves as a multifaceted denominator, contributing to the clinical manifestations of these disorders. There is a compelling hypothesis that therapeutic strategies capable of mitigating misfolded protein accumulation and disrupting ongoing pathogenic processes may slow or even halt disease progression. Recent research has linked disease-associated microglia to their transition into a senescent state-characterized by irreversible cell cycle arrest-in aging populations and NDDs. Although senescent microglia are consistently observed in NDDs, few studies have utilized animal models to explore their role in disease pathology. Emerging evidence from experimental rat models suggests that disease-associated microglia exhibit characteristics of senescence, indicating that deeper exploration of microglial senescence could enhance our understanding of NDD pathogenesis and reveal novel therapeutic targets. This review underscores the importance of investigating microglial senescence and its potential contributions to the pathophysiology of NDDs, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Additionally, it highlights the potential of targeting microglial senescence through iron chelation and senolytic therapies as innovative approaches for treating age-related NDDs.
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Affiliation(s)
- Tobiloba Samuel Olajide
- Laboratory for Experimental and Translational Neurobiology, University of Medical Sciences, Ondo, Ondo, Nigeria
| | - Toheeb O. Oyerinde
- Laboratory for Experimental and Translational Neurobiology, University of Medical Sciences, Ondo, Ondo, Nigeria
| | - Omolabake I. Omotosho
- Laboratory for Experimental and Translational Neurobiology, University of Medical Sciences, Ondo, Ondo, Nigeria
| | - Oritoke M. Okeowo
- Laboratory for Experimental and Translational Neurobiology, University of Medical Sciences, Ondo, Ondo, Nigeria
- Department of Physiology, School of Basic Medical Science, Federal University of Technology, Akure, Ondo, Nigeria
| | - Olayemi J. Olajide
- Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, Montreal, Quebec, Canada
- Division of Neurobiology, Department of Anatomy, Faculty of Basic Medical Sciences, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Omamuyouwi M. Ijomone
- Laboratory for Experimental and Translational Neurobiology, University of Medical Sciences, Ondo, Ondo, Nigeria
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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20
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Ho PC, Hsieh TC, Tsai KJ. TDP-43 proteinopathy in frontotemporal lobar degeneration and amyotrophic lateral sclerosis: From pathomechanisms to therapeutic strategies. Ageing Res Rev 2024; 100:102441. [PMID: 39069095 DOI: 10.1016/j.arr.2024.102441] [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: 05/31/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Proteostasis failure is a common pathological characteristic in neurodegenerative diseases. Revitalizing clearance systems could effectively mitigate these diseases. The transactivation response (TAR) DNA-binding protein 43 (TDP-43) plays a critical role as an RNA/DNA-binding protein in RNA metabolism and synaptic function. Accumulation of TDP-43 aggregates in the central nervous system is a hallmark of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Autophagy, a major and highly conserved degradation pathway, holds the potential for degrading aggregated TDP-43 and alleviating FTLD/ALS. This review explores the causes of TDP-43 aggregation, FTLD/ALS-related genes, key autophagy factors, and autophagy-based therapeutic strategies targeting TDP-43 proteinopathy. Understanding the underlying pathological mechanisms of TDP-43 proteinopathy can facilitate therapeutic interventions.
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Affiliation(s)
- Pei-Chuan Ho
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung-Chi Hsieh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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21
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Zeng J, Tang Y, Dong X, Li F, Wei G. Influence of ALS-linked M337V mutation on the conformational ensembles of TDP-43 321-340 peptide monomer and dimer. Proteins 2024; 92:1059-1069. [PMID: 36841957 DOI: 10.1002/prot.26482] [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: 01/09/2023] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
The transactive response (TAR) DNA/RNA-binding protein 43 (TDP-43) can self-assemble into both functional stress granules via liquid-liquid phase separation (LLPS) and pathogenic amyloid fibrillary aggregates that are closely linked to amyotrophic lateral sclerosis. Previous experimental studies reported that the low complexity domain (LCD) of TDP-43 plays an essential role in the LLPS and aggregation of the full-length protein, and it alone can also undergo LLPS to form liquid droplets mainly via intermolecular interactions in the 321-340 region. And the ALS-associated M337V mutation impairs LCD's LLPS and facilitates liquid-solid phase transition. However, the underlying atomistic mechanism is not well understood. Herein, as a first step to understand the M337V-caused LLPS disruption of TDP-43 LCD mediated by the 321-340 region and the fibrillization enhancement, we investigated the conformational properties of monomer/dimer of TDP-43321-340 peptide and its M337V mutant by performing extensive all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations demonstrate that M337V mutation alters the residue regions with high helix/β-structure propensities and thus affects the conformational ensembles of both monomer and dimer. M337V mutation inhibits helix formation in the N-terminal Ala-rich region and the C-terminal mutation site region, while facilitating their long β-sheet formation, albeit with a minor impact on the average probability of both helix structure and β-structure. Further analysis of dimer system shows that M337V mutation disrupts inter-molecular helix-helix interactions and W334-W334 π-π stacking interactions which were reported to be important for the LLPS of TDP-43 LCD, whereas enhances the overall peptide residue-residue interactions and weakens peptide-water interactions, which is conducive to peptide fibrillization. This study provides mechanistic insights into the M337V-mutation-induced impairment of phase separation and facilitation of fibril formation of TDP-43 LCD.
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Affiliation(s)
- Jiyuan Zeng
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
| | - Xuewei Dong
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai, China
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22
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Ceron-Codorniu M, Torres P, Fernàndez-Bernal A, Rico-Rios S, Serrano JC, Miralles MP, Beltran M, Garcera A, Soler RM, Pamplona R, Portero-Otín M. TDP-43 dysfunction leads to bioenergetic failure and lipid metabolic rewiring in human cells. Redox Biol 2024; 75:103301. [PMID: 39116527 PMCID: PMC11362800 DOI: 10.1016/j.redox.2024.103301] [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: 06/04/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024] Open
Abstract
The dysfunction of TAR DNA-binding protein 43 (TDP-43) is implicated in various neurodegenerative diseases, though the specific contributions of its toxic gain-of-function versus loss-of-function effects remain unclear. This study investigates the impact of TARDBP loss on cellular metabolism and viability using human-induced pluripotent stem cell-derived motor neurons and HeLa cells. TARDBP silencing led to reduced metabolic activity and cell growth, accompanied by neurite degeneration and decreased oxygen consumption rates in both cell types. Notably, TARDBP depletion induced a metabolic shift, impairing ATP production, increasing metabolic inflexibility, and elevating free radical production, indicating a critical role for TDP-43 in maintaining cellular bioenergetics. Furthermore, TARDBP loss triggered non-apoptotic cell death, increased ACSL4 expression, and reprogrammed lipid metabolism towards lipid droplet accumulation, while paradoxically enhancing resilience to ferroptosis inducers. Overall, our findings highlight those essential cellular traits such as ATP production, metabolic activity, oxygen consumption, and cell survival are highly dependent on TARDBP function.
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Affiliation(s)
- Miriam Ceron-Codorniu
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Pascual Torres
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Anna Fernàndez-Bernal
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Santiago Rico-Rios
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - José Ce Serrano
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Maria P Miralles
- Neuronal Signaling Unit, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Maria Beltran
- Neuronal Signaling Unit, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Ana Garcera
- Neuronal Signaling Unit, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Rosa M Soler
- Neuronal Signaling Unit, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Reinald Pamplona
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain
| | - Manuel Portero-Otín
- Metabolic Pathophysiology Research Group, Universitat de Lleida-IRBLleida, 25198, Lleida, Spain.
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23
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Thompson EG, Spead O, Akerman SC, Curcio C, Zaepfel BL, Kent ER, Philips T, Vijayakumar BG, Zacco A, Zhou W, Nagappan G, Rothstein JD. A robust evaluation of TDP-43, poly GP, cellular pathology and behavior in a AAV-C9ORF72 (G 4C 2) 66 mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.607409. [PMID: 39253499 PMCID: PMC11383318 DOI: 10.1101/2024.08.27.607409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
The G4C2 hexanucleotide repeat expansion in C9ORF72 is the major genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9-ALS/FTD). Despite considerable efforts, the development of mouse models of C9-ALS/FTD useful for therapeutic development has proven challenging due to the intricate interplay of genetic and molecular factors underlying this neurodegenerative disorder, in addition to species differences. This study presents a robust investigation of the cellular pathophysiology and behavioral outcomes in a previously described AAV mouse model of C9-ALS expressing 66 G4C2 hexanucleotide repeats. Despite displaying key molecular ALS pathological markers including RNA foci, dipeptide repeat (DPR) protein aggregation, p62 positive stress granule formation as well as mild gliosis, the AAV-(G4C2)66 mouse model in this study exhibits negligible neuronal loss, no motor deficits, and functionally unimpaired TAR DNA-binding protein-43 (TDP-43). While our findings indicate and support that this is a robust and pharmacologically tractable model for investigating the molecular mechanisms and cellular consequences of (G4C2) repeat driven DPR pathology, it is not suitable for investigating the development of disease associated neurodegeneration, TDP-43 dysfunction, gliosis, and motor performance. Our findings underscore the complexity of ALS pathogenesis involving genetic mutations and protein dysregulation and highlight the need for more comprehensive model systems that reliably replicate the multifaceted cellular and behavioral aspects of C9-ALS.
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Affiliation(s)
- Emily G Thompson
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Olivia Spead
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - S Can Akerman
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Carrie Curcio
- Glaxo Smith Kline Research and Development, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Benjamin L Zaepfel
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Erica R Kent
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Thomas Philips
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Balaji G Vijayakumar
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Anna Zacco
- Glaxo Smith Kline Research and Development, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Weibo Zhou
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Guhan Nagappan
- Glaxo Smith Kline Research and Development, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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24
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Bai D, Deng F, Jia Q, Ou K, Wang X, Hou J, Zhu L, Guo M, Yang S, Jiang G, Li S, Li XJ, Yin P. Pathogenic TDP-43 accelerates the generation of toxic exon1 HTT in Huntington's disease knock-in mice. Aging Cell 2024:e14325. [PMID: 39185703 DOI: 10.1111/acel.14325] [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: 04/03/2024] [Revised: 08/05/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
Huntington's disease (HD) is caused by a CAG repeat expansion in exon1 of the HTT gene that encodes a polyglutamine tract in huntingtin protein. The formation of HTT exon1 fragments with an expanded polyglutamine repeat has been implicated as a key step in the pathogenesis of HD. It was reported that the CAG repeat length-dependent aberrant splicing of exon1 HTT results in a short polyadenylated mRNA that is translated into an exon1 HTT protein. Under normal conditions, TDP-43 is predominantly found in the nucleus, where it regulates gene expression. However, in various pathological conditions, TDP-43 is mislocalized in the cytoplasm. By investigating HD knock-in mice, we explore whether the pathogenic TDP-43 in the cytoplasm contributes to HD pathogenesis, through expressing the cytoplasmic TDP-43 without nuclear localization signal. We found that the cytoplasmic TDP-43 is increased in the HD mouse brain and that its mislocalization could deteriorate the motor and gait behavior. Importantly, the cytoplasmic TDP-43, via its binding to the intron1 sequence (GU/UG)n of the mouse Htt pre-mRNA, promotes the transport of exon1-intron1 Htt onto ribosome, resulting in the aberrant generation of exon1 Htt. Our findings suggest that cytoplasmic TDP-43 contributes to HD pathogenesis via its binding to and transport of nuclear un-spliced mRNA to the ribosome for the generation of a toxic protein product.
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Affiliation(s)
- Dazhang Bai
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Fuyu Deng
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
- Shenzhen Institute for Drug Control, Shenzhen Testing Center of Medical Devices, In Vitro Diagnostic Reagents Testing Department, Shenzhen, Guangdong, China
| | - Qingqing Jia
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Kaili Ou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Xiang Wang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Junqi Hou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Longhong Zhu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Mingwei Guo
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Su Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Guohui Jiang
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shihua Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Xiao-Jiang Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
| | - Peng Yin
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Key Laboratory of non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China
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25
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Wenzhi Y, Xiangyi L, Dongsheng F. The prion-like effect and prion-like protein targeting strategy in amyotrophic lateral sclerosis. Heliyon 2024; 10:e34963. [PMID: 39170125 PMCID: PMC11336370 DOI: 10.1016/j.heliyon.2024.e34963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/09/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
Pathological proteins in amyotrophic lateral sclerosis (ALS), such as superoxide dismutase 1, TAR DNA-binding protein 43, and fused in sarcoma, exhibit a prion-like pattern. All these proteins have a low-complexity domain and seeding activity in cells. In this review, we summarize the studies on the prion-like effect of these proteins and list six prion-like protein targeting strategies that we believe have potential for ALS therapy, including antisense oligonucleotides, antibody-based technology, peptide, protein chaperone, autophagy enhancement, and heteromultivalent compounds. Considering the pathological complexity and heterogeneity of ALS, we believe that the final solution to ALS therapy is most likely to be an individualized cocktail therapy, including clearance of toxicity, blockage of pathological progress, and protection of neurons.
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Affiliation(s)
- Yang Wenzhi
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Liu Xiangyi
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Fan Dongsheng
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
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26
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Bedja-Iacona L, Richard E, Marouillat S, Brulard C, Alouane T, Beltran S, Andres CR, Blasco H, Corcia P, Veyrat-Durebex C, Vourc’h P. Post-Translational Variants of Major Proteins in Amyotrophic Lateral Sclerosis Provide New Insights into the Pathophysiology of the Disease. Int J Mol Sci 2024; 25:8664. [PMID: 39201350 PMCID: PMC11354932 DOI: 10.3390/ijms25168664] [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: 06/30/2024] [Revised: 08/04/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Post-translational modifications (PTMs) affecting proteins during or after their synthesis play a crucial role in their localization and function. The modification of these PTMs under pathophysiological conditions, i.e., their appearance, disappearance, or variation in quantity caused by a pathological environment or a mutation, corresponds to post-translational variants (PTVs). These PTVs can be directly or indirectly involved in the pathophysiology of diseases. Here, we present the PTMs and PTVs of four major amyotrophic lateral sclerosis (ALS) proteins, SOD1, TDP-43, FUS, and TBK1. These modifications involve acetylation, phosphorylation, methylation, ubiquitination, SUMOylation, and enzymatic cleavage. We list the PTM positions known to be mutated in ALS patients and discuss the roles of PTVs in the pathophysiological processes of ALS. In-depth knowledge of the PTMs and PTVs of ALS proteins is needed to better understand their role in the disease. We believe it is also crucial for developing new therapies that may be more effective in ALS.
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Affiliation(s)
- Léa Bedja-Iacona
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
| | - Elodie Richard
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
| | - Sylviane Marouillat
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
| | | | | | - Stéphane Beltran
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Neurologie, CHRU de Tours, 37000 Tours, France
| | - Christian R. Andres
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
| | - Hélène Blasco
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
| | - Philippe Corcia
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- Service de Neurologie, CHRU de Tours, 37000 Tours, France
| | - Charlotte Veyrat-Durebex
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- UTTIL, CHRU de Tours, 37000 Tours, France
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
| | - Patrick Vourc’h
- UMR 1253, iBraiN, Université de Tours, Inserm, 37000 Tours, France; lea.bedja-- (L.B.-I.); (E.R.)
- UTTIL, CHRU de Tours, 37000 Tours, France
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37000 Tours, France
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27
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Gatch AJ, Ding F. TDP-43 Promotes Amyloid-Beta Toxicity by Delaying Fibril Maturation via Direct Molecular Interaction. ACS Chem Neurosci 2024; 15:2936-2953. [PMID: 39073874 PMCID: PMC11323227 DOI: 10.1021/acschemneuro.4c00334] [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] [Indexed: 07/30/2024] Open
Abstract
Amyloid-β (Aβ) is a peptide that undergoes self-assembly into amyloid fibrils, which compose the hallmark plaques observed in Alzheimer's disease (AD). TAR DNA-binding protein 43 (TDP-43) is a protein with mislocalization and aggregation implicated in amyotrophic lateral sclerosis and other neurodegenerative diseases. Recent work suggests that TDP-43 may interact with Aβ, inhibiting the formation of amyloid fibrils and worsening AD pathology, but the molecular details of their interaction remain unknown. Using all-atom discrete molecular dynamics simulations, we systematically investigated the direct molecular interaction between Aβ and TDP-43. We found that Aβ monomers were able to bind near the flexible nuclear localization sequence of the N-terminal domain (NTD) of TDP-43, adopting β-sheet rich conformations that were promoted by the interaction. Furthermore, Aβ associated with the nucleic acid binding interface of the tandem RNA recognition motifs of TDP-43 via electrostatic interactions. Using the computational peptide array method, we found the strongest C-terminal domain interaction with Aβ to be within the amyloidogenic core region of TDP-43. With experimental evidence suggesting that the NTD is necessary for inhibiting Aβ fibril growth, we also simulated the NTD with an Aβ40 fibril seed. We found that the NTD was able to strongly bind the elongation surface of the fibril seed via extensive hydrogen bonding and could also diffuse along the lateral surface via electrostatic interactions. Our results suggest that TDP-43 binding to the elongation surface, thereby sterically blocking Aβ monomer addition, is responsible for the experimentally observed inhibition of fibril growth. We conclude that TDP-43 may promote Aβ toxicity by stabilizing the oligomeric state and kinetically delaying fibril maturation.
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Affiliation(s)
- Adam J. Gatch
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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28
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Luan T, Li Q, Huang Z, Feng Y, Xu D, Zhou Y, Hu Y, Wang T. Axonopathy Underlying Amyotrophic Lateral Sclerosis: Unraveling Complex Pathways and Therapeutic Insights. Neurosci Bull 2024:10.1007/s12264-024-01267-2. [PMID: 39097850 DOI: 10.1007/s12264-024-01267-2] [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: 02/15/2024] [Accepted: 04/08/2024] [Indexed: 08/05/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a complex neurodegenerative disorder characterized by progressive axonopathy, jointly leading to the dying back of the motor neuron, disrupting both nerve signaling and motor control. In this review, we highlight the roles of axonopathy in ALS progression, driven by the interplay of multiple factors including defective trafficking machinery, protein aggregation, and mitochondrial dysfunction. Dysfunctional intracellular transport, caused by disruptions in microtubules, molecular motors, and adaptors, has been identified as a key contributor to disease progression. Aberrant protein aggregation involving TDP-43, FUS, SOD1, and dipeptide repeat proteins further amplifies neuronal toxicity. Mitochondrial defects lead to ATP depletion, oxidative stress, and Ca2+ imbalance, which are regarded as key factors underlying the loss of neuromuscular junctions and axonopathy. Mitigating these defects through interventions including neurotrophic treatments offers therapeutic potential. Collaborative research efforts aim to unravel ALS complexities, opening avenues for holistic interventions that target diverse pathological mechanisms.
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Affiliation(s)
- Tongshu Luan
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qing Li
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhi Huang
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yu Feng
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Duo Xu
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yujie Zhou
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yiqing Hu
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Tong Wang
- The Brain Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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29
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Soubannier V, Chaineau M, Gursu L, Lépine S, Kalaydjian D, Sirois J, Haghi G, Rouleau G, Durcan TM, Stifani S. Early nuclear phenotypes and reactive transformation in human iPSC-derived astrocytes from ALS patients with SOD1 mutations. Glia 2024. [PMID: 39092466 DOI: 10.1002/glia.24598] [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: 10/13/2023] [Revised: 06/13/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the progressive death of motor neurons (MNs). Glial cells play roles in MN degeneration in ALS. More specifically, astrocytes with mutations in the ALS-associated gene Cu/Zn superoxide dismutase 1 (SOD1) promote MN death. The mechanisms by which SOD1-mutated astrocytes reduce MN survival are incompletely understood. To characterize the impact of SOD1 mutations on astrocyte physiology, we generated astrocytes from human induced pluripotent stem cell (iPSC) derived from ALS patients carrying SOD1 mutations, together with control isogenic iPSCs. We report that astrocytes harboring SOD1(A4V) and SOD1(D90A) mutations exhibit molecular and morphological changes indicative of reactive astrogliosis when compared to isogenic astrocytes. We show further that a number of nuclear phenotypes precede, or coincide with, reactive transformation. These include increased nuclear oxidative stress and DNA damage, and accumulation of the SOD1 protein in the nucleus. These findings reveal early cell-autonomous phenotypes in SOD1-mutated astrocytes that may contribute to the acquisition of a reactive phenotype involved in alterations of astrocyte-MN communication in ALS.
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Affiliation(s)
- Vincent Soubannier
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Mathilde Chaineau
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Lale Gursu
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Sarah Lépine
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - David Kalaydjian
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Julien Sirois
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Ghazal Haghi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Guy Rouleau
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Thomas M Durcan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Neuro's Early Drug Discovery Unit, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
- The Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Stefano Stifani
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
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30
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Jacob SM, Lee S, Kim SH, Sharkey KA, Pfeffer G, Nguyen MD. Brain-body mechanisms contribute to sexual dimorphism in amyotrophic lateral sclerosis. Nat Rev Neurol 2024; 20:475-494. [PMID: 38965379 DOI: 10.1038/s41582-024-00991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common form of human motor neuron disease. It is characterized by the progressive degeneration of upper and lower motor neurons, leading to generalized motor weakness and, ultimately, respiratory paralysis and death within 3-5 years. The disease is shaped by genetics, age, sex and environmental stressors, but no cure or routine biomarkers exist for the disease. Male individuals have a higher propensity to develop ALS, and a different manifestation of the disease phenotype, than female individuals. However, the mechanisms underlying these sex differences remain a mystery. In this Review, we summarize the epidemiology of ALS, examine the sexually dimorphic presentation of the disease and highlight the genetic variants and molecular pathways that might contribute to sex differences in humans and animal models of ALS. We advance the idea that sexual dimorphism in ALS arises from the interactions between the CNS and peripheral organs, involving vascular, metabolic, endocrine, musculoskeletal and immune systems, which are strikingly different between male and female individuals. Finally, we review the response to treatments in ALS and discuss the potential to implement future personalized therapeutic strategies for the disease.
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Affiliation(s)
- Sarah M Jacob
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sukyoung Lee
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Seung Hyun Kim
- Department of Neurology, Hanyang University Hospital, Seoul, South Korea
| | - Keith A Sharkey
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Gerald Pfeffer
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
| | - Minh Dang Nguyen
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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31
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Mazzotta GM, Conte C. Alpha Synuclein Toxicity and Non-Motor Parkinson's. Cells 2024; 13:1265. [PMID: 39120295 PMCID: PMC11311369 DOI: 10.3390/cells13151265] [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: 06/13/2024] [Revised: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Parkinson's disease (PD) is a common multisystem neurodegenerative disorder affecting 1% of the population over the age of 60 years. The main neuropathological features of PD are the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the presence of alpha synuclein (αSyn)-rich Lewy bodies both manifesting with classical motor signs. αSyn has emerged as a key protein in PD pathology as it can spread through synaptic networks to reach several anatomical regions of the body contributing to the appearance of non-motor symptoms (NMS) considered prevalent among individuals prior to PD diagnosis and persisting throughout the patient's life. NMS mainly includes loss of taste and smell, constipation, psychiatric disorders, dementia, impaired rapid eye movement (REM) sleep, urogenital dysfunction, and cardiovascular impairment. This review summarizes the more recent findings on the impact of αSyn deposits on several prodromal NMS and emphasizes the importance of early detection of αSyn toxic species in biofluids and peripheral biopsies as prospective biomarkers in PD.
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Affiliation(s)
| | - Carmela Conte
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
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32
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Rajabi D, Khanmohammadi S, Rezaei N. The role of long noncoding RNAs in amyotrophic lateral sclerosis. Rev Neurosci 2024; 35:533-547. [PMID: 38452377 DOI: 10.1515/revneuro-2023-0155] [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: 12/14/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a poor prognosis leading to death. The diagnosis and treatment of ALS are inherently challenging due to its complex pathomechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides involved in different cellular processes, incisively gene expression. In recent years, more studies have been conducted on lncRNA classes and interference in different disease pathologies, showing their promising contribution to diagnosing and treating neurodegenerative diseases. In this review, we discussed the role of lncRNAs like NEAT1 and C9orf72-as in ALS pathogenesis mechanisms caused by mutations in different genes, including TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), superoxide dismutase type 1 (SOD1). NEAT1 is a well-established lncRNA in ALS pathogenesis; hence, we elaborate on its involvement in forming paraspeckles, stress response, inflammatory response, and apoptosis. Furthermore, antisense lncRNAs (as-lncRNAs), a key group of transcripts from the opposite strand of genes, including ZEB1-AS1 and ATXN2-AS, are discussed as newly identified components in the pathology of ALS. Ultimately, we review the current standing of using lncRNAs as biomarkers and therapeutic agents and the future vision of further studies on lncRNA applications.
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Affiliation(s)
- Darya Rajabi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
| | - Shaghayegh Khanmohammadi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
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33
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Percio A, Cicchinelli M, Masci D, Summo M, Urbani A, Greco V. Oxidative Cysteine Post Translational Modifications Drive the Redox Code Underlying Neurodegeneration and Amyotrophic Lateral Sclerosis. Antioxidants (Basel) 2024; 13:883. [PMID: 39199129 PMCID: PMC11351139 DOI: 10.3390/antiox13080883] [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: 06/23/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024] Open
Abstract
Redox dysregulation, an imbalance between oxidants and antioxidants, is crucial in the pathogenesis of various neurodegenerative diseases. Within this context, the "redoxome" encompasses the network of redox molecules collaborating to maintain cellular redox balance and signaling. Among these, cysteine-sensitive proteins are fundamental for this homeostasis. Due to their reactive thiol groups, cysteine (Cys) residues are particularly susceptible to oxidative post-translational modifications (PTMs) induced by free radicals (reactive oxygen, nitrogen, and sulfur species) which profoundly affect protein functions. Cys-PTMs, forming what is referred to as "cysteinet" in the redox proteome, are essential for redox signaling in both physiological and pathological conditions, including neurodegeneration. Such modifications significantly influence protein misfolding and aggregation, key hallmarks of neurodegenerative diseases such as Alzheimer's, Parkinson's, and notably, amyotrophic lateral sclerosis (ALS). This review aims to explore the complex landscape of cysteine PTMs in the cellular redox environment, elucidating their impact on neurodegeneration at protein level. By investigating specific cysteine-sensitive proteins and the regulatory networks involved, particular emphasis is placed on the link between redox dysregulation and ALS, highlighting this pathology as a prime example of a neurodegenerative disease wherein such redox dysregulation is a distinct hallmark.
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Affiliation(s)
- Anna Percio
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.P.); (M.C.); (D.M.); (M.S.); (A.U.)
- Department of Laboratory Diagnostic and Infectious Diseases, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy
| | - Michela Cicchinelli
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.P.); (M.C.); (D.M.); (M.S.); (A.U.)
- Department of Laboratory Diagnostic and Infectious Diseases, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy
| | - Domiziana Masci
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.P.); (M.C.); (D.M.); (M.S.); (A.U.)
| | - Mariagrazia Summo
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.P.); (M.C.); (D.M.); (M.S.); (A.U.)
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.P.); (M.C.); (D.M.); (M.S.); (A.U.)
- Department of Laboratory Diagnostic and Infectious Diseases, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (A.P.); (M.C.); (D.M.); (M.S.); (A.U.)
- Department of Laboratory Diagnostic and Infectious Diseases, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy
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Sharma H, Koirala S, Chew YL, Konopka A. DNA Damage and Chromatin Rearrangement Work Together to Promote Neurodegeneration. Mol Neurobiol 2024:10.1007/s12035-024-04331-0. [PMID: 38977621 DOI: 10.1007/s12035-024-04331-0] [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] [Accepted: 06/21/2024] [Indexed: 07/10/2024]
Abstract
Neurodegenerative diseases have a complex origin and are composed of genetic and environmental factors. Both DNA damage and chromatin rearrangement are important processes that occur under pathological conditions and in neurons functioning properly. While numerous studies have demonstrated the inseparable relationship between DNA damage and chromatin organization, understanding of this relationship, especially in neurodegenerative diseases, requires further study. Interestingly, recent studies revealed that known hallmark proteins involved in neurodegenerative diseases function in both DNA damage and chromatin reorganization, and this review discusses the current knowledge of this relationship. This review focused on hallmark proteins involved in various neurodegenerative diseases, such as the microtubule-associated protein tau, TAR DNA/RNA binding protein 43 (TDP-43), superoxide dismutase 1 (SOD1), fused in sarcoma (FUS), huntingtin (HTT), α-synuclein, and β-amyloid precursor protein (APP). Hence, DNA damage and chromatin rearrangement are associated with disease mechanisms in distinct neurodegenerative diseases. Targeting common modulators of DNA repair and chromatin reorganization may lead to promising therapies for treating neurodegeneration.
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35
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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36
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Xu Z, Zhang J, Tang J, Gong Y, Zou Y, Zhang Q. Dissecting the effect of ALS mutation S375G on the conformational properties and aggregation dynamics of TDP-43 370-375 fragment. Biophys Chem 2024; 310:107230. [PMID: 38615537 DOI: 10.1016/j.bpc.2024.107230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024]
Abstract
The aggregation of transactive response deoxyribonucleic acid (DNA) binding protein of 43 kDa (TDP-43) into ubiquitin-positive inclusions is closely associated with amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and chronic traumatic encephalopathy. The 370-375 fragment of TDP-43 (370GNNSYS375, TDP-43370-375), the amyloidogenic hexapeptides, can be prone to forming pathogenic amyloid fibrils with the characteristic of steric zippers. Previous experiments reported the ALS-associated mutation, serine 375 substituted by glycine (S375G) is linked to early onset disease and protein aggregation of TDP-43. Based on this, it is necessary to explore the underlying molecular mechanisms. By utilizing all-atom molecular dynamics (MD) simulations of 102 μs in total, we investigated the impact of S375G mutation on the conformational ensembles and oligomerization dynamics of TDP-43370-375 peptides. Our replica exchange MD simulations show that S375G mutation could promote the unstructured conformation formation and induce peptides to form a loose packed oligomer, thus inhibiting the aggregation of TDP-43370-375. Further analyses suggest that S375G mutation displays a reduction effect on the number of total hydrogen bonds and contacts among TDP-43370-375 peptides. Hydrogen bonding and polar interactions among TDP-43370-375 peptides, as well as Y374-Y374 π-π stacking interaction, are attenuated by S375G mutation. Additional microsecond MD simulations demonstrate that S375G mutation could prohibit the conformational conversion to β-structure-rich aggregates and possess an inhibitory effect on the oligomerization dynamics of TDP-43370-375. This study offers for the first time of molecular insights into the S375G mutation affecting the aggregation of TDP-43370-375 at the atomic level, and may open new avenues in the development of future site-specific mutation therapeutics.
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Affiliation(s)
- Zhengdong Xu
- Department of Physical Education, Shanghai University of Engineering Science, 333 Long Teng Road, Shanghai 201620, People's Republic of China
| | - Jianxin Zhang
- Department of Physical Education, Shanghai University of Engineering Science, 333 Long Teng Road, Shanghai 201620, People's Republic of China
| | - Jiaxing Tang
- College of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China
| | - Yehong Gong
- General Education Center, Westlake University, 600 Dunyu Road, Hangzhou 310030, People's Republic of China
| | - Yu Zou
- Department Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310007, Zhejiang, People's Republic of China.
| | - Qingwen Zhang
- College of Physical Education, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, People's Republic of China.
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37
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Chahla C, Kovacic H, Ferhat L, Leloup L. Pathological Impact of Redox Post-Translational Modifications. Antioxid Redox Signal 2024; 41:152-180. [PMID: 38504589 DOI: 10.1089/ars.2023.0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Oxidative stress is involved in the development of several pathologies. The different reactive oxygen species (ROS) produced during oxidative stress are at the origin of redox post-translational modifications (PTMs) on proteins and impact nucleic acids and lipids. This review provides an overview of recent data on cysteine and methionine oxidation and protein carbonylation following oxidative stress in a pathological context. Oxidation, like nitration, is a selective process and not all proteins are impacted. It depends on multiple factors, including amino acid environment, accessibility, and physical and chemical properties, as well as protein structures. Thiols can undergo reversible oxidations and others that are irreversible. On the contrary, carbonylation represents irreversible PTM. To date, hundreds of proteins were shown to be modified by ROS and reactive nitrogen species (RNS). We reviewed recent advances in the impact of redox-induced PTMs on protein functions and activity, as well as its involvement in disease development or treatment. These data show a complex situation of the involvement of redox PTM on the function of targeted proteins. Many proteins can have their activity decreased by the oxidation of cysteine thiols or methionine S-methyl thioethers, while for other proteins, this oxidation will be activating. This complexity of redox PTM regulation suggests that a global antioxidant therapeutic approach, as often proposed, is unlikely to be effective. However, the specificity of the effect obtained by targeting a cysteine or methionine residue to be able to inactivate or activate a particular protein represents a major interest if it is possible to consider this targeting from a therapeutic point of view with our current pharmacological tools. Antioxid. Redox Signal. 41, 152-180.
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Affiliation(s)
- Charbel Chahla
- Faculté de Médecine, INP, Institut de neurophysiopathologie, Aix Marseille Université, CNRS, Marseille, France
| | - Hervé Kovacic
- Faculté de Médecine, INP, Institut de neurophysiopathologie, Aix Marseille Université, CNRS, Marseille, France
| | - Lotfi Ferhat
- Faculté de Médecine, INP, Institut de neurophysiopathologie, Aix Marseille Université, CNRS, Marseille, France
| | - Ludovic Leloup
- Faculté de Médecine, INP, Institut de neurophysiopathologie, Aix Marseille Université, CNRS, Marseille, France
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38
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Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
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Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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39
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Bonanni R, Cariati I, Cifelli P, Frank C, Annino G, Tancredi V, D'Arcangelo G. Exercise to Counteract Alzheimer's Disease: What Do Fluid Biomarkers Say? Int J Mol Sci 2024; 25:6951. [PMID: 39000060 PMCID: PMC11241657 DOI: 10.3390/ijms25136951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/14/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Neurodegenerative diseases (NDs) represent an unsolved problem to date with an ever-increasing population incidence. Particularly, Alzheimer's disease (AD) is the most widespread ND characterized by an accumulation of amyloid aggregates of beta-amyloid (Aβ) and Tau proteins that lead to neuronal death and subsequent cognitive decline. Although neuroimaging techniques are needed to diagnose AD, the investigation of biomarkers within body fluids could provide important information on neurodegeneration. Indeed, as there is no definitive solution for AD, the monitoring of these biomarkers is of strategic importance as they are useful for both diagnosing AD and assessing the progression of the neurodegenerative state. In this context, exercise is known to be an effective non-pharmacological management strategy for AD that can counteract cognitive decline and neurodegeneration. However, investigation of the concentration of fluid biomarkers in AD patients undergoing exercise protocols has led to unclear and often conflicting results, suggesting the need to clarify the role of exercise in modulating fluid biomarkers in AD. Therefore, this critical literature review aims to gather evidence on the main fluid biomarkers of AD and the modulatory effects of exercise to clarify the efficacy and usefulness of this non-pharmacological strategy in counteracting neurodegeneration in AD.
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Affiliation(s)
- Roberto Bonanni
- Department of Biomedicine and Prevention, "Tor Vergata" University of Rome, 00133 Rome, Italy
| | - Ida Cariati
- Department of Systems Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
| | - Pierangelo Cifelli
- Department of Applied Clinical and Biotechnological Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Claudio Frank
- UniCamillus-Saint Camillus International University of Health Sciences, 00131 Rome, Italy
| | - Giuseppe Annino
- Department of Systems Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
- Centre of Space Bio-Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
- Sports Engineering Laboratory, Department of Industrial Engineering, "Tor Vergata" University of Rome, 00133 Rome, Italy
| | - Virginia Tancredi
- Department of Systems Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
- Centre of Space Bio-Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
| | - Giovanna D'Arcangelo
- Department of Systems Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
- Centre of Space Bio-Medicine, "Tor Vergata" University of Rome, 00133 Rome, Italy
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40
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Zhang X, Das T, Chao TF, Trinh V, Carmen-Orozco RP, Ling JP, Kalab P, Hayes LR. Multivalent GU-rich oligonucleotides sequester TDP-43 in the nucleus by inducing high molecular weight RNP complexes. iScience 2024; 27:110109. [PMID: 38989321 PMCID: PMC11233918 DOI: 10.1016/j.isci.2024.110109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/22/2024] [Accepted: 05/23/2024] [Indexed: 07/12/2024] Open
Abstract
TDP-43 nuclear clearance and cytoplasmic aggregation are hallmarks of TDP-43 proteinopathies. We recently demonstrated that binding to endogenous nuclear GU-rich RNAs sequesters TDP-43 in the nucleus by restricting its passive nuclear export. Here, we tested the feasibility of synthetic RNA oligonucleotide-mediated augmentation of TDP-43 nuclear localization. Using biochemical assays, we compared the ability of GU-rich oligonucleotides to engage in multivalent, RRM-dependent binding with TDP-43. When transfected into cells, (GU)16 attenuated TDP-43 mislocalization induced by transcriptional blockade or RanGAP1 ablation. Clip34nt and (GU)16 accelerated TDP-43 nuclear re-import after cytoplasmic mislocalization. RNA pulldowns confirmed that multivalent GU-oligonucleotides induced high molecular weight RNP complexes, incorporating TDP-43 and possibly other GU-binding proteins. Transfected GU-repeat oligos disrupted TDP-43 cryptic exon repression, likely by diverting TDP-43 from endogenous RNAs, except for Clip34nt that contains interspersed A and C. Thus, exogenous multivalent GU-RNAs can promote TDP-43 nuclear localization, though pure GU-repeat motifs impair TDP-43 function.
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Affiliation(s)
- Xi Zhang
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tanuza Das
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Tiffany F. Chao
- Johns Hopkins University Whiting School of Engineering, Baltiomre, MD 21218, USA
| | - Vickie Trinh
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | - Jonathan P. Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Petr Kalab
- Johns Hopkins University Whiting School of Engineering, Baltiomre, MD 21218, USA
| | - Lindsey R. Hayes
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Johns Hopkins Brain Science Institute, Baltimore, MD 21205, USA
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41
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Doke AA, Jha SK. Electrostatics Choreographs the Aggregation Dynamics of Full-Length TDP-43 via a Monomeric Amyloid Precursor. Biochemistry 2024; 63:1553-1568. [PMID: 38820318 DOI: 10.1021/acs.biochem.4c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
TDP-43 is a ubiquitously expressed, multidomain functional protein that is distinctively known to form aggregates in many fatal neurodegenerative disorders. However, the information for arresting TDP-43 aggregation is missing due to a lack of understanding of the molecular mechanism of the aggregation and structural properties of TDP-43. TDP-43 is inherently prone to aggregation and has minimal protein solubility. Multiple studies have been performed on the smaller parts of TDP-43 or the full-length protein attached to a large solubilization tag. However, the presence of co-solutes or solubilization tags is observed to interfere with the molecular properties and aggregation mechanism of full-length TDP-43. Notably, this study populated and characterized the native, dimeric state of TDP-43 without the interference of co-solutes or protein modifications. We observed that the electrostatics of the local environment is capable of the partial unfolding and monomerization of the native dimeric state of TDP-43 into an amyloidogenic molten globule. By employing the tools of thermodynamics and kinetics, we reveal the structural characteristics and temporal order of the early intermediates and transition states during the transition of the molten globule to β-rich, amyloid-like aggregates of TDP-43, which is governed by the electrostatics of the environment. The current advanced understanding of the nature of native and early aggregation-prone intermediates, early steps, and the influence of electrostatics in TDP-43 aggregation is essential for drug design.
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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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Ko VI, Ong K, Cleveland DW, Yu H, Ravits JM. CK1δ/ε kinases regulate TDP-43 phosphorylation and are therapeutic targets for ALS-related TDP-43 hyperphosphorylation. Neurobiol Dis 2024; 196:106516. [PMID: 38677657 DOI: 10.1016/j.nbd.2024.106516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024] Open
Abstract
Hyperphosphorylated TAR DNA-binding protein 43 (TDP-43) aggregates in the cytoplasm of neurons is the neuropathological hallmark of amyotrophic lateral sclerosis (ALS) and a group of neurodegenerative diseases collectively referred to as TDP-43 proteinopathies that includes frontotemporal dementia, Alzheimer's disease, and limbic onset age-related TDP-43 encephalopathy. The mechanism of TDP-43 phosphorylation is poorly understood. Previously we reported casein kinase 1 epsilon gene (CSNK1E gene encoding CK1ε protein) as being tightly correlated with phosphorylated TDP-43 (pTDP-43) pathology. Here we pursued studies to investigate in cellular models and in vitro how CK1ε and CK1δ (a closely related family sub-member) mediate TDP-43 phosphorylation in disease. We first validated the binding interaction between TDP-43 and either CK1δ and CK1ε using kinase activity assays and predictive bioinformatic database. We utilized novel inducible cellular models that generated translocated phosphorylated TDP-43 (pTDP-43) and cytoplasmic aggregation. Reducing CK1 kinase activity with siRNA or small molecule chemical inhibitors resulted in significant reduction of pTDP-43, in both soluble and insoluble protein fractions. We also established CK1δ and CK1ε are the primary kinases that phosphorylate TDP-43 compared to CK2α, CDC7, ERK1/2, p38α/MAPK14, and TTBK1, other identified kinases that have been implicated in TDP-43 phosphorylation. Throughout our studies, we were careful to examine both the soluble and insoluble TDP-43 protein fractions, the critical protein fractions related to protein aggregation diseases. These results identify CK1s as critical kinases involved in TDP-43 hyperphosphorylation and aggregation in cellular models and in vitro, and in turn are potential therapeutic targets by way of CK1δ/ε inhibitors.
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Affiliation(s)
- Vivian I Ko
- Neuroscience Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - Kailee Ong
- Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - Haiyang Yu
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - John M Ravits
- Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA.
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Ho DM, Shaban M, Mahmood F, Ganguly P, Todeschini L, Van Vactor D, Artavanis-Tsakonas S. cAMP/PKA signaling regulates TDP-43 aggregation and mislocalization. Proc Natl Acad Sci U S A 2024; 121:e2400732121. [PMID: 38838021 PMCID: PMC11181030 DOI: 10.1073/pnas.2400732121] [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: 01/12/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Cytoplasmic mislocalization and aggregation of TDP-43 protein are hallmarks of amyotrophic lateral sclerosis (ALS) and are observed in the vast majority of both familial and sporadic cases. How these two interconnected processes are regulated on a molecular level, however, remains enigmatic. Genome-wide screens for modifiers of the ALS-associated genes TDP-43 and FUS have identified the phospholipase D (Pld) pathway as a key regulator of ALS-related phenotypes in the fruit fly Drosophila melanogaster [M. W. Kankel et al., Genetics 215, 747-766 (2020)]. Here, we report the results of our search for downstream targets of the enzymatic product of Pld, phosphatidic acid. We identify two conserved negative regulators of the cAMP/PKA signaling pathway, the phosphodiesterase dunce and the inhibitory subunit PKA-R2, as modifiers of pathogenic phenotypes resulting from overexpression of the Drosophila TDP-43 ortholog TBPH. We show that knockdown of either of these genes results in a mitigation of both TBPH aggregation and mislocalization in larval motor neuron cell bodies, as well as an amelioration of adult-onset motor defects and shortened lifespan induced by TBPH. We determine that PKA kinase activity is downstream of both TBPH and Pld and that overexpression of the PKA target CrebA can rescue TBPH mislocalization. These findings suggest a model whereby increasing cAMP/PKA signaling can ameliorate the molecular and functional effects of pathological TDP-43.
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Affiliation(s)
- Diana M. Ho
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Muhammad Shaban
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA02114
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA02142
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA02114
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA02115
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA02142
| | - Payel Ganguly
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | | | - David Van Vactor
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
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Adler GL, Le K, Fu Y, Kim WS. Human Endogenous Retroviruses in Neurodegenerative Diseases. Genes (Basel) 2024; 15:745. [PMID: 38927681 PMCID: PMC11202925 DOI: 10.3390/genes15060745] [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: 05/10/2024] [Revised: 05/25/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are DNA transposable elements that have integrated into the human genome via an ancestral germline infection. The potential importance of HERVs is underscored by the fact that they comprise approximately 8% of the human genome. HERVs have been implicated in the pathogenesis of neurodegenerative diseases, a group of CNS diseases characterized by a progressive loss of structure and function of neurons, resulting in cell death and multiple physiological dysfunctions. Much evidence indicates that HERVs are initiators or drivers of neurodegenerative processes in multiple sclerosis and amyotrophic lateral sclerosis, and clinical trials have been designed to target HERVs. In recent years, the role of HERVs has been explored in other major neurodegenerative diseases, including frontotemporal dementia, Alzheimer's disease and Parkinson's disease, with some interesting discoveries. This review summarizes and evaluates the past and current research on HERVs in neurodegenerative diseases. It discusses the potential role of HERVs in disease manifestation and neurodegeneration. It critically reviews antiretroviral strategies used in the therapeutic intervention of neurodegenerative diseases.
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Affiliation(s)
- Gabrielle L. Adler
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Kelvin Le
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - YuHong Fu
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Woojin Scott Kim
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Droppelmann CA, Campos-Melo D, Noches V, McLellan C, Szabla R, Lyons TA, Amzil H, Withers B, Kaplanis B, Sonkar KS, Simon A, Buratti E, Junop M, Kramer JM, Strong MJ. Mitigation of TDP-43 toxic phenotype by an RGNEF fragment in amyotrophic lateral sclerosis models. Brain 2024; 147:2053-2068. [PMID: 38739752 PMCID: PMC11146434 DOI: 10.1093/brain/awae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/24/2024] [Accepted: 02/08/2024] [Indexed: 05/16/2024] Open
Abstract
Aggregation of the RNA-binding protein TAR DNA binding protein (TDP-43) is a hallmark of TDP-proteinopathies including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As TDP-43 aggregation and dysregulation are causative of neuronal death, there is a special interest in targeting this protein as a therapeutic approach. Previously, we found that TDP-43 extensively co-aggregated with the dual function protein GEF (guanine exchange factor) and RNA-binding protein rho guanine nucleotide exchange factor (RGNEF) in ALS patients. Here, we show that an N-terminal fragment of RGNEF (NF242) interacts directly with the RNA recognition motifs of TDP-43 competing with RNA and that the IPT/TIG domain of NF242 is essential for this interaction. Genetic expression of NF242 in a fruit fly ALS model overexpressing TDP-43 suppressed the neuropathological phenotype increasing lifespan, abolishing motor defects and preventing neurodegeneration. Intracerebroventricular injections of AAV9/NF242 in a severe TDP-43 murine model (rNLS8) improved lifespan and motor phenotype, and decreased neuroinflammation markers. Our results demonstrate an innovative way to target TDP-43 proteinopathies using a protein fragment with a strong affinity for TDP-43 aggregates and a mechanism that includes competition with RNA sequestration, suggesting a promising therapeutic strategy for TDP-43 proteinopathies such as ALS and FTD.
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Affiliation(s)
- Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Crystal McLellan
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Robert Szabla
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Taylor A Lyons
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Hind Amzil
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Benjamin Withers
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Brianna Kaplanis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Kirti S Sonkar
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, 34149 Trieste, Italy
| | - Anne Simon
- Department of Biology, Faculty of Science, Western University, London, Ontario N6A 5B7, Canada
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), AREA Science Park, 34149 Trieste, Italy
| | - Murray Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
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Stuwe H, Reardon PN, Yu Z, Shah S, Hughes K, Barbar EJ. Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix. J Biol Chem 2024; 300:107354. [PMID: 38718862 PMCID: PMC11180338 DOI: 10.1016/j.jbc.2024.107354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, evading host immunity, and virus maturation. N is a multidomain protein composed of an independently folded monomeric N-terminal domain that is the primary site for RNA binding and a dimeric C-terminal domain that is essential for efficient phase separation and condensate formation with RNA. The domains are separated by a disordered Ser/Arg-rich region preceding a self-associating Leu-rich helix. Phosphorylation in the Ser/Arg region in infected cells decreases the viscosity of N:RNA condensates promoting viral replication and host immune evasion. The molecular level effect of phosphorylation, however, is missing from our current understanding. Using NMR spectroscopy and analytical ultracentrifugation, we show that phosphorylation destabilizes the self-associating Leu-rich helix 30 amino-acids distant from the phosphorylation site. NMR and gel shift assays demonstrate that RNA binding by the linker is dampened by phosphorylation, whereas RNA binding to the full-length protein is not significantly affected presumably due to retained strong interactions with the primary RNA-binding domain. Introducing a switchable self-associating domain to replace the Leu-rich helix confirms the importance of linker self-association to droplet formation and suggests that phosphorylation not only increases solubility of the positively charged elongated Ser/Arg region as observed in other RNA-binding proteins but can also inhibit self-association of the Leu-rich helix. These data highlight the effect of phosphorylation both at local sites and at a distant self-associating hydrophobic helix in regulating liquid-liquid phase separation of the entire protein.
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Affiliation(s)
- Hannah Stuwe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | | | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Sahana Shah
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
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47
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Xiong B, Yang C, Yang X, Luo S, Li S, Chen C, He K, Nie L, Li P, Li S, Huang H, Liu J, Zhang Z, Xie Y, Zou L, Yang X. Arctigenin derivative A-1 ameliorates motor dysfunction and pathological manifestations in SOD1 G93A transgenic mice via the AMPK/SIRT1/PGC-1α and AMPK/SIRT1/IL-1β/NF-κB pathways. CNS Neurosci Ther 2024; 30:e14692. [PMID: 38872258 PMCID: PMC11176200 DOI: 10.1111/cns.14692] [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: 10/29/2023] [Revised: 02/15/2024] [Accepted: 03/10/2024] [Indexed: 06/15/2024] Open
Abstract
AIM Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disease characterized by progressive death of upper and lower motor neurons, leading to generalized muscle atrophy, paralysis, and even death. Mitochondrial damage and neuroinflammation play key roles in the pathogenesis of ALS. In the present study, the efficacy of A-1, a derivative of arctigenin with AMP-activated protein kinase (AMPK) and silent information regulator 1 (SIRT1) activation for ALS, was investigated. METHODS A-1 at 33.3 mg/kg was administrated in SOD1G93A transgenic mice orally from the 13th week for a 6-week treatment period. Motor ability was assessed before terminal anesthesia. Muscle atrophy and fibrosis, motor neurons, astrocytes, and microglia in the spinal cord were evaluated by H&E, Masson, Sirius Red, Nissl, and immunohistochemistry staining. Protein expression was detected with proteomics analysis, Western blotting, and ELISA. Mitochondrial adenosine triphosphate (ATP) and malondialdehyde (MDA) levels were measured using an assay kit. RESULTS A-1 administration in SOD1G93A mice enhanced mobility, decreased skeletal muscle atrophy and fibrosis, mitigated loss of spinal motor neurons, and reduced glial activation. Additionally, A-1 treatment improved mitochondrial function, evidenced by elevated ATP levels and increased expression of key mitochondrial-related proteins. The A-1 treatment group showed decreased levels of IL-1β, pIκBα/IκBα, and pNF-κB/NF-κB. CONCLUSIONS A-1 treatment reduced motor neuron loss, improved gastrocnemius atrophy, and delayed ALS progression through the AMPK/SIRT1/PGC-1α pathway, which promotes mitochondrial biogenesis. Furthermore, the AMPK/SIRT1/IL-1β/NF-κB pathway exerted neuroprotective effects by reducing neuroinflammation. These findings suggest A-1 as a promising therapeutic approach for ALS.
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Affiliation(s)
- Bocheng Xiong
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Chao Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Xiao Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Song Luo
- Department of NeurologyThe First Affiliated Hospital of Bengbu Medical UniversityBengbuChina
- Department of NeurologyShenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdongChina
| | - Shangming Li
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Chongyang Chen
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Kaiwu He
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Lulin Nie
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Peimao Li
- Medical LaboratoryShenzhen Prevention and Treatment Center for Occupational DiseasesShenzhenChina
| | - Shupeng Li
- State Key Laboratory of OncogenomicsSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate SchoolShenzhenChina
| | - Haiyan Huang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Jianjun Liu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Zaijun Zhang
- Institute of New Drug Research, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of ChinaJinan UniversityGuangzhouChina
| | - Yongmei Xie
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for BiotherapySichuan UniversityChengduChina
| | - Liangyu Zou
- Department of NeurologyShenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), ShenzhenGuangdongChina
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020‐2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
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Lee K, Ku J, Ku D, Kim Y. Inverted Alu repeats: friends or foes in the human transcriptome. Exp Mol Med 2024; 56:1250-1262. [PMID: 38871814 PMCID: PMC11263572 DOI: 10.1038/s12276-024-01177-3] [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: 10/09/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/15/2024] Open
Abstract
Alu elements are highly abundant primate-specific short interspersed nuclear elements that account for ~10% of the human genome. Due to their preferential location in gene-rich regions, especially in introns and 3' UTRs, Alu elements can exert regulatory effects on the expression of both host and neighboring genes. When two Alu elements with inverse orientations are positioned in close proximity, their transcription results in the generation of distinct double-stranded RNAs (dsRNAs), known as inverted Alu repeats (IRAlus). IRAlus are key immunogenic self-dsRNAs and post-transcriptional cis-regulatory elements that play a role in circular RNA biogenesis, as well as RNA transport and stability. Recently, IRAlus dsRNAs have emerged as regulators of transcription and activators of Z-DNA-binding proteins. The formation and activity of IRAlus can be modulated through RNA editing and interactions with RNA-binding proteins, and misregulation of IRAlus has been implicated in several immune-associated disorders. In this review, we summarize the emerging functions of IRAlus dsRNAs, the regulatory mechanisms governing IRAlus activity, and their relevance in the pathogenesis of human diseases.
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Affiliation(s)
- Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury (KIB), Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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50
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Murage B, Tan H, Mashimo T, Jackson M, Skehel PA. Spinal cord neurone loss and foot placement changes in a rat knock-in model of amyotrophic lateral sclerosis Type 8. Brain Commun 2024; 6:fcae184. [PMID: 38846532 PMCID: PMC11154649 DOI: 10.1093/braincomms/fcae184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 04/10/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Amyotrophic lateral sclerosis is an age-dependent cell type-selective degenerative disease. Genetic studies indicate that amyotrophic lateral sclerosis is part of a spectrum of disorders, ranging from spinal muscular atrophy to frontotemporal dementia that share common pathological mechanisms. Amyotrophic lateral sclerosis Type 8 is a familial disease caused by mis-sense mutations in VAPB. VAPB is localized to the cytoplasmic surface of the endoplasmic reticulum, where it serves as a docking point for cytoplasmic proteins and mediates inter-organelle interactions with the endoplasmic reticulum membrane. A gene knock-in model of amyotrophic lateral sclerosis Type 8 based on the VapBP56S mutation and VapB gene deletion has been generated in rats. These animals display a range of age-dependent phenotypes distinct from those previously reported in mouse models of amyotrophic lateral sclerosis Type 8. A loss of motor neurones in VapBP56S/+ and VapBP56S/P56S animals is indicated by a reduction in the number of large choline acetyl transferase-staining cells in the spinal cord. VapB-/- animals exhibit a relative increase in cytoplasmic TDP-43 levels compared with the nucleus, but no large protein aggregates. Concomitant with these spinal cord pathologies VapBP56S/+ , VapBP56S/P56S and VapB-/- animals exhibit age-dependent changes in paw placement and exerted pressures when traversing a CatWalk apparatus, consistent with a somatosensory dysfunction. Extramotor dysfunction is reported in half the cases of motor neurone disease, and this is the first indication of an associated sensory dysfunction in a rodent model of amyotrophic lateral sclerosis. Different rodent models may offer complementary experimental platforms with which to understand the human disease.
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Affiliation(s)
- Brenda Murage
- Centre for Discovery Brain Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
- Euan MacDonald Centre for MND Research, Edinburgh University, Edinburgh EH16 4SB, UK
| | - Han Tan
- Centre for Discovery Brain Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mandy Jackson
- Centre for Discovery Brain Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
- Euan MacDonald Centre for MND Research, Edinburgh University, Edinburgh EH16 4SB, UK
| | - Paul A Skehel
- Centre for Discovery Brain Sciences, Edinburgh University, Edinburgh EH8 9XD, UK
- Euan MacDonald Centre for MND Research, Edinburgh University, Edinburgh EH16 4SB, UK
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