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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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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 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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3
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Liu K, Tao Y, Zhao Q, Xia W, Li X, Zhang S, Yao Y, Xiang H, Han C, Tan L, Sun B, Li D, Li A, Liu C. Binding adaptability of chemical ligands to polymorphic α-synuclein amyloid fibrils. Proc Natl Acad Sci U S A 2024; 121:e2321633121. [PMID: 39172784 DOI: 10.1073/pnas.2321633121] [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: 12/08/2023] [Accepted: 07/17/2024] [Indexed: 08/24/2024] Open
Abstract
α-synuclein (α-syn) assembles into structurally distinct fibril polymorphs seen in different synucleinopathies, such as Parkinson's disease and multiple system atrophy. Targeting these unique fibril structures using chemical ligands holds diagnostic significance for different disease subtypes. However, the molecular mechanisms governing small molecules interacting with different fibril polymorphs remain unclear. Here, we investigated the interactions of small molecules belonging to four distinct scaffolds, with different α-syn fibril polymorphs. Using cryo-electron microscopy, we determined the structures of these molecules when bound to the fibrils formed by E46K mutant α-syn and compared them to those bound with wild-type α-syn fibrils. Notably, we observed that these ligands exhibit remarkable binding adaptability, as they engage distinct binding sites across different fibril polymorphs. While the molecular scaffold primarily steered the binding locations and geometries on specific sites, the conjugated functional groups further refined this adaptable binding by fine-tuning the geometries and binding sites. Overall, our finding elucidates the adaptability of small molecules binding to different fibril structures, which sheds light on the diagnostic tracer and drug developments tailored to specific pathological fibril polymorphs.
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Affiliation(s)
- Kaien Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qinyue Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shenqing Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuxuan Yao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ang Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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4
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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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Zampar S, Di Gregorio SE, Grimmer G, Watts JC, Ingelsson M. "Prion-like" seeding and propagation of oligomeric protein assemblies in neurodegenerative disorders. Front Neurosci 2024; 18:1436262. [PMID: 39161653 PMCID: PMC11330897 DOI: 10.3389/fnins.2024.1436262] [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: 05/21/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
Intra- or extracellular aggregates of proteins are central pathogenic features in most neurodegenerative disorders. The accumulation of such proteins in diseased brains is believed to be the end-stage of a stepwise aggregation of misfolded monomers to insoluble cross-β fibrils via a series of differently sized soluble oligomers/protofibrils. Several studies have shown how α-synuclein, amyloid-β, tau and other amyloidogenic proteins can act as nucleating particles and thereby share properties with misfolded forms, or strains, of the prion protein. Although the roles of different protein assemblies in the respective aggregation cascades remain unclear, oligomers/protofibrils are considered key pathogenic species. Numerous observations have demonstrated their neurotoxic effects and a growing number of studies have indicated that they also possess seeding properties, enabling their propagation within cellular networks in the nervous system. The seeding behavior of oligomers differs between the proteins and is also affected by various factors, such as size, shape and epitope presentation. Here, we are providing an overview of the current state of knowledge with respect to the "prion-like" behavior of soluble oligomers for several of the amyloidogenic proteins involved in neurodegenerative diseases. In addition to providing new insight into pathogenic mechanisms, research in this field is leading to novel diagnostic and therapeutic opportunities for neurodegenerative diseases.
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Affiliation(s)
- Silvia Zampar
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Sonja E. Di Gregorio
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Gustavo Grimmer
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Joel C. Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Martin Ingelsson
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Public Health/Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Müller KJ, Schmidbauer ML, Schönecker S, Kamm K, Pelz JO, Holzapfel K, Papadopoulou M, Bakola E, Tsivgoulis G, Naumann M, Hermann A, Walter U, Dimitriadis K, Reilich P, Schöberl F. Diagnostic accuracy and confounders of vagus nerve ultrasound in amyotrophic lateral sclerosis-a single-center case series and pooled individual patient data meta-analysis. J Neurol 2024:10.1007/s00415-024-12601-z. [PMID: 39085618 DOI: 10.1007/s00415-024-12601-z] [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: 06/09/2024] [Revised: 07/11/2024] [Accepted: 07/20/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Several single-center studies proposed utility of vagus nerve (VN) ultrasound for detecting disease severity, autonomic dysfunction, and bulbar phenotype in amyotrophic lateral sclerosis (ALS). However, the resulting body of literature shows opposing results, leaving considerable uncertainty on the clinical benefits of VN ultrasound in ALS. METHODS Relevant studies were identified up to 04/2024 and individual patient data (IPD) obtained from the respective authors were pooled with a so far unpublished cohort (from Munich). An IPD meta-analysis of 109 patients with probable or definite ALS (El Escorial criteria) and available VN cross-sectional area (CSA) was performed, with age, sex, ALS Functional Rating Scale-revised (ALSFRS-R), disease duration, and bulbar phenotype as independent variables. RESULTS Mean age was 65 years (± 12) and 47% of patients (± 12) had bulbar ALS. Mean ALSFRS-R was 38 (± 7), and mean duration was 18 months (± 18). VN atrophy was highly prevalent [left: 67% (± 5), mean CSA 1.6mm2 (± 0.6); right: 78% (± 21), mean CSA 1.8 mm2 (± 0.7)]. VN CSA correlated with disease duration (mean slope: left - 0.01; right - 0.01), but not with ALSFRS-R (mean slope: left 0.004; mean slope: right - 0.002). Test accuracy for phenotyping bulbar vs. non-bulbar ALS was poor (summary receiver operating characteristic area under the curve: left 0.496; right 0.572). CONCLUSION VN atrophy in ALS is highly prevalent and correlates with disease duration, but not with ALSFRS-R. VN CSA is insufficient to differentiate bulbar from non-bulbar ALS phenotypes. Further studies are warranted to analyze the link between VN atrophy, autonomic impairment, and survival in ALS.
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Affiliation(s)
- Katharina J Müller
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany
| | - Moritz L Schmidbauer
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany
| | - Sonja Schönecker
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany
| | - Katharina Kamm
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany
| | - Johann O Pelz
- Department of Neurology, Leipzig University Hospital, Leipzig, Germany
| | - Korbinian Holzapfel
- Department of Neurology and Clinical Neurophysiology, University of Augsburg, Augsburg, Germany
| | - Marianna Papadopoulou
- Department of Physiotherapy, Laboratory of Neuromuscular and Cardiovascular Study of Motion, University of West Attica, Athens, Greece
| | - Eleni Bakola
- Second Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Markus Naumann
- Department of Neurology and Clinical Neurophysiology, University of Augsburg, Augsburg, Germany
| | - Andreas Hermann
- Deutsches Zentrum Für Neurodegenerative, Erkrankungen Rostock/Greifswald, Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock, Rostock University Medical Center, Rostock, Germany
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, Rostock University Medical Center, Rostock, Germany
| | - Uwe Walter
- Deutsches Zentrum Für Neurodegenerative, Erkrankungen Rostock/Greifswald, Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock, Rostock University Medical Center, Rostock, Germany
- Department of Neurology, Rostock University Medical Center, Rostock, Germany
| | - Konstantinos Dimitriadis
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany
| | - Peter Reilich
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany
| | - Florian Schöberl
- Department of Neurology With Friedrich Baur Institute, LMU University Hospital, LMU Munich, Munich, Germany.
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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] [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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Rowe RK, Schulz P, He P, Mannino GS, Opp MR, Sierks MR. Acute sleep deprivation in mice generates protein pathology consistent with neurodegenerative diseases. Front Neurosci 2024; 18:1436966. [PMID: 39114483 PMCID: PMC11303328 DOI: 10.3389/fnins.2024.1436966] [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: 05/22/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Insufficient or disturbed sleep is strongly associated with adverse health conditions, including various neurodegenerative disorders. While the relationship between sleep and neurodegenerative disease is likely bidirectional, sleep disturbances often predate the onset of other hallmark clinical symptoms. Neuronal waste clearance is significantly more efficient during sleep; thus, disturbed sleep may lead to the accumulation of neuronal proteins that underlie neurodegenerative diseases. Key pathological features of neurodegenerative diseases include an accumulation of misfolded or misprocessed variants of amyloid beta (Aβ), tau, alpha synuclein (α-syn), and TarDNA binding protein 43 (TDP-43). While the presence of fibrillar protein aggregates of these neuronal proteins are characteristic of neurodegenerative diseases, the presence of small soluble toxic oligomeric variants of these different proteins likely precedes the formation of the hallmark aggregates. Methods We hypothesized that sleep deprivation would lead to accumulation of toxic oligomeric variants of Aβ, tau, α-syn, and TDP-43 in brain tissue of wild-type mice. Adult mice were subjected to 6 h of sleep deprivation (zeitgeber 0-6) for 5 consecutive days or were left undisturbed as controls. Following sleep deprivation, brains were collected, and protein pathology was assessed in multiple brain regions using an immunostain panel of reagents selectively targeting neurodegenerative disease-related variants of Aβ, tau, α-syn, and TDP-43. Results Overall, sleep deprivation elevated levels of all protein variants in at least one of the brain regions of interest. The reagent PDTDP, targeting a TDP-43 variant present in Parkinson's disease, was elevated throughout the brain. The cortex, caudoputamen, and corpus callosum brain regions showed the highest accumulation of pathology following sleep deprivation. Discussion These data provide a direct mechanistic link between sleep deprivation, and the hallmark protein pathologies of neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Rachel K. Rowe
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, United States
| | - Philip Schulz
- Chemical Engineering, The School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Ping He
- Chemical Engineering, The School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Grant S. Mannino
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, United States
| | - Mark R. Opp
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, United States
| | - Michael R. Sierks
- Chemical Engineering, The School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
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Lv G, Sayles NM, Huang Y, Mancinelli CD, McAvoy K, Shneider NA, Manfredi G, Kawamata H, Eliezer D. Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604174. [PMID: 39091724 PMCID: PMC11291021 DOI: 10.1101/2024.07.18.604174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
CHCHD10 is mutated in rare cases of FTD and ALS and aggregates in mouse models of disease. Here we show that the disordered N-terminal domain of CHCHD10 forms amyloid fibrils and report their cryoEM structure. Disease-associated mutations cannot be accommodated by the WT fibril structure, while sequence differences between CHCHD10 and CHCHD2 are tolerated, explaining the co-aggregation of the two proteins and linking CHCHD10 and CHCHD2 amyloid fibrils to neurodegeneration.
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Affiliation(s)
- Guohua Lv
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, United States
| | - Nicole M Sayles
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 E 61 Street, New York, NY 10065, United States
| | - Yun Huang
- Department of Physiology & Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Chiara D Mancinelli
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, United States
| | - Kevin McAvoy
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 E 61 Street, New York, NY 10065, United States
| | - Neil A Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, 630 W 168 Street, New York, NY 10032
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 E 61 Street, New York, NY 10065, United States
| | - Hibiki Kawamata
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 E 61 Street, New York, NY 10065, United States
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10021, United States
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 E 61 Street, New York, NY 10065, United States
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10
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Todd TW, Islam NN, Cook CN, Caulfield TR, Petrucelli L. Cryo-EM structures of pathogenic fibrils and their impact on neurodegenerative disease research. Neuron 2024; 112:2269-2288. [PMID: 38834068 PMCID: PMC11257806 DOI: 10.1016/j.neuron.2024.05.012] [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: 08/22/2023] [Revised: 03/13/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Neurodegenerative diseases are commonly associated with the formation of aberrant protein aggregates within the brain, and ultrastructural analyses have revealed that the proteins within these inclusions often assemble into amyloid filaments. Cryoelectron microscopy (cryo-EM) has emerged as an effective method for determining the near-atomic structure of these disease-associated filamentous proteins, and the resulting structures have revolutionized the way we think about aberrant protein aggregation and propagation during disease progression. These structures have also revealed that individual fibril conformations may dictate different disease conditions, and this newfound knowledge has improved disease modeling in the lab and advanced the ongoing pursuit of clinical tools capable of distinguishing and targeting different pathogenic entities within living patients. In this review, we summarize some of the recently developed cryo-EM structures of ex vivo α-synuclein, tau, β-amyloid (Aβ), TAR DNA-binding protein 43 (TDP-43), and transmembrane protein 106B (TMEM106B) fibrils and discuss how these structures are being leveraged toward mechanistic research and therapeutic development.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Naeyma N Islam
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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11
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Rizuan A, Shenoy J, Mohanty P, dos Passos PMS, Mercado Ortiz JF, Bai L, Viswanathan R, Wang SH, Johnson V, Mamede LD, Ayala YM, Ghirlando R, Mittal J, Fawzi NL. Structural details of helix-mediated TDP-43 C-terminal domain multimerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602258. [PMID: 39005345 PMCID: PMC11245101 DOI: 10.1101/2024.07.05.602258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The primarily disordered C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43), a key nuclear protein in RNA metabolism, forms neuronal inclusions in several neurodegenerative diseases. A conserved region (CR, spanning residues 319-341) in CTD forms transient helix-helix contacts important for its higher-order oligomerization and function that are disrupted by ALS-associated mutations. However, the structural details of CR assembly and the explanation for several ALS-associated variants' impact on phase separation and function remain unclear due to challenges in analyzing the dynamic association of TDP-43 CTD using traditional structural biology approaches. By employing an integrative approach, combining biophysical experiments, biochemical assays, AlphaFold2-Multimer (AF2-Multimer), and atomistic simulations, we generated structural models of helical oligomerization of TDP-43 CR. Using NMR, we first established that the native state of TDP-43 CR under physiological conditions is α-helical. Next, alanine scanning mutagenesis revealed that while hydrophobic residues in the CR are important for CR assembly, phase separation and TDP-43 nuclear retention function, polar residues down regulate these processes. Finally, pairing AF2-Multimer modeling with AAMD simulations indicated that dynamic, oligomeric assemblies of TDP-43 that are stabilized by a methionine-rich core with specific contributions from a tryptophan/leucine pair. In conclusion, our results advance the structural understanding of the mechanisms driving TDP-43 function and provide a window into the initial stages of its conversion into pathogenic aggregates.
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Affiliation(s)
- Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Patricia M. S. dos Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - José F. Mercado Ortiz
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Leanna Bai
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Renjith Viswanathan
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Victoria Johnson
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Lohany D. Mamede
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Yuna M. Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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12
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Morelli C, Faltova L, Capasso Palmiero U, Makasewicz K, Papp M, Jacquat RPB, Pinotsi D, Arosio P. RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates. Nat Chem 2024; 16:1052-1061. [PMID: 38472406 PMCID: PMC11230912 DOI: 10.1038/s41557-024-01467-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Several RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein-RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid-protein interactions affect the kinetics and molecular pathways of amyloid formation.
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Affiliation(s)
- Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Raphaël P B Jacquat
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zürich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland.
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13
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Arseni D, Nonaka T, Jacobsen MH, Murzin AG, Cracco L, Peak-Chew SY, Garringer HJ, Kawakami I, Suzuki H, Onaya M, Saito Y, Murayama S, Geula C, Vidal R, Newell KL, Mesulam M, Ghetti B, Hasegawa M, Ryskeldi-Falcon B. Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP Type C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600403. [PMID: 38979278 PMCID: PMC11230283 DOI: 10.1101/2024.06.25.600403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Neurodegenerative diseases are characterised by the abnormal filamentous assembly of specific proteins in the central nervous system 1 . Human genetic studies established a causal role for protein assembly in neurodegeneration 2 . However, the underlying molecular mechanisms remain largely unknown, which is limiting progress in developing clinical tools for these diseases. Recent advances in electron cryo-microscopy (cryo-EM) have enabled the structures of the protein filaments to be determined from patient brains 1 . All diseases studied to date have been characterised by the self-assembly of a single intracellular protein in homomeric amyloid filaments, including that of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) Types A and B 3,4 . Here, we used cryo-EM to determine filament structures from the brains of individuals with FTLD-TDP Type C, one of the most common forms of sporadic FTLD-TDP. Unexpectedly, the structures revealed that a second protein, annexin A11 (ANXA11), co-assembles with TDP-43 in heteromeric amyloid filaments. The ordered filament fold is formed by TDP-43 residues G282/284-N345 and ANXA11 residues L39-L74 from their respective low-complexity domains (LCDs). Regions of TDP-43 and ANXA11 previously implicated in protein-protein interactions form an extensive hydrophobic interface at the centre of the filament fold. Immunoblots of the filaments revealed that the majority of ANXA11 exists as a ∼22 kDa N-terminal fragment (NTF) lacking the annexin core domain. Immunohistochemistry of brain sections confirmed the co-localisation of ANXA11 and TDP-43 in inclusions, redefining the histopathology of FTLD-TDP Type C. This work establishes a central role for ANXA11 in FTLD-TDP Type C. The unprecedented formation of heteromeric amyloid filaments in human brain revises our understanding of amyloid assembly and may be of significance for the pathogenesis of neurodegenerative diseases.
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14
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Kitamura A, Fujimoto A, Kawashima R, Lyu Y, Sasaki K, Hamada Y, Moriya K, Kurata A, Takahashi K, Brielmann R, Bott LC, Morimoto RI, Kinjo M. Hetero-oligomerization of TDP-43 carboxy-terminal fragments with cellular proteins contributes to proteotoxicity. Commun Biol 2024; 7:743. [PMID: 38902525 PMCID: PMC11190292 DOI: 10.1038/s42003-024-06410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
Carboxy terminal fragments (CTFs) of TDP-43 contain an intrinsically disordered region (IDR) and form cytoplasmic condensates containing amyloid fibrils. Such condensates are toxic and associated with pathogenicity in amyotrophic lateral sclerosis. However, the molecular details of how the domain of TDP-43 CTFs leads to condensation and cytotoxicity remain elusive. Here, we show that truncated RNA/DNA-recognition motif (RRM) at the N-terminus of TDP-43 CTFs leads to the structural transition of the IDR, whereas the IDR itself of TDP-43 CTFs is difficult to assemble even if they are proximate intermolecularly. Hetero-oligomers of TDP-43 CTFs that have recruited other proteins are more toxic than homo-oligomers, implicating loss-of-function of the endogenous proteins by such oligomers is associated with cytotoxicity. Furthermore, such toxicity of TDP-43 CTFs was cell-nonautonomously affected in the nematodes. Therefore, misfolding and oligomeric characteristics of the truncated RRM at the N-terminus of TDP-43 CTFs define their condensation properties and toxicity.
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Affiliation(s)
- Akira Kitamura
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan.
- PRIME, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, 100-0004, Japan.
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan.
| | - Ai Fujimoto
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Rei Kawashima
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Yidan Lyu
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kotetsu Sasaki
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Yuta Hamada
- Laboratory of Cellular and Molecular Sciences, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kanami Moriya
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Ayumi Kurata
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Kazuho Takahashi
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
| | - Reneé Brielmann
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Laura C Bott
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Richard I Morimoto
- Department of Molecular Bioscience, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, 60208, USA
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, N21W11, Kita-ku, Sapporo, 001-0021, Japan
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15
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Bacioglu M, Schweighauser M, Gray D, Lövestam S, Katsinelos T, Quaegebeur A, van Swieten J, Jaunmuktane Z, Davies SW, Scheres SHW, Goedert M, Ghetti B, Spillantini MG. Cleaved TMEM106B forms amyloid aggregates in central and peripheral nervous systems. Acta Neuropathol Commun 2024; 12:99. [PMID: 38886865 PMCID: PMC11181561 DOI: 10.1186/s40478-024-01813-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 06/01/2024] [Indexed: 06/20/2024] Open
Abstract
Filaments made of residues 120-254 of transmembrane protein 106B (TMEM106B) form in an age-dependent manner and can be extracted from the brains of neurologically normal individuals and those of subjects with a variety of neurodegenerative diseases. TMEM106B filament formation requires cleavage at residue 120 of the 274 amino acid protein; at present, it is not known if residues 255-274 form the fuzzy coat of TMEM106B filaments. Here we show that a second cleavage appears likely, based on staining with an antibody raised against residues 263-274 of TMEM106B. We also show that besides the brain TMEM106B inclusions form in dorsal root ganglia and spinal cord, where they were mostly found in non-neuronal cells. We confirm that in the brain, inclusions were most abundant in astrocytes. No inclusions were detected in heart, liver, spleen or hilar lymph nodes. Based on their staining with luminescent conjugated oligothiophenes, we confirm that TMEM106B inclusions are amyloids. By in situ immunoelectron microscopy, TMEM106B assemblies were often found in structures resembling endosomes and lysosomes.
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Affiliation(s)
- Mehtap Bacioglu
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Derrick Gray
- IUSM Center for Electron Microscopy (ICEM), Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sofia Lövestam
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Annelies Quaegebeur
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust and the Cambridge Brain Bank, Cambridge, UK
| | - John van Swieten
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Zane Jaunmuktane
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Stephen W Davies
- Department of Cell and Developmental Biology, University College, London, UK
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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16
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Glynn C, Rodriguez JA, Hyman BT. The structural line between prion and "prion-like": Insights from prion protein and tau. Curr Opin Neurobiol 2024; 86:102857. [PMID: 38489865 PMCID: PMC11162956 DOI: 10.1016/j.conb.2024.102857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/15/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
The concept of 'prion-like' behavior has emerged in the study of diseases involving protein misfolding where fibrillar structures, called amyloids, self-propagate and induce disease in a fashion similar to prions. From a biological standpoint, in order to be considered 'prion-like,' a protein must traverse cells and tissues and further propagate via a templated conformational change. Since 2017, cryo-electron microscopy structures from patient-derived 'prion-like' amyloids, in particular tau, have been presented and revealed structural similarities shared across amyloids. Since 2021, cryo-EM structures from prions of known infectivity have been added to the ex vivo amyloid structure family. In this review, we discuss current proposals for the 'prion-like' mechanisms of spread for tau and prion protein as well as discuss different influencers on structures of aggregates from tauopathies and prion diseases. Lastly, we discuss some of the current hypotheses for what may distinguish structures that are 'prion-like' from transmissible prion structures.
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Affiliation(s)
- Calina Glynn
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA.
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17
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024; 26:851-858. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [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: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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18
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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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19
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Yan X, Kuster D, Mohanty P, Nijssen J, Pombo-García K, Rizuan A, Franzmann TM, Sergeeva A, Passos PM, George L, Wang SH, Shenoy J, Danielson HL, Honigmann A, Ayala YM, Fawzi NL, Mittal J, Alberti S, Hyman AA. Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576837. [PMID: 38328053 PMCID: PMC10849624 DOI: 10.1101/2024.01.23.576837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cytosolic aggregation of the nuclear protein TDP-43 is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43 enriched phase within stress granules, which subsequently transitions into pathological aggregates. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We conclude that up-concentration inside condensates and simultaneous exposure to environmental stress could be a general pathway for protein aggregation, with intra-condensate demixing constituting a key intermediate step.
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Affiliation(s)
- Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
| | - David Kuster
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
- These authors contributed equally
| | - Jik Nijssen
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- These authors contributed equally
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
| | - Titus M. Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Aleksandra Sergeeva
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Patricia M. Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Leah George
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Helen L. Danielson
- Center for Biomedical Engineering, Brown University; Providence, RI 02912; USA
| | - Alf Honigmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Yuna M. Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University; St. Louis, MO 63104; USA
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University; Providence, RI 02912; USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University; College Station, TX 77843; USA
- Department of Chemistry, Texas A&M University; College Station, TX 77843; USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University; College Station, TX 77843; USA
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden; Dresden, Saxony, 01307; Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG); Dresden, Saxony, 01307; Germany
- Lead contact
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20
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Fernandez-Ramirez MDC, Nguyen BA, Singh V, Afrin S, Evers B, Basset P, Wang L, Pękała M, Ahmed Y, Singh P, Canepa J, Wosztyl A, Li Y, Saelices L. Multi-organ structural homogeneity of amyloid fibrils in ATTRv-T60A amyloidosis patients, revealed by Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594218. [PMID: 38798519 PMCID: PMC11118364 DOI: 10.1101/2024.05.14.594218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
ATTR amyloidosis is a degenerative disorder characterized by the systemic deposition of the protein transthyretin. These amyloid aggregates of transthyretin (ATTR) can deposit in different parts of the body causing diverse clinical manifestations. Our laboratory aims to investigate a potential relationship between the different genotypes, organ of deposition, clinical phenotypes, and the structure of ATTR fibrils. Using cryo-electron microscopy, we have recently described how the neuropathic related mutations ATTRv-I84S and ATTRv-V122∆ can drive structural polymorphism in ex vivo fibrils. Here we question whether the mutation ATTRv-T60A, that commonly triggers cardiac and neuropathic symptoms, has a similar effect. To address this question, we extracted and determined the structure of ATTR-T60A fibrils from multiple organs (heart, thyroid, kidney, and liver) from the same patient and from the heart of two additional patients. We have found a consistent conformation among all the fibril structures, acquiring the "closed-gate morphology" previously found in ATTRwt and others ATTRv related to cardiac or mixed manifestations. The closed-gate morphology is composed by two segments of the protein that interact together forming a polar channel, where the residues glycine 57 to isoleucine 68 act as a gate of the polar cavity. Our study indicates that ATTR-T60A fibrils present in peripheral organs adopt the same structural conformation in all patients, regardless of the organ of deposition.
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Affiliation(s)
- Maria del Carmen Fernandez-Ramirez
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Binh A. Nguyen
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Virender Singh
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Shumaila Afrin
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Bret Evers
- Department of Pathology, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Parker Basset
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Lanie Wang
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maja Pękała
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Yasmin Ahmed
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Preeti Singh
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Jacob Canepa
- Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aleksandra Wosztyl
- Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lorena Saelices
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
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21
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Ahmed Y, Nguyen BA, Afrin S, Singh V, Evers B, Singh P, Pedretti R, Wang L, Bassett P, del Carmen Fernandez-Ramirez M, Pekala M, Kluve-Beckerman B, Saelices L. Amyloid fibril polymorphism in the heart of an ATTR amyloidosis patient with polyneuropathy attributed to the V122Δ variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593396. [PMID: 38766262 PMCID: PMC11100820 DOI: 10.1101/2024.05.09.593396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
ATTR amyloidosis is a phenotypically heterogeneous disease characterized by the pathological deposition of transthyretin in the form of amyloid fibrils into various organs. ATTR amyloidosis may stem from mutations in variant (ATTRv) amyloidosis, or aging in wild-type (ATTRwt) amyloidosis. ATTRwt generally manifests as a cardiomyopathy phenotype, whereas ATTRv may present as polyneuropathy, cardiomyopathy, or mixed, in combination with many other symptoms deriving from secondary organ involvement. Over 130 different mutational variants of transthyretin have been identified, many of them being linked to specific disease symptoms. Yet, the role of these mutations in the differential disease manifestation remains elusive. Using cryo-electron microscopy, here we structurally characterized fibrils from the heart of an ATTRv patient carrying the V122Δ mutation, predominantly associated with polyneuropathy. Our results show that these fibrils are polymorphic, presenting as both single and double filaments. Our study alludes to a structural connection contributing to phenotypic variation in ATTR amyloidosis, as polymorphism in ATTR fibrils may manifest in patients with predominantly polyneuropathic phenotypes.
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Affiliation(s)
- Yasmin Ahmed
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Binh An Nguyen
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Shumaila Afrin
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Virender Singh
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Bret Evers
- Department of Pathology, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Preeti Singh
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Rose Pedretti
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Lanie Wang
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Parker Bassett
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maria del Carmen Fernandez-Ramirez
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maja Pekala
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Barbara Kluve-Beckerman
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lorena Saelices
- Center for Alzheimer’s and Neurodegenerative Diseases, Department of Biophysics, Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
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22
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Xin J, Huang S, Wen J, Li Y, Li A, Satyanarayanan SK, Yao X, Su H. Drug Screening and Validation Targeting TDP-43 Proteinopathy for Amyotrophic Lateral Sclerosis. Aging Dis 2024:AD.2024.0440. [PMID: 38739934 DOI: 10.14336/ad.2024.0440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) stands as a rare, yet severely debilitating disorder marked by the deterioration of motor neurons (MNs) within the brain and spinal cord, which is accompanied by degenerated corticobulbar/corticospinal tracts and denervation in skeletal muscles. Despite ongoing research efforts, ALS remains incurable, attributed to its intricate pathogenic mechanisms. A notable feature in the pathology of ALS is the prevalence of TAR DNA-binding protein 43 (TDP-43) proteinopathy, detected in approximately 97% of ALS cases, underscoring its significance in the disease's progression. As a result, strategies targeting the aberrant TDP-43 protein have garnered attention as a potential avenue for ALS therapy. This review delves into the existing drug screening systems aimed at TDP-43 proteinopathy and the models employed for drug efficacy validation. It also explores the hurdles encountered in the quest to develop potent medications against TDP-43 proteinopathy, offering insights into the intricacies of drug discovery and development for ALS. Through this comprehensive analysis, the review sheds light on the critical aspects of identifying and advancing therapeutic solutions for ALS.
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Affiliation(s)
- Jiaqi Xin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Sen Huang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Jing Wen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yunhao Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ang Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Senthil Kumaran Satyanarayanan
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong Science Park, Hong Kong, China
| | - Xiaoli Yao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases; National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Huanxing Su
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
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23
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Huettemann P, Mahadevan P, Lempart J, Tse E, Dehury B, Edwards BFP, Southworth DR, Sahoo BR, Jakob U. Amyloid Accelerator Polyphosphate Implicated as the Mystery Density in α-Synuclein Fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592011. [PMID: 38746133 PMCID: PMC11092616 DOI: 10.1101/2024.05.01.592011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Aberrant aggregation of α-Synuclein is the pathological hallmark of a set of neurodegenerative diseases termed synucleinopathies. Recent advances in cryo-electron microscopy have led to the structural determination of the first synucleinopathy-derived α-Synuclein fibrils, which contain a non-proteinaceous, "mystery density" at the core of the protofilaments, hypothesized to be highly negatively charged. Guided by previous studies that demonstrated that polyphosphate (polyP), a universally conserved polyanion, significantly accelerates α-Synuclein fibril formation, we conducted blind docking and molecular dynamics simulation experiments to model the polyP binding site in α-Synuclein fibrils. Here we demonstrate that our models uniformly place polyP into the lysine-rich pocket, which coordinates the mystery density in patient-derived fibrils. Subsequent in vitro studies and experiments in cells revealed that substitution of the two critical lysine residues K43 and K45 leads to a loss of all previously reported effects of polyP binding on α-Synuclein, including stimulation of fibril formation, change in filament conformation and stability as well as alleviation of cytotoxicity. In summary, our study demonstrates that polyP fits the unknown electron density present in in vivo α-Synuclein fibrils and suggests that polyP exerts its functions by neutralizing charge repulsion between neighboring lysine residues.
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24
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Sun X, Li W, Li G, Yang H, Jiang Z, Shen L, Shen Y, Liu Y, Wang G. A novel long non-coding RNA LINC00524 facilitates invasion and metastasis through interaction with TDP43 in breast cancer. J Cell Mol Med 2024; 28:e18275. [PMID: 38568058 PMCID: PMC10989564 DOI: 10.1111/jcmm.18275] [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: 10/12/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024] Open
Abstract
Breast cancer (BC) remains a significant health concern worldwide, with metastasis being a primary contributor to patient mortality. While advances in understanding the disease's progression continue, the underlying mechanisms, particularly the roles of long non-coding RNAs (lncRNAs), are not fully deciphered. In this study, we examined the influence of the lncRNA LINC00524 on BC invasion and metastasis. Through meticulous analyses of TCGA and GEO data sets, we observed a conspicuous elevation of LINC00524 expression in BC tissues. This increased expression correlated strongly with a poorer prognosis for BC patients. A detailed Gene Ontology analysis suggested that LINC00524 likely exerts its effects through RNA-binding proteins (RBPs) mechanisms. Experimentally, LINC00524 was demonstrated to amplify BC cell migration, invasion and proliferation in vitro. Additionally, in vivo tests showed its potent role in promoting BC cell growth and metastasis. A pivotal discovery was LINC00524's interaction with TDP43, which leads to the stabilization of TDP43 protein expression, an element associated with unfavourable BC outcomes. In essence, our comprehensive study illuminates how LINC00524 accelerates BC invasion and metastasis by binding to TDP43, presenting potential avenues for therapeutic interventions.
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Affiliation(s)
- Xianglin Sun
- Department of Physiology and Hypoxic Biomedicine, Institute of Special Environmental MedicineNantong UniversityNantongChina
| | - Wenfeng Li
- Department of Physiology and Hypoxic Biomedicine, Institute of Special Environmental MedicineNantong UniversityNantongChina
| | - Gang Li
- Department of Physiology and Hypoxic Biomedicine, Institute of Special Environmental MedicineNantong UniversityNantongChina
| | - Huan Yang
- Department of Physiology and Hypoxic Biomedicine, Institute of Special Environmental MedicineNantong UniversityNantongChina
| | - Zhenglin Jiang
- Department of Physiology and Hypoxic Biomedicine, Institute of Special Environmental MedicineNantong UniversityNantongChina
| | - Lihua Shen
- Department of PathologyAffiliated Hospital of Nantong UniversityNantongChina
| | | | - Yifei Liu
- Department of PathologyAffiliated Hospital of Nantong UniversityNantongChina
| | - Guohua Wang
- Department of Physiology and Hypoxic Biomedicine, Institute of Special Environmental MedicineNantong UniversityNantongChina
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25
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586202. [PMID: 38585945 PMCID: PMC10996529 DOI: 10.1101/2024.03.21.586202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
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 Ser-to-Asp substitutions at residues S403, S404, S409 and S410 alter the LLPS behavior of TDP-43 LCD. In particular, in contrast to the unmodified protein, the phosphomimetic variants display 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 the TDP-43 in a more complex cellular environment.
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Affiliation(s)
- Raza Haider
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
| | - Brandon Shipley
- Department of Physics, Case Western Reserve University, Cleveland, United States
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, United States
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
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26
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Creekmore BC, Kixmoeller K, Black BE, Lee EB, Chang YW. Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling. Nat Commun 2024; 15:2660. [PMID: 38531877 PMCID: PMC10965902 DOI: 10.1038/s41467-024-47066-1] [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: 09/27/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) allows higher resolution imaging of unfixed cellular samples while preserving architecture, but it requires samples to be vitreous and thin enough for transmission EM. Due to these requirements, cryo-ET has yet to be employed to investigate unfixed, never previously frozen human brain tissue. Here we present a method for generating lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue via plunge-freezing and use xenon plasma focused ion beam (FIB) milling to generate lamellae directly on-grid at variable depth inside the tissue. Lamellae generated in Alzheimer's disease brain tissue reveal intact subcellular structures including components of autophagy and potential pathologic tau fibrils. Furthermore, we reveal intact compact myelin and functional cytoplasmic expansions. These images indicate that plasma FIB milling with cryo-ET may be used to elucidate nanoscale structures within the human brain.
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Affiliation(s)
- Benjamin C Creekmore
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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27
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Salaikumaran M, Gopal PP. Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders. ACS Chem Neurosci 2024; 15:1096-1109. [PMID: 38466778 PMCID: PMC10959110 DOI: 10.1021/acschemneuro.3c00659] [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: 10/12/2023] [Revised: 01/21/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
TDP-43, an essential RNA/DNA-binding protein, is central to the pathology of neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. Pathological mislocalization and aggregation of TDP-43 disrupt RNA splicing, mRNA stability, and mRNA transport, thereby impairing neuronal function and survival. The formation of amyloid-like TDP-43 filaments is largely facilitated by the destabilization of an α-helical segment within the disordered C-terminal region. In this study, we hypothesized that preventing the destabilization of the α-helical domain could potentially halt the growth of these pathological filaments. To explore this, we utilized a range of in silico techniques to design and evaluate peptide-based therapeutics that bind to pathological TDP-43 amyloid-like filament crystal structures and resist β sheet conversion. Our computational approaches, including biophysical and secondary structure property prediction, molecular docking, 3D structure prediction, and molecular dynamics simulations, were used to assess the structure, stability, and binding affinity of these peptides in relation to pathological TDP-43 filaments. The results of our in silico analyses identified a selection of promising peptides which displayed a stable α-helical structure, exhibited an increased number of intramolecular hydrogen bonds within the helical domain, and demonstrated high binding affinities for pathological TDP-43 amyloid-like filaments. Molecular dynamics simulations provided further support for the structural and thermodynamic stability of these peptides, as they exhibited lower root-mean-square deviation and more favorable free energy landscapes over 300 ns. These findings establish α-helical propensity peptides as potential lead molecules for the development of novel therapeutics against TDP-43 aggregation. This structure-based computational approach for the rational design of peptide inhibitors opens a new direction in the search for effective interventions for ALS, FTD, and other related neurodegenerative diseases. The peptides identified as the most promising candidates in this study are currently subject to further testing and validation through both in vitro and in vivo experiments.
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Affiliation(s)
- Muthu
Raj Salaikumaran
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Pallavi P. Gopal
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Program
in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, Connecticut 06520-8055, United States
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28
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Amartumur S, Nguyen H, Huynh T, Kim TS, Woo RS, Oh E, Kim KK, Lee LP, Heo C. Neuropathogenesis-on-chips for neurodegenerative diseases. Nat Commun 2024; 15:2219. [PMID: 38472255 PMCID: PMC10933492 DOI: 10.1038/s41467-024-46554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Developing diagnostics and treatments for neurodegenerative diseases (NDs) is challenging due to multifactorial pathogenesis that progresses gradually. Advanced in vitro systems that recapitulate patient-like pathophysiology are emerging as alternatives to conventional animal-based models. In this review, we explore the interconnected pathogenic features of different types of ND, discuss the general strategy to modelling NDs using a microfluidic chip, and introduce the organoid-on-a-chip as the next advanced relevant model. Lastly, we overview how these models are being applied in academic and industrial drug development. The integration of microfluidic chips, stem cells, and biotechnological devices promises to provide valuable insights for biomedical research and developing diagnostic and therapeutic solutions for NDs.
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Affiliation(s)
- Sarnai Amartumur
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Huong Nguyen
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Thuy Huynh
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Testaverde S Kim
- Center for Integrated Nanostructure Physics (CINAP), Institute for Basic Science (IBS), Suwon, 16419, Korea
| | - Ran-Sook Woo
- Department of Anatomy and Neuroscience, College of Medicine, Eulji University, Daejeon, 34824, Korea
| | - Eungseok Oh
- Department of Neurology, Chungnam National University Hospital, Daejeon, 35015, Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Luke P Lee
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea.
- Harvard Medical School, Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, 94720, USA.
| | - Chaejeong Heo
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, 16419, Korea.
- Center for Integrated Nanostructure Physics (CINAP), Institute for Basic Science (IBS), Suwon, 16419, Korea.
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29
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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30
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Suresh K, Dahal E, Badano A. Synthetic β-sheets mimicking fibrillar and oligomeric structures for evaluation of spectral X-ray scattering technique for biomarker quantification. Cell Biosci 2024; 14:26. [PMID: 38374092 PMCID: PMC10877803 DOI: 10.1186/s13578-024-01208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Archetypical cross-β spines sharpen the boundary between functional and pathological proteins including β-amyloid, tau, α-synuclein and transthyretin are linked to many debilitating human neurodegenerative and non-neurodegenerative amyloidoses. An increased focus on development of pathogenic β-sheet specific fluid and imaging structural biomarkers and conformation-specific monoclonal antibodies in targeted therapies has been recently observed. Identification and quantification of pathogenic oligomers remain challenging for existing neuroimaging modalities. RESULTS We propose two artificial β-sheets which can mimic the nanoscopic structural characteristics of pathogenic oligomers and fibrils for evaluating the performance of a label free, X-ray based biomarker detection and quantification technique. Highly similar structure with elliptical cross-section and parallel cross-β motif is observed among recombinant α-synuclein fibril, Aβ-42 fibril and artificial β-sheet fibrils. We then use these β-sheet models to assess the performance of spectral small angle X-ray scattering (sSAXS) technique for detecting β-sheet structures. sSAXS showed quantitatively accurate detection of antiparallel, cross-β artificial oligomers from a tissue mimicking environment and significant distinction between different oligomer packing densities such as diffuse and dense packings. CONCLUSION The proposed synthetic β-sheet models mimicked the nanoscopic structural characteristics of β-sheets of fibrillar and oligomeric states of Aβ and α-synuclein based on the ATR-FTIR and SAXS data. The tunability of β-sheet proportions and shapes of structural motifs, and the low-cost of these β-sheet models can become useful test materials for evaluating β-sheet or amyloid specific biomarkers in a wide range of neurological diseases. By using the proposed synthetic β-sheet models, our study indicates that the sSAXS has potential to evaluate different stages of β-sheet-enriched structures including oligomers of pathogenic proteins.
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Affiliation(s)
- Karthika Suresh
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA.
| | - Eshan Dahal
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Aldo Badano
- Division of Imaging, Diagnostics, and Software Reliability, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA
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31
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Haider R, Penumutchu S, Boyko S, Surewicz WK. Phosphomimetic substitutions in TDP-43's transiently α-helical region suppress phase separation. Biophys J 2024; 123:361-373. [PMID: 38178578 PMCID: PMC10870169 DOI: 10.1016/j.bpj.2024.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/10/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024] Open
Abstract
Phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) is present within the aggregates of several age-related neurodegenerative disorders, such as amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and Alzheimer's disease, to the point that the presence of phosphorylated TDP-43 is considered a hallmark of some of these diseases. The majority of known TDP-43 phosphorylation sites detected in amyotrophic lateral sclerosis and frontotemporal lobar degeneration patients is located in the low-complexity domain (LCD), the same domain that has been shown to be critical for TDP-43 liquid-liquid phase separation (LLPS). However, the effect of these LCD phosphorylation sites on TDP-43 LLPS has been largely unexplored, and any work that has been done has mainly focused on sites near the C-terminal end of the LCD. Here, we used a phosphomimetic approach to explore the impact of phosphorylation at residues S332 and S333, sites located within the transiently α-helical region of TDP-43 that have been observed to be phosphorylated in disease, on protein LLPS. Our turbidimetry and fluorescence microscopy data demonstrate that these phosphomimetic substitutions greatly suppress LLPS, and solution NMR data strongly suggest that this effect is at least in part due to the loss of α-helical propensity of the phosphomimetic protein variant. We also show that the S332D and S333D substitutions slow TDP-43 LCD droplet aging and fibrillation of the protein. Overall, these findings provide a biophysical basis for understanding the effect of phosphorylation within the transiently α-helical region of TDP-43 LCD on protein LLPS and fibrillation, suggesting that phosphorylation at residues 332 and 333 is not necessarily directly related to the pathogenic process.
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Affiliation(s)
- Raza Haider
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Srinivasa Penumutchu
- Northeast Ohio High Field NMR Facility, Case Western Reserve University, Cleveland, Ohio
| | - Solomiia Boyko
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio.
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32
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Garcia-Pardo J, Ventura S. Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies. Trends Biochem Sci 2024; 49:119-133. [PMID: 37926650 DOI: 10.1016/j.tibs.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Amyloids are implicated in neurodegenerative and systemic diseases, yet they serve important functional roles in numerous organisms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that control central events of RNA biogenesis in normal and diseased cellular conditions. Many of these proteins contain prion-like sequences of low complexity, which not only assemble into functional fibrils in response to cellular cues but can also lead to disease when missense mutations arise in their sequences. Recent advances in cryo-electron microscopy (cryo-EM) have provided unprecedented high-resolution structural insights into diverse amyloid assemblies formed by hnRNPs and structurally related RBPs, including TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Orb2, hnRNPA1, hnRNPA2, and hnRNPDL-2. This review provides a comprehensive overview of these structures and explores their functional and pathological implications.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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33
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Liu Z, Qiang Y, Shan S, Wang S, Song F. Carbon disulfide induces accumulation of TDP-43 in the cytoplasm and mitochondrial dysfunction in rat spinal cords. Cereb Cortex 2024; 34:bhad526. [PMID: 38185999 DOI: 10.1093/cercor/bhad526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/09/2024] Open
Abstract
The relationship between environmental neurotoxicant exposure and neurodegenerative diseases is being extensively investigated. Carbon disulfide, a classic neurotoxicant and prototype of dithiocarbamates fungicides and anti-inflammatory agents, has been detected in urban adults, raising questions about whether exposure to carbon disulfide is associated with a high incidence of neurodegenerative diseases. Here, using rat models and SH-SY5Y cells, we investigated the possible mechanistic linkages between carbon disulfide neurotoxicity and the expression of TDP-43 protein, a marker of amyotrophic lateral sclerosis/frontotemporal lobar degeneration. Our results showed that rats exhibited severe dyskinesia and increased TDP-43 expression in the spinal cord following carbon disulfide exposure. Moreover, carbon disulfide exposure induced abnormal cytoplasmic localization and phosphorylation of TDP-43 in motor neurons. Importantly, carbon disulfide treatment led to the accumulation of TDP-43 in the mitochondria of motor neurons and resulted in subsequent mitochondrial damage, including mitochondrial structural disruption, mitochondrial respiratory chain complex I inhibition, and impaired VCP/p97-dependent mitophagy. In summary, our study provides support for carbon disulfide exposure-mediated TDP-43 mislocalization and mitochondrial dysfunction, contributes to understanding the pathogenesis of environmental neurotoxin-induced neurodegeneration, and provides inspiration for potential therapeutic strategies.
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Affiliation(s)
- Zhidan Liu
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Yalong Qiang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Shulin Shan
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Shuai Wang
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Fuyong Song
- Department of Toxicology and Nutrition, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
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34
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Creekmore BC, Watanabe R, Lee EB. Neurodegenerative Disease Tauopathies. ANNUAL REVIEW OF PATHOLOGY 2024; 19:345-370. [PMID: 37832941 PMCID: PMC11009985 DOI: 10.1146/annurev-pathmechdis-051222-120750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Tauopathies are a diverse group of progressive and fatal neurodegenerative diseases characterized by aberrant tau inclusions in the central nervous system. Tau protein forms pathologic fibrillar aggregates that are typically closely associated with neuronal cell death, leading to varied clinical phenotypes including dementia, movement disorders, and motor neuron disease. In this review, we describe the clinicopathologic features of tauopathies and highlight recent advances in understanding the mechanisms that lead to spread of pathologic aggregates through interconnected neuronal pathways. The cell-to-cell propagation of tauopathy is then linked to posttranslational modifications, tau fibril structural variants, and the breakdown of cellular protein quality control.
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Affiliation(s)
- Benjamin C Creekmore
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Ryohei Watanabe
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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35
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Khalil B, Linsenmeier M, Smith CL, Shorter J, Rossoll W. Nuclear-import receptors as gatekeepers of pathological phase transitions in ALS/FTD. Mol Neurodegener 2024; 19:8. [PMID: 38254150 PMCID: PMC10804745 DOI: 10.1186/s13024-023-00698-1] [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: 06/05/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders on a disease spectrum that are characterized by the cytoplasmic mislocalization and aberrant phase transitions of prion-like RNA-binding proteins (RBPs). The common accumulation of TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), and other nuclear RBPs in detergent-insoluble aggregates in the cytoplasm of degenerating neurons in ALS/FTD is connected to nuclear pore dysfunction and other defects in the nucleocytoplasmic transport machinery. Recent advances suggest that beyond their canonical role in the nuclear import of protein cargoes, nuclear-import receptors (NIRs) can prevent and reverse aberrant phase transitions of TDP-43, FUS, and related prion-like RBPs and restore their nuclear localization and function. Here, we showcase the NIR family and how they recognize cargo, drive nuclear import, and chaperone prion-like RBPs linked to ALS/FTD. We also discuss the promise of enhancing NIR levels and developing potentiated NIR variants as therapeutic strategies for ALS/FTD and related neurodegenerative proteinopathies.
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Affiliation(s)
- Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - Miriam Linsenmeier
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Neuroscience Track, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A..
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A..
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36
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Nguyen BA, Singh V, Afrin S, Yakubovska A, Wang L, Ahmed Y, Pedretti R, Fernandez-Ramirez MDC, Singh P, Pękała M, Cabrera Hernandez LO, Kumar S, Lemoff A, Gonzalez-Prieto R, Sawaya MR, Eisenberg DS, Benson MD, Saelices L. Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy. Nat Commun 2024; 15:581. [PMID: 38233397 PMCID: PMC10794703 DOI: 10.1038/s41467-024-44820-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024] Open
Abstract
ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies.
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Affiliation(s)
- Binh An Nguyen
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Virender Singh
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Shumaila Afrin
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Anna Yakubovska
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Lanie Wang
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Yasmin Ahmed
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Rose Pedretti
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maria Del Carmen Fernandez-Ramirez
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Preeti Singh
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Maja Pękała
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Luis O Cabrera Hernandez
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Siddharth Kumar
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roman Gonzalez-Prieto
- Andalusian Center for Molecular Biology and regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Departmento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Michael R Sawaya
- Department of Biological Chemistry, University of California, Los Angeles, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - David S Eisenberg
- Department of Biological Chemistry, University of California, Los Angeles, Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Merrill Douglas Benson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lorena Saelices
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
- Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
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37
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Yang L, Jasiqi Y, Zettor A, Vadas O, Chiaravalli J, Agou F, Lashuel HA. Effective Inhibition of TDP-43 Aggregation by Native State Stabilization. Angew Chem Int Ed Engl 2024; 63:e202314587. [PMID: 37949836 DOI: 10.1002/anie.202314587] [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: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Preventing the misfolding or aggregation of transactive response DNA binding protein with 43 kDa (TDP-43) is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis and other neurodegenerative diseases. In this work, we provide proof of concept that native state stabilization of TDP-43 is a viable and effective strategy for treating TDP-43 proteinopathies. Firstly, we leveraged the Cryo-EM structures of TDP-43 fibrils to design C-terminal substitutions that disrupt TDP-43 aggregation. Secondly, we showed that these substitutions (S333D/S342D) stabilize monomeric TDP-43 without altering its physiological properties. Thirdly, we demonstrated that binding native oligonucleotide ligands stabilized monomeric TDP-43 and prevented its fibrillization and phase separation in the absence of direct binding to the aggregation-prone C-terminal domain. Fourthly, we showed that the monomeric TDP-43 variant could be induced to aggregate in a controlled manner, which enabled the design and implementation of a high-throughput screening assay to identify native state stabilizers of TDP-43. Altogether, our findings demonstrate that different structural domains in TDP-43 could be exploited and targeted to develop drugs that stabilize the native state of TDP-43 and provide a platform to discover novel drugs to treat TDP-43 proteinopathies.
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Affiliation(s)
- Lixin Yang
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| | - Yllza Jasiqi
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| | - Agnès Zettor
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Université Paris Cité, CNRS, UMR 3523, C2RT, Paris, France
| | - Oscar Vadas
- Protein Platform, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211, Geneva, Switzerland
| | - Jeanne Chiaravalli
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Université Paris Cité, CNRS, UMR 3523, C2RT, Paris, France
| | - Fabrice Agou
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Université Paris Cité, CNRS, UMR 3523, C2RT, Paris, France
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
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38
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Sharma K, Stockert F, Shenoy J, Berbon M, Abdul-Shukkoor MB, Habenstein B, Loquet A, Schmidt M, Fändrich M. Cryo-EM observation of the amyloid key structure of polymorphic TDP-43 amyloid fibrils. Nat Commun 2024; 15:486. [PMID: 38212334 PMCID: PMC10784485 DOI: 10.1038/s41467-023-44489-0] [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: 06/20/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024] Open
Abstract
The transactive response DNA-binding protein-43 (TDP-43) is a multi-facet protein involved in phase separation, RNA-binding, and alternative splicing. In the context of neurodegenerative diseases, abnormal aggregation of TDP-43 has been linked to amyotrophic lateral sclerosis and frontotemporal lobar degeneration through the aggregation of its C-terminal domain. Here, we report a cryo-electron microscopy (cryo-EM)-based structural characterization of TDP-43 fibrils obtained from the full-length protein. We find that the fibrils are polymorphic and contain three different amyloid structures. The structures differ in the number and relative orientation of the protofilaments, although they share a similar fold containing an amyloid key motif. The observed fibril structures differ from previously described conformations of TDP-43 fibrils and help to better understand the structural landscape of the amyloid fibril structures derived from this protein.
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Affiliation(s)
- Kartikay Sharma
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
| | - Fabian Stockert
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Jayakrishna Shenoy
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | | | - Birgit Habenstein
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Antoine Loquet
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
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39
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Tetter S, Arseni D, Murzin AG, Buhidma Y, Peak-Chew SY, Garringer HJ, Newell KL, Vidal R, Apostolova LG, Lashley T, Ghetti B, Ryskeldi-Falcon B. TAF15 amyloid filaments in frontotemporal lobar degeneration. Nature 2024; 625:345-351. [PMID: 38057661 PMCID: PMC10781619 DOI: 10.1038/s41586-023-06801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders1. The pathological hallmarks of FTLD are neuronal inclusions of specific, abnormally assembled proteins2. In the majority of cases the inclusions contain amyloid filament assemblies of TAR DNA-binding protein 43 (TDP-43) or tau, with distinct filament structures characterizing different FTLD subtypes3,4. The presence of amyloid filaments and their identities and structures in the remaining approximately 10% of FTLD cases are unknown but are widely believed to be composed of the protein fused in sarcoma (FUS, also known as translocated in liposarcoma). As such, these cases are commonly referred to as FTLD-FUS. Here we used cryogenic electron microscopy (cryo-EM) to determine the structures of amyloid filaments extracted from the prefrontal and temporal cortices of four individuals with FTLD-FUS. Surprisingly, we found abundant amyloid filaments of the FUS homologue TATA-binding protein-associated factor 15 (TAF15, also known as TATA-binding protein-associated factor 2N) rather than of FUS itself. The filament fold is formed from residues 7-99 in the low-complexity domain (LCD) of TAF15 and was identical between individuals. Furthermore, we found TAF15 filaments with the same fold in the motor cortex and brainstem of two of the individuals, both showing upper and lower motor neuron pathology. The formation of TAF15 amyloid filaments with a characteristic fold in FTLD establishes TAF15 proteinopathy in neurodegenerative disease. The structure of TAF15 amyloid filaments provides a basis for the development of model systems of neurodegenerative disease, as well as for the design of diagnostic and therapeutic tools targeting TAF15 proteinopathy.
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Affiliation(s)
| | - Diana Arseni
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Yazead Buhidma
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liana G Apostolova
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tammaryn Lashley
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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40
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Zhang Y, Xia Y, Sun J. Probiotics and microbial metabolites maintain barrier and neuromuscular functions and clean protein aggregation to delay disease progression in TDP43 mutation mice. Gut Microbes 2024; 16:2363880. [PMID: 38860943 PMCID: PMC11174066 DOI: 10.1080/19490976.2024.2363880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neuromuscular disease. The ALS mice expressing human mutant of transactive response DNA binding protein of 43 kDa (hmTDP43) showed intestinal dysfunction before neuromuscular symptoms. We hypothesize that restoring the intestinal and microbial homeostasis with a bacterial metabolite or probiotics delays the ALS disease onset. We investigate the pathophysiological changes in the intestine and neurons, intestinal and blood-brain barriers, and inflammation during the ALS progression. We then cultured enteric glial cells (EGCs) isolated from TDP43 mice for mechanistic studies. TDP43 mice had significantly decreased intestinal mobility, increased permeability, and weakened muscle, compared with the age-matched wild-type mice. We observed increased hmTDP43 and Glial fibrillary acidic protein (GFAP), and decreased expression of α-smooth muscle actin (α-SMA), tight junction proteins (ZO-1 and Claudin-5) in the colon, spinal cord, and brain in TDP43 mice. TDP43 mice had reduced Butyryl-coenzyme A CoA transferase, decreased butyrate-producing bacteria Butyrivibrio fibrisolvens, and increased Bacteroides fragilis, compared to the WT mice. Serum inflammation cytokines (IL-6, IL-17, and IFN-γ) and LPS were elevated in TDP43 mice. EGCs from TDP43 mice showed aggregation of hmTDP43 associated with increased GFAP and ionized calcium-binding adaptor molecule (IBA1, a microglia marker). TDP43 mice treated with butyrate or probiotic VSL#3 had significantly increased rotarod time, increased intestinal mobility and decreased permeability, compared to the untreated group. Butyrate or probiotics treatment decreased the expression of GFAP, TDP43, and increased α-SMA, ZO-1, and Claudin-5 in the colon, spinal cord, and brain. Also, butyrate or probiotics treatment enhanced the Butyryl-coenzyme A CoA transferase, Butyrivibrio fibrisolvens, and reduced inflammatory cytokines in TDP43 mice. The TDP43 EGCs treated with butyrate or probiotics showed reduced GFAP, IBA1, and TDP43 aggregation. Restoring the intestinal and microbial homeostasis by beneficial bacteria and metabolites provide a potential therapeutic strategy to treat ALS.
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Affiliation(s)
- Yongguo Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
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41
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Fukui Y, Shirakawa H, Kaneko S, Nagayasu K. Wild-Type DCTN1 Suppresses the Aggregation of DCTN1 Mutants Associated with Perry Disease. Biol Pharm Bull 2024; 47:253-258. [PMID: 38267040 DOI: 10.1248/bpb.b23-00828] [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: 01/26/2024]
Abstract
Perry disease, a rare autosomal dominant neurodegenerative disorder, is characterized by parkinsonism, depression or apathy, unexpected weight loss, and central hypoventilation. Genetic analyses have revealed a strong association between point mutations in the dynactin I gene (DCTN1) coding p150glued and Perry disease. Although previous reports have suggested a critical role of p150glued aggregation in Perry disease pathology, whether and how p150glued mutations affect protein aggregation is not fully understood. In this study, we comprehensively investigated the intracellular distribution of the p150glued mutants in HEK293T cells. We further assessed the effect of co-overexpression of the wild-type p150glued protein with mutants on the formation of mutant aggregates. Notably, overexpression of p150glued mutants identified in healthy controls, which is also associated with amyotrophic lateral sclerosis, showed a thread-like cytoplasmic distribution, similar to the wild-type p150glued. In contrast, p150glued mutants in Perry disease and motor neuron disease caused aggregation. In addition, the co-overexpression of the wild-type protein with p150glued mutants in Perry disease suppressed aggregate formation. In contrast, the p150glued aggregation of motor neuron disease mutants was less affected by the wild-type p150glued. Further investigation of the mechanism of aggregate formation, contents of the aggregates, and biological mechanisms of Perry disease could help develop novel therapeutics.
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Affiliation(s)
- Yuto Fukui
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Hisashi Shirakawa
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Shuji Kaneko
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Kazuki Nagayasu
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University
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Lövestam S, Li D, Wagstaff JL, Kotecha A, Kimanius D, McLaughlin SH, Murzin AG, Freund SMV, Goedert M, Scheres SHW. Disease-specific tau filaments assemble via polymorphic intermediates. Nature 2024; 625:119-125. [PMID: 38030728 PMCID: PMC10764278 DOI: 10.1038/s41586-023-06788-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023]
Abstract
Intermediate species in the assembly of amyloid filaments are believed to play a central role in neurodegenerative diseases and may constitute important targets for therapeutic intervention1,2. However, structural information about intermediate species has been scarce and the molecular mechanisms by which amyloids assemble remain largely unknown. Here we use time-resolved cryogenic electron microscopy to study the in vitro assembly of recombinant truncated tau (amino acid residues 297-391) into paired helical filaments of Alzheimer's disease or into filaments of chronic traumatic encephalopathy3. We report the formation of a shared first intermediate amyloid filament, with an ordered core comprising residues 302-316. Nuclear magnetic resonance indicates that the same residues adopt rigid, β-strand-like conformations in monomeric tau. At later time points, the first intermediate amyloid disappears and we observe many different intermediate amyloid filaments, with structures that depend on the reaction conditions. At the end of both assembly reactions, most intermediate amyloids disappear and filaments with the same ordered cores as those from human brains remain. Our results provide structural insights into the processes of primary and secondary nucleation of amyloid assembly, with implications for the design of new therapies.
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Affiliation(s)
| | - David Li
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Abhay Kotecha
- Thermo Fisher Scientific, Eindhoven, The Netherlands
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43
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Forgrave LM, Moon K, Hamden JE, Li Y, Lu P, Foster LJ, Mackenzie IRA, DeMarco ML. Truncated TDP-43 proteoforms diagnostic of frontotemporal dementia with TDP-43 pathology. Alzheimers Dement 2024; 20:103-111. [PMID: 37461300 PMCID: PMC10917011 DOI: 10.1002/alz.13368] [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: 04/12/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 01/18/2024]
Abstract
INTRODUCTION Biomarkers of TDP-43 pathology are needed to distinguish frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP) from phenotypically related disorders. While normal physiological TDP-43 is not a promising biomarker, low-resolution techniques have suggested truncated forms of TDP-43 may be specific to TDP-43 pathology. To advance biomarker efforts for FTLD-TDP, we employed a high-resolution structural technique to characterize TDP-43 post-translational modifications in FTLD-TDP. METHODS High-resolution mass spectrometry was used to characterize TDP-43 proteoforms in brain tissue from FTLD-TDP, non-TDP-43 dementias and neuropathologically unaffected cases. Findings were then verified in a larger cohort of FTLD-TDP and non-TDP-43 dementias via targeted quantitative mass spectrometry. RESULTS In the discovery phase, truncated TDP-43 identified FTLD-TDP with 85% sensitivity and 100% specificity. The verification phase revealed similar findings, with 83% sensitivity and 89% specificity. DISCUSSION The concentration of truncated TDP-43 proteoforms-in particular, in vivo generated C-terminal fragments-have high diagnostic accuracy for FTLD-TDP. HIGHLIGHTS Discovery: Truncated TDP-43 differentiates FTLD-TDP from related dementias. Verification: Truncated TDP-43 concentration has high accuracy for FTLD-TDP. TDP-43 proteoforms <28 kDa have highest discriminatory power for TDP-43 pathology.
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Affiliation(s)
- Lauren M. Forgrave
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - Kyung‐Mee Moon
- Department of Biochemistry and Molecular Biology and Michael Smith LaboratoriesUniversity of British ColumbiaVancouverCanada
| | - Jordan E. Hamden
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - Yun Li
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - Phoebe Lu
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - Leonard J. Foster
- Department of Biochemistry and Molecular Biology and Michael Smith LaboratoriesUniversity of British ColumbiaVancouverCanada
| | - Ian R. A. Mackenzie
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
- Department of Pathology and Laboratory MedicineVancouver General HospitalVancouverCanada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
- Department of Pathology and Laboratory MedicineSt. Paul's Hospital, Providence Health CareVancouverCanada
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44
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Qi C, Verheijen BM, Kokubo Y, Shi Y, Tetter S, Murzin AG, Nakahara A, Morimoto S, Vermulst M, Sasaki R, Aronica E, Hirokawa Y, Oyanagi K, Kakita A, Ryskeldi-Falcon B, Yoshida M, Hasegawa M, Scheres SHW, Goedert M. Tau filaments from amyotrophic lateral sclerosis/parkinsonism-dementia complex adopt the CTE fold. Proc Natl Acad Sci U S A 2023; 120:e2306767120. [PMID: 38100415 PMCID: PMC10743375 DOI: 10.1073/pnas.2306767120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023] Open
Abstract
The amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterized by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here, we used electron cryo-microscopy to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in three Kii cases and tau filaments with the corticobasal degeneration fold in one Kii case. We identified a new Type III CTE tau filament, where protofilaments pack against each other in an antiparallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors.
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Affiliation(s)
- Chao Qi
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Bert M. Verheijen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Yasumasa Kokubo
- Graduate School of Regional Innovation Studies, Mie University, Tsu514-8507, Japan
| | - Yang Shi
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Stephan Tetter
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Alexey G. Murzin
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Asa Nakahara
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Satoru Morimoto
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Tsu514-8507, Japan
| | - Marc Vermulst
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Ryogen Sasaki
- Department of Nursing, Suzuka University of Medical Science, Suzuka513-8670, Japan
| | - Eleonora Aronica
- Department of Neuropathology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam Neuroscience, Amsterdam1105 AZ, The Netherlands
| | - Yoshifumi Hirokawa
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Tsu514-8507, Japan
| | - Kiyomitsu Oyanagi
- Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto390-8621, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | | | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute480-1195, Japan
| | - Masato Hasegawa
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, Tokyo156-8506, Japan
| | - Sjors H. W. Scheres
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Michel Goedert
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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Mishra S. Emerging Trends in Cryo-EM-based Structural Studies of Neuropathological Amyloids. J Mol Biol 2023; 435:168361. [PMID: 37949311 DOI: 10.1016/j.jmb.2023.168361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tauopathies, synucleinopathies, Aβ amyloidosis, TDP-43 proteinopathies, and prion diseases- these neurodegenerative diseases have in common the formation of amyloid filaments rich in cross-β sheets. Cryo-electron microscopy now permits the visualization of amyloid assemblies at atomic resolution, ushering a wide range of structural studies on several of these poorly understood amyloidogenic proteins. Amyloids are polymorphic with minor modulations in reaction environment affecting the overall architecture of their assembly, making amyloids an extremely challenging venture for structure-based therapeutic intervention. In 2017, the first cryo-EM structure of tau filaments from an Alzheimer's disease-affected brain established that in vitro assemblies might not necessarily reflect the native amyloid fold. Since then, brain-derived amyloid structures for several proteins across many neurodegenerative diseases have uncovered the disease-relevant amyloid folds. It has now been shown for tauopathies, synucleinopathies and TDP-43 proteinopathies, that distinct amyloid folds of the same protein might be related to different diseases. Salient features of each of these brain-derived folds are discussed in detail. It was also recently observed that seeded aggregation does not necessarily replicate the brain-derived structural fold. Owing to high throughput structure determination, some of these native amyloid folds have also been successfully replicated in vitro. In vitro replication of disease-relevant filaments will aid development of imaging ligands and defibrillating drugs. Towards this direction, recent high-resolution structures of tau filaments with positron emission tomography tracers and a defibrillating drug are also discussed. This review summarizes and celebrates the recent advancements in structural understanding of neuropathological amyloid filaments using cryo-EM.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Biological Sciences Division, Indian Institute of Science, Bengaluru 560 012, Karnataka, India.
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46
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Schiano G, Lake J, Mariniello M, Schaeffer C, Harvent M, Rampoldi L, Olinger E, Devuyst O. Allelic effects on uromodulin aggregates drive autosomal dominant tubulointerstitial kidney disease. EMBO Mol Med 2023; 15:e18242. [PMID: 37885358 PMCID: PMC10701617 DOI: 10.15252/emmm.202318242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Missense mutations in the uromodulin (UMOD) gene cause autosomal dominant tubulointerstitial kidney disease (ADTKD), one of the most common monogenic kidney diseases. The unknown impact of the allelic and gene dosage effects and fate of mutant uromodulin leaves open the gap between postulated gain-of-function mutations, end-organ damage and disease progression in ADTKD. Based on two prevalent missense UMOD mutations with divergent disease progression, we generated UmodC171Y and UmodR186S knock-in mice that showed strong allelic and gene dosage effects on uromodulin aggregates and activation of ER stress and unfolded protein and immune responses, leading to variable kidney damage. Deletion of the wild-type Umod allele in heterozygous UmodR186S mice increased the formation of uromodulin aggregates and ER stress. Studies in kidney tubular cells confirmed differences in uromodulin aggregates, with activation of mutation-specific quality control and clearance mechanisms. Enhancement of autophagy by starvation and mTORC1 inhibition decreased uromodulin aggregates. These studies substantiate the role of toxic aggregates as driving progression of ADTKD-UMOD, relevant for therapeutic strategies to improve clearance of mutant uromodulin.
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Affiliation(s)
- Guglielmo Schiano
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
| | - Jennifer Lake
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
| | - Marta Mariniello
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
| | - Céline Schaeffer
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Marianne Harvent
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
- Institut de Recherche Expérimentale et CliniqueUCLouvainBrusselsBelgium
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Eric Olinger
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
- Translational and Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
- Center for Human GeneticsCliniques Universitaires Saint‐Luc, UCLouvainBrusselsBelgium
| | - Olivier Devuyst
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
- Institut de Recherche Expérimentale et CliniqueUCLouvainBrusselsBelgium
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47
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Cascella R, Banchelli M, Abolghasem Ghadami S, Ami D, Gagliani MC, Bigi A, Staderini T, Tampellini D, Cortese K, Cecchi C, Natalello A, Adibi H, Matteini P, Chiti F. An in situ and in vitro investigation of cytoplasmic TDP-43 inclusions reveals the absence of a clear amyloid signature. Ann Med 2023; 55:72-88. [PMID: 36495262 PMCID: PMC9746631 DOI: 10.1080/07853890.2022.2148734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction: Several neurodegenerative conditions are associated with a common histopathology within neurons of the central nervous system, consisting of the deposition of cytoplasmic inclusions of TAR DNA-binding protein 43 (TDP-43). Such inclusions have variably been described as morphologically and molecularly ordered aggregates having amyloid properties, as filaments without the cross-β-structure and dye binding specific for amyloid, or as amorphous aggregates with no defined structure and fibrillar morphology.Aims and Methods: Here we have expressed human full-length TDP-43 in neuroblastoma x spinal cord 34 (NSC-34) cells to investigate the morphological, structural, and tinctorial properties of TDP-43 inclusions in situ. We have used last-generation amyloid diagnostic probes able to cross the cell membrane and detect amyloid in the cytoplasm and have adopted Raman and Fourier transform infrared microspectroscopies to study in situ the secondary structure of the TDP-43 protein in the inclusions. We have then used transmission electron microscopy to study the morphology of the TDP-43 inclusions.Results: The results show the absence of amyloid dye binding, the lack of an enrichment of cross-β structure in the inclusions, and of a fibrillar texture in the round inclusions. The aggregates formed in vitro from the purified protein under conditions in which it is initially native also lack all these characteristics, ruling out a clear amyloid-like signature.Conclusions: These findings indicate a low propensity of TDP-43 to form amyloid fibrils and even non-amyloid filaments, under conditions in which the protein is initially native and undergoes its typical nucleus-to-cell mislocalization. It cannot be excluded that filaments emerge on the long time scale from such inclusions, but the high propensity of the protein to form initially other types of inclusions appear to be an essential characteristic of TDP-43 proteinopathies.KEY MESSAGESCytoplasmic inclusions of TDP-43 formed in NSC-34 cells do not stain with amyloid-diagnostic dyes, are not enriched with cross-β structure, and do not show a fibrillar morphology.TDP-43 assemblies formed in vitro from pure TDP-43 do not have any hallmarks of amyloid.
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Affiliation(s)
- Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Martina Banchelli
- Institute of Applied Physics "Nello Carrara", National Research Council, Sesto Fiorentino, Italy
| | | | - Diletta Ami
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy.,Milan Center of Neuroscience (NeuroMI), Milan, Italy
| | - Maria Cristina Gagliani
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine, University of Genova, Genoa, Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Tommaso Staderini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Davide Tampellini
- U 1195 INSERM-Université Paris-Saclay, Paris, France.,Institut Professeur Baulieu, Paris, France
| | - Katia Cortese
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine, University of Genova, Genoa, Italy
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Antonino Natalello
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy.,Milan Center of Neuroscience (NeuroMI), Milan, Italy
| | - Hadi Adibi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Paolo Matteini
- Institute of Applied Physics "Nello Carrara", National Research Council, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
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48
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Tan RH, McCann H, Shepherd CE, Pinkerton M, Mazumder S, Devenney EM, Adler GL, Rowe DB, Kril J, Halliday GM, Kiernan MC. Heterogeneity of cortical pTDP-43 inclusion morphologies in amyotrophic lateral sclerosis. Acta Neuropathol Commun 2023; 11:180. [PMID: 37957721 PMCID: PMC10642010 DOI: 10.1186/s40478-023-01670-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Despite the presence of significant cortical pTDP-43 inclusions of heterogeneous morphologies in patients diagnosed with amyotrophic lateral sclerosis (ALS), pathological subclassification is routinely performed in the minority of patients with concomitant frontotemporal dementia (FTD). OBJECTIVE In order to improve current understanding of the presence and relevance of pathological pTDP-43 subtypes in ALS, the present study examined the pattern of cortical pTDP-43 aggregates in 61 ALS cases without FTD. RESULTS Based on the presence, morphology and composition of pTDP-43 pathology, three distinct ALS-TDP subtypes were delineated: (1) A predominant pattern of pTDP-43 granulofilamentous neuronal inclusions (GFNIs) and grains that were immuno-negative for p62 was identified in 18% of cases designated ALS-TDP type E; (2) neuronal cytoplasmic inclusions (NCIs) that were immuno-positive for both pTDP-43 and p62 were observed in 67% of cases assigned ALS-TDP type B; and (3) scarce cortical pTDP-43 and p62 aggregates were identified in 15% of cases coined ALS-TDP type SC (scarce cortical). Quantitative analyses revealed a significantly greater burden of pTDP-43 GFNI and grains in ALS-TDP type E. Principal component analysis demonstrated significant relationships between GFNIs, grains and ALS-TDP subtypes to support the distinction of subtypes E and B. No significant difference in age at death or disease duration was found between ALS-TDP subgroups to suggest that these subtypes represent earlier or later stages of the same disease process. Instead, a significantly higher ALS-TDP stage, indicating greater topographical spread of pTDP-43, was identified in ALS-TDP type E. Alzheimer's disease neuropathological change (ABC score ≥ intermediate) and Lewy body disease (Braak stage ≥ IV) was more prevalent in the ALS-TDP type SC cohort, which also demonstrated a significantly lower overall cognitive score. CONCLUSION In summary, the present study demonstrates that ALS-TDP does not represent a single homogenous neuropathology. We propose the subclassification of ALS-TDP into three distinct subtypes using standard immuno-stains for pTDP-43 and p62 in the motor cortex, which is routinely sampled and evaluated for diagnostic neuropathological characterisation of ALS. We propose that future studies specify both clinicopathological group and pTDP-43 subtype to advance current understanding of the pathogenesis of clinical phenotypes in pTDP-43 proteinopathies, which will have significant relevance to the development of targeted therapies for this heterogeneous disorder.
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Affiliation(s)
- Rachel H Tan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia.
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia.
| | - Heather McCann
- Neuroscience Research Australia, Randwick, NSW, Australia
| | | | - Monica Pinkerton
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Srestha Mazumder
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - Emma M Devenney
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
| | - Gabrielle L Adler
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Dominic B Rowe
- Macquarie University Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Jillian Kril
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
- Dementia Research Centre, Macquarie Medical School, Macquarie University, Sydney, NSW, Australia
| | - Glenda M Halliday
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, Australia
- Institute of Clinical Neurosciences, Royal Prince Alfred Hospital, Sydney, NSW, Australia
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49
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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50
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Audrain M, Egesipe AL, Tentillier N, Font L, Ratnam M, Mottier L, Clavel M, Le Roux-Bourdieu M, Fenyi A, Ollier R, Chevalier E, Guilhot F, Fuchs A, Piorkowska K, Carlyle B, Arnold SE, Berry JD, Luthi-Carter R, Adolfsson O, Pfeifer A, Kosco-Vilbois M, Seredenina T, Afroz T. Targeting amyotrophic lateral sclerosis by neutralizing seeding-competent TDP-43 in CSF. Brain Commun 2023; 5:fcad306. [PMID: 38025276 PMCID: PMC10644982 DOI: 10.1093/braincomms/fcad306] [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: 06/12/2023] [Revised: 09/08/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
In amyotrophic lateral sclerosis, a disease driven by abnormal transactive response DNA-binding protein of 43 kDa aggregation, CSF may contain pathological species of transactive response DNA-binding protein of 43 kDa contributing to the propagation of pathology and neuronal toxicity. These species, released in part by degenerating neurons, would act as a template for the aggregation of physiological protein contributing to the spread of pathology in the brain and spinal cord. In this study, a robust seed amplification assay was established to assess the presence of seeding-competent transactive response DNA-binding protein of 43 kDa species in CSF of apparently sporadic amyotrophic lateral sclerosis patients. These samples resulted in a significant acceleration of substrate aggregation differentiating the kinetics from healthy controls. In parallel, a second assay was developed to determine the level of target engagement that would be necessary to neutralize such species in human CSF by a therapeutic monoclonal antibody targeting transactive response DNA-binding protein of 43 kDa. For this, evaluation of the pharmacokinetic/pharmacodynamic effect for the monoclonal antibody, ACI-5891.9, in vivo and in vitro confirmed that a CSF concentration of ≍1100 ng/mL would be sufficient for sustained target saturation. Using this concentration in the seed amplification assay, ACI-5891.9 was able to neutralize the transactive response DNA-binding protein of 43 kDa pathogenic seeds derived from amyotrophic lateral sclerosis patient CSF. This translational work adds to the evidence of transmission of transactive response DNA-binding protein of 43 kDa pathology via CSF that could contribute to the non-contiguous pattern of clinical manifestations observed in amyotrophic lateral sclerosis and demonstrates the ability of a therapeutic monoclonal antibody to neutralize the toxic, extracellular seeding-competent transactive response DNA-binding protein of 43 kDa species in the CSF of apparently sporadic amyotrophic lateral sclerosis patients.
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Affiliation(s)
| | | | | | - Laure Font
- Research, AC Immune SA, 1015 Lausanne, Switzerland
| | | | | | | | | | - Alexis Fenyi
- Research, AC Immune SA, 1015 Lausanne, Switzerland
| | | | | | | | - Aline Fuchs
- Research, AC Immune SA, 1015 Lausanne, Switzerland
| | | | - Becky Carlyle
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Steven E Arnold
- Department of Neurology and the Massachusetts Alzheimer’s Disease Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - James D Berry
- Sean M. Healey & AMG Center for ALS & the Neurological Clinical Research Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | | | | | | | | | | | - Tariq Afroz
- Research, AC Immune SA, 1015 Lausanne, Switzerland
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