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Pillay K, Chiliza TE, Senzani S, Pillay B, Pillay M. In silico design of Mycobacterium tuberculosis multi-epitope adhesin protein vaccines. Heliyon 2024; 10:e37536. [PMID: 39323805 PMCID: PMC11422057 DOI: 10.1016/j.heliyon.2024.e37536] [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: 07/31/2024] [Accepted: 09/04/2024] [Indexed: 09/27/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) adhesin proteins are promising candidates for subunit vaccine design. Multi-epitope Mtb vaccine and diagnostic candidates were designed using immunoinformatic tools. The antigenic potential of 26 adhesin proteins were determined using VaxiJen 2.0. The truncated heat shock protein 70 (tnHSP70), 19 kDa antigen lipoprotein (lpqH), Mtb curli pili (MTP), and Phosphate transport protein S1 (PstS1) were selected based on the number of known epitopes on the Immune Epitope Database (IEDB). B- and T-cell epitopes were identified using BepiPred2.0, ABCpred, SVMTriP, and IEDB, respectively. Population coverage was analysed using prominent South African specific alleles on the IEDB. The allergenicity, physicochemical characteristics and tertiary structure of the tri-fusion proteins were determined. The in silico immune simulation was performed using C-ImmSim. Three truncated sequences, with predicted B and T cell epitopes, and without allergenicity or signal peptides were linked by three glycine-serine residues, resulting in the stable, hydrophilic molecules, tnlpqH-tnPstS1-tnHSP70 (64,86 kDa) and tnMTP-tnPstS1-tnHSP70 (63,96 kDa). Restriction endonuclease recognition sequences incorporated at the N- and C-terminal ends of each construct, facilitated virtual cloning using Snapgene, into pGEX6P-1, resulting in novel, highly immunogenic vaccine candidates (0,912-0,985). Future studies will involve the cloning, recombinant protein expression and purification of these constructs for downstream applications.
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Affiliation(s)
- Koobashnee Pillay
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, South Africa
| | - Thamsanqa E. Chiliza
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa
| | - Sibusiso Senzani
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, South Africa
| | - Balakrishna Pillay
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, South Africa
| | - Manormoney Pillay
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, South Africa
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Mondal M, Jankoski PE, Lee LD, Dinakarapandian DM, Chiu TY, Swetman WS, Wu H, Paravastu AK, Clemons TD, Rangachari V. Reversible Disulfide Bond Cross-Links as Tunable Levers of Phase Separation in Designer Biomolecular Condensates. J Am Chem Soc 2024; 146:25299-25311. [PMID: 39196681 PMCID: PMC11403603 DOI: 10.1021/jacs.4c09557] [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] [Indexed: 08/30/2024]
Abstract
Biomolecular condensates (BCs) are membraneless hubs enriched with proteins and nucleic acids that have emerged as important players in many cellular functions. Uncovering the sequence determinants of proteins for phase separation is essential in understanding the biophysical and biochemical properties of BCs. Despite significant discoveries in the past decade, the role of cysteine residues in BC formation and dissolution has remained unknown. Here, to uncover the involvement of disulfide cross-links and their redox sensitivity in BCs, we designed a "stickers and spacers" model of phase-separating peptides interspersed with cysteines. Through biophysical investigations, we learned that cysteines promote liquid-liquid phase separation in oxidizing conditions and perpetuate liquid condensates through disulfide cross-links, which can be reversibly tuned with redox chemistry. By varying the composition of cysteines, subtle but distinct changes in the viscoelastic behavior of the condensates were observed. Empirically, we conclude that cysteines function neither as stickers nor spacers but as covalent nodes to lower the effective concentrations for sticker interactions and inhibit system-spanning percolation networks. Together, we unmask the possible role of cysteines in the formation of biomolecular condensates and their potential use as tunable covalent cross-linkers in developing redox-sensitive viscoelastic materials.
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Affiliation(s)
- Malay Mondal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Penelope E Jankoski
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Landon D Lee
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Daniel M Dinakarapandian
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0002, United States
| | - Tzu-Ying Chiu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0002, United States
| | - Windfield S Swetman
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Hongwei Wu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0002, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0002, United States
| | - Tristan D Clemons
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
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3
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Mondal M, Jankoski PE, Lee LD, Dinakarapandian DM, Chiu TY, Swetman WS, Wu H, Paravastu AK, Clemons TD, Rangachari V. Reversible disulfide bond crosslinks as tunable levers of phase separation in designer biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603402. [PMID: 39071339 PMCID: PMC11275914 DOI: 10.1101/2024.07.13.603402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Biomolecular condensates (BCs) are membraneless hubs enriched in proteins and nucleic acids that have become important players in many cellular functions. Uncovering the sequence determinants of proteins for phase separation is important in understanding the biophysical and biochemical properties of BCs. Despite significant discoveries in the last decade, the role of cysteine residues in BC formation and dissolution has remained unknown. Here, to determine the involvement of disulfide crosslinks and their redox sensitivity in BCs, we designed a 'stickers and spacers' model of phase-separating peptides interspersed with cysteines. Through biophysical investigations, we learned that cysteines promote liquid-liquid phase separation in oxidizing conditions and perpetuate liquid condensates through disulfide crosslinks, which can be reversibly tuned with redox chemistry. By varying the composition of cysteines, subtle but distinct changes in the viscoelastic behavior of the condensates were observed. Empirically, we conclude that cysteines are neither stickers nor spacers but function as covalent nodes to lower the effective concentrations for sticker interactions and inhibit system-spanning percolation networks. Together, we unmask the role of cysteines in protein phase behavior and the potential to develop tunable, redox-sensitive viscoelastic materials.
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4
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Clayton EL, Huggon L, Cousin MA, Mizielinska S. Synaptopathy: presynaptic convergence in frontotemporal dementia and amyotrophic lateral sclerosis. Brain 2024; 147:2289-2307. [PMID: 38451707 PMCID: PMC11224618 DOI: 10.1093/brain/awae074] [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: 08/18/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are common forms of neurodegenerative disease that share overlapping genetics and pathologies. Crucially, no significantly disease-modifying treatments are available for either disease. Identifying the earliest changes that initiate neuronal dysfunction is important for designing effective intervention therapeutics. The genes mutated in genetic forms of frontotemporal dementia and amyotrophic lateral sclerosis have diverse cellular functions, and multiple disease mechanisms have been proposed for both. Identification of a convergent disease mechanism in frontotemporal dementia and amyotrophic lateral sclerosis would focus research for a targetable pathway, which could potentially effectively treat all forms of frontotemporal dementia and amyotrophic lateral sclerosis (both familial and sporadic). Synaptopathies are diseases resulting from physiological dysfunction of synapses, and define the earliest stages in multiple neuronal diseases, with synapse loss a key feature in dementia. At the presynapse, the process of synaptic vesicle recruitment, fusion and recycling is necessary for activity-dependent neurotransmitter release. The unique distal location of the presynaptic terminal means the tight spatio-temporal control of presynaptic homeostasis is dependent on efficient local protein translation and degradation. Recently, numerous publications have shown that mutations associated with frontotemporal dementia and amyotrophic lateral sclerosis present with synaptopathy characterized by presynaptic dysfunction. This review will describe the complex local signalling and membrane trafficking events that occur at the presynapse to facilitate neurotransmission and will summarize recent publications linking frontotemporal dementia/amyotrophic lateral sclerosis genetic mutations to presynaptic function. This evidence indicates that presynaptic synaptopathy is an early and convergent event in frontotemporal dementia and amyotrophic lateral sclerosis and illustrates the need for further research in this area, to identify potential therapeutic targets with the ability to impact this convergent pathomechanism.
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Affiliation(s)
- Emma L Clayton
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
| | - Laura Huggon
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
- Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Sarah Mizielinska
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
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Wang X, Hu Y, Xu R. The pathogenic mechanism of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis. Neural Regen Res 2024; 19:800-806. [PMID: 37843214 PMCID: PMC10664110 DOI: 10.4103/1673-5374.382233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 10/17/2023] Open
Abstract
The onset of amyotrophic lateral sclerosis is usually characterized by focal death of both upper and/or lower motor neurons occurring in the motor cortex, basal ganglia, brainstem, and spinal cord, and commonly involves the muscles of the upper and/or lower extremities, and the muscles of the bulbar and/or respiratory regions. However, as the disease progresses, it affects the adjacent body regions, leading to generalized muscle weakness, occasionally along with memory, cognitive, behavioral, and language impairments; respiratory dysfunction occurs at the final stage of the disease. The disease has a complicated pathophysiology and currently, only riluzole, edaravone, and phenylbutyrate/taurursodiol are licensed to treat amyotrophic lateral sclerosis in many industrialized countries. The TAR DNA-binding protein 43 inclusions are observed in 97% of those diagnosed with amyotrophic lateral sclerosis. This review provides a preliminary overview of the potential effects of TAR DNA-binding protein 43 in the pathogenesis of amyotrophic lateral sclerosis, including the abnormalities in nucleoplasmic transport, RNA function, post-translational modification, liquid-liquid phase separation, stress granules, mitochondrial dysfunction, oxidative stress, axonal transport, protein quality control system, and non-cellular autonomous functions (e.g., glial cell functions and prion-like propagation).
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Affiliation(s)
- Xinxin Wang
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Yushu Hu
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Renshi Xu
- Medical College of Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
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Sung W, Noh MY, Nahm M, Kim YS, Ki CS, Kim YE, Kim HJ, Kim SH. Progranulin haploinsufficiency mediates cytoplasmic TDP-43 aggregation with lysosomal abnormalities in human microglia. J Neuroinflammation 2024; 21:47. [PMID: 38347588 PMCID: PMC10863104 DOI: 10.1186/s12974-024-03039-1] [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: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Progranulin (PGRN) haploinsufficiency due to progranulin gene (GRN) variants can cause frontotemporal dementia (FTD) with aberrant TAR DNA-binding protein 43 (TDP-43) accumulation. Despite microglial burden with TDP-43-related pathophysiology, direct microglial TDP-43 pathology has not been clarified yet, only emphasized in neuronal pathology. Thus, the objective of this study was to investigate TDP-43 pathology in microglia of patients with PGRN haploinsufficiency. METHODS To design a human microglial cell model with PGRN haploinsufficiency, monocyte-derived microglia (iMGs) were generated from FTD-GRN patients carrying pathogenic or likely pathogenic variants (p.M1? and p.W147*) and three healthy controls. RESULTS iMGs from FTD-GRN patients with PGRN deficiency exhibited severe neuroinflammation phenotype and failure to maintain their homeostatic molecular signatures, along with impaired phagocytosis. In FTD-GRN patients-derived iMGs, significant cytoplasmic TDP-43 aggregation and accumulation of lipid droplets with profound lysosomal abnormalities were observed. These pathomechanisms were mediated by complement C1q activation and upregulation of pro-inflammatory cytokines. CONCLUSIONS Our study provides considerable cellular and molecular evidence that loss-of-function variants of GRN in human microglia can cause microglial dysfunction with abnormal TDP-43 aggregation induced by inflammatory milieu as well as the impaired lysosome. Elucidating the role of microglial TDP-43 pathology in intensifying neuroinflammation in individuals with FTD due to PGRN deficiency and examining consequential effects on microglial dysfunction might yield novel insights into the mechanisms underlying FTD and neurodegenerative disorders.
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Affiliation(s)
- Wonjae Sung
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | - Min-Young Noh
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | - Minyeop Nahm
- Dementia Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Yong Sung Kim
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | | | - Young-Eun Kim
- Department of Laboratory Medicine, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hee-Jin Kim
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea
| | - Seung Hyun Kim
- Department of Neurology, College of Medicine, Hanyang University, 222, Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Republic of Korea.
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Ducharme S, Pijnenburg Y, Rohrer JD, Huey E, Finger E, Tatton N. Identifying and Diagnosing TDP-43 Neurodegenerative Diseases in Psychiatry. Am J Geriatr Psychiatry 2024; 32:98-113. [PMID: 37741764 PMCID: PMC11270911 DOI: 10.1016/j.jagp.2023.08.017] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/24/2023] [Indexed: 09/25/2023]
Abstract
Neuropsychiatric symptoms (NPS) are common manifestations of neurodegenerative disorders and are often early signs of those diseases. Among those neurodegenerative diseases, TDP-43 proteinopathies are an increasingly recognized cause of early neuropsychiatric manifestations. TDP-43-related diseases include frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), and Limbic-Predominant Age-Related TDP-43 Encephalopathy (LATE). The majority of TDP-43-related diseases are sporadic, but a significant proportion is hereditary, with progranulin (GRN) mutations and C9orf72 repeat expansions as the most common genetic etiologies. Studies reveal that NPS can be the initial manifestation of those diseases or can complicate disease course, but there is a lack of awareness among clinicians about TDP-43-related diseases, which leads to common diagnostic mistakes or delays. There is also emerging evidence that TDP-43 accumulations could play a role in late-onset primary psychiatric disorders. In the absence of robust biomarkers for TDP-43, the diagnosis remains primarily based on clinical assessment and neuroimaging. Given the association with psychiatric symptoms, clinical psychiatrists have a key role in the early identification of patients with TDP-43-related diseases. This narrative review provides a comprehensive overview of the pathobiology of TDP-43, resulting clinical presentations, and associated neuropsychiatric manifestations to help guide clinical practice.
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Affiliation(s)
- Simon Ducharme
- Department of Psychiatry (SD), Douglas Mental Health University Institute, McGill University, Montreal, Canada; McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.
| | - Yolande Pijnenburg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience (YP), Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jonathan D Rohrer
- Dementia Research Centre, Department of Neurodegenerative Disease (JDR), UCL Queen Square Institute of Neurology, London, UK
| | - Edward Huey
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Psychiatry (EH), Columbia University, New York, NY
| | - Elizabeth Finger
- London Health Sciences Centre Parkwood Institute (EF), London, ON, Canada
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Foressi NN, Rodríguez LC, Celej MS. Heterotypic liquid-liquid phase separation of tau and α-synuclein: Implications for overlapping neuropathologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140950. [PMID: 37574035 DOI: 10.1016/j.bbapap.2023.140950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Tauopathies and synucleinopathies are characterized by the aggregation of Tau and α-synuclein (AS) into amyloid structures, respectively. Individuals with these neuropathies have an elevated risk of developing subsequent neurodegenerative or comorbid disorders. Intriguingly, post-mortem brain examinations have revealed co-localization of Tau and AS aggregates, suggesting a synergistic pathological relationship with an adverse prognosis. The role of liquid-liquid phase separation (LLPS) in the development of neurodegenerative diseases is currently receiving significant attention, as it can contribute to the aggregation and co-deposition of amyloidogenic proteins. In this study, we investigated the phase separation behavior of Tau and AS under various insults, some of which are implicated in disease progression. Our findings demonstrate the formation of heterotypic droplets composed of Tau and AS at physiologically relevant mole ratios that mimic neurons' soma and terminal buttons. Importantly, these heterotypic droplets exhibit increased resistance to electrostatic screening compared to homotypic condensates. Moreover, we observed that biologically relevant biomolecules, known to be dysregulated in disease, exert different effects on these droplets. Additionally, we provide evidence that phase separation itself influences the amyloid aggregation of Tau and AS, underscoring the significance of this process in the development of aggregopathies.
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Affiliation(s)
- Nahuel N Foressi
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Leandro Cruz Rodríguez
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
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Kamagata K, Kanbayashi S, Koda S, Kadotani A, Ubukata O, Tashima T. Suppression of TDP-43 aggregation by artificial peptide binder targeting to its low complexity domain. Biochem Biophys Res Commun 2023; 662:119-125. [PMID: 37104882 DOI: 10.1016/j.bbrc.2023.04.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/16/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023]
Abstract
TAR DNA-binding protein 43 (TDP-43), aggregation prone protein, is a potential target of drug discovery for amyotrophic lateral sclerosis. The molecular binders, targeting the disordered low complexity domain (LCD) relevant to the aggregation, may suppress the aggregation. Recently, Kamagata et al. developed a rational design of peptide binders targeting intrinsically disordered proteins based on contact energies between residue pairs. In this study, we designed 18 producible peptide binder candidates to TDP-43 LCD by using this method. Fluorescence anisotropy titration and surface plasmon resonance assays demonstrated that one of the designed peptides bound to TDP-43 LCD at 30 μM. Thioflavin-T fluorescence and sedimentation assays showed that the peptide binder suppressed the aggregation of TDP-43. In summary, this study highlights the potential applicability of peptide binder design for aggregation prone proteins.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | | | - Akito Kadotani
- Daiichi Sankyo RD Novare Co. Ltd., Tokyo, 134-0081, Japan
| | - Osamu Ubukata
- Daiichi Sankyo RD Novare Co. Ltd., Tokyo, 134-0081, Japan
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Doke AA, Jha SK. Shapeshifter TDP-43: Molecular mechanism of structural polymorphism, aggregation, phase separation and their modulators. Biophys Chem 2023; 295:106972. [PMID: 36812677 DOI: 10.1016/j.bpc.2023.106972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
TDP-43 is a nucleic acid-binding protein that performs physiologically essential functions and is known to undergo phase separation and aggregation during stress. Initial observations have shown that TDP-43 forms heterogeneous assemblies, including monomer, dimer, oligomers, aggregates, phase-separated assemblies, etc. However, the significance of each assembly of TDP-43 concerning its function, phase separation, and aggregation is poorly known. Furthermore, how different assemblies of TDP-43 are related to each other is unclear. In this review, we focus on the various assemblies of TDP-43 and discuss the plausible origin of the structural heterogeneity of TDP-43. TDP-43 is involved in multiple physiological processes like phase separation, aggregation, prion-like seeding, and performing physiological functions. However, the molecular mechanism behind the physiological process performed by TDP-43 is not well understood. The current review discusses the plausible molecular mechanism of phase separation, aggregation, and prion-like propagation of TDP-43.
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Affiliation(s)
- Abhilasha A Doke
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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11
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Ma L, Fang X, Wang C. Peptide-based coacervates in therapeutic applications. Front Bioeng Biotechnol 2023; 10:1100365. [PMID: 36686257 PMCID: PMC9845597 DOI: 10.3389/fbioe.2022.1100365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.
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Affiliation(s)
- Lilusi Ma
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaocui Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
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12
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TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury. Nat Neurosci 2022; 25:1608-1625. [PMID: 36424432 DOI: 10.1038/s41593-022-01199-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/11/2022] [Indexed: 11/27/2022]
Abstract
Decreasing the activation of pathology-activated microglia is crucial to prevent chronic inflammation and tissue scarring. In this study, we used a stab wound injury model in zebrafish and identified an injury-induced microglial state characterized by the accumulation of lipid droplets and TAR DNA-binding protein of 43 kDa (TDP-43)+ condensates. Granulin-mediated clearance of both lipid droplets and TDP-43+ condensates was necessary and sufficient to promote the return of microglia back to the basal state and achieve scarless regeneration. Moreover, in postmortem cortical brain tissues from patients with traumatic brain injury, the extent of microglial activation correlated with the accumulation of lipid droplets and TDP-43+ condensates. Together, our results reveal a mechanism required for restoring microglia to a nonactivated state after injury, which has potential for new therapeutic applications in humans.
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13
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Samulevich ML, Shamilov R, Aneskievich BJ. Thermostable Proteins from HaCaT Keratinocytes Identify a Wide Breadth of Intrinsically Disordered Proteins and Candidates for Liquid-Liquid Phase Separation. Int J Mol Sci 2022; 23:ijms232214323. [PMID: 36430801 PMCID: PMC9692912 DOI: 10.3390/ijms232214323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) move through an ensemble of conformations which allows multitudinous roles within a cell. Keratinocytes, the predominant cell type in mammalian epidermis, have had only a few individual proteins assessed for intrinsic disorder and its possible contribution to liquid-liquid phase separation (LLPS), especially in regard to what functions or structures these proteins provide. We took a holistic approach to keratinocyte IDPs starting with enrichment via the isolation of thermostable proteins. The keratinocyte protein involucrin, known for its resistance to heat denaturation, served as a marker. It and other thermostable proteins were identified by liquid chromatography tandem mass spectrometry and subjected to extensive bioinformatic analysis covering gene ontology, intrinsic disorder, and potential for LLPS. Numerous proteins unique to keratinocytes and other proteins with shared expression in multiple cell types were identified to have IDP traits (e.g., compositional bias, nucleic acid binding, and repeat motifs). Among keratinocyte-specific proteins, many that co-assemble with involucrin into the cell-specific structure known as the cornified envelope scored highly for intrinsic disorder and potential for LLPS. This suggests intrinsic disorder and LLPS are previously unrecognized traits for assembly of the cornified envelope, echoing the contribution of intrinsic disorder and LLPS to more widely encountered features such as stress granules and PML bodies.
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Affiliation(s)
- Michael L. Samulevich
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06292-3092, USA
| | - Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06292-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269-3092, USA
- Correspondence: ; Tel.: +1-860-486-3053; Fax: +1-860-486-5792
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14
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Gracia P, Polanco D, Tarancón-Díez J, Serra I, Bracci M, Oroz J, Laurents DV, García I, Cremades N. Molecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau. Nat Commun 2022; 13:4586. [PMID: 35933508 PMCID: PMC9357037 DOI: 10.1038/s41467-022-32350-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
Amyloid aggregation of α-synuclein (αS) is the hallmark of Parkinson's disease and other synucleinopathies. Recently, Tau protein, generally associated with Alzheimer's disease, has been linked to αS pathology and observed to co-localize in αS-rich disease inclusions, although the molecular mechanisms for the co-aggregation of both proteins remain elusive. We report here that αS phase-separates into liquid condensates by electrostatic complex coacervation with positively charged polypeptides such as Tau. Condensates undergo either fast gelation or coalescence followed by slow amyloid aggregation depending on the affinity of αS for the poly-cation and the rate of valence exhaustion of the condensate network. By combining a set of advanced biophysical techniques, we have been able to characterize αS/Tau liquid-liquid phase separation and identified key factors that lead to the formation of hetero-aggregates containing both proteins in the interior of the liquid protein condensates.
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Affiliation(s)
- Pablo Gracia
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain
| | - David Polanco
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain
| | - Jorge Tarancón-Díez
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain
| | - Ilenia Serra
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009, Zaragoza, Spain
| | - Maruan Bracci
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009, Zaragoza, Spain
| | - Javier Oroz
- "Rocasolano" Institute for Physical Chemistry, CSIC, Serrano 119, Madrid, E-28006, Spain
| | - Douglas V Laurents
- "Rocasolano" Institute for Physical Chemistry, CSIC, Serrano 119, Madrid, E-28006, Spain
| | - Inés García
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009, Zaragoza, Spain
- Centro Universitario de la Defensa, Academia General Militar, Ctra. de Huesca s/n, 50090, Zaragoza, Spain
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018, Zaragoza, Spain.
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, 50009, Zaragoza, Spain.
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15
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Bhopatkar AA, Dhakal S, Abernathy HG, Morgan SE, Rangachari V. Charge and Redox States Modulate Granulin-TDP-43 Coacervation Toward Phase Separation or Aggregation. Biophys J 2022; 121:2107-2126. [PMID: 35490297 DOI: 10.1016/j.bpj.2022.04.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/05/2022] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
Abstract
Cytoplasmic inclusions containing aberrant proteolytic fragments of TDP-43 are associated with frontotemporal lobar degeneration (FTLD) and other related pathologies. In FTLD, TDP-43 is translocated into the cytoplasm and proteolytically cleaved to generate a prion-like domain (PrLD) containing C-terminal fragments (C25 and C35) that form toxic inclusions. Under stress, TDP-43 partitions into membraneless organelles called stress granules (SGs) by coacervating with RNA and other proteins. To glean into the factors that influence the dynamics between these cytoplasmic foci, we investigated the effects of cysteine-rich granulins (GRNs 1-7), which are the proteolytic products of progranulin, a protein implicated in FTLD, on TDP-43. We show that extracellular GRNs, typically generated during inflammation, internalize and colocalize with PrLD as puncta in the cytoplasm of neuroblastoma cells but show less likelihood of their presence in SGs. In addition, we show GRNs and PrLD coacervate to undergo liquid-liquid phase separation (LLPS) or form gel- or solid-like aggregates. Using charge patterning and conserved cysteines among the wild-type GRNs as guides, along with specifically engineered mutants, we discover that the negative charges on GRNs drive LLPS while the positive charges and the redox state of cysteines modulate these phase transitions. Furthermore, RNA and GRNs compete and expel one another from PrLD condensates, providing a basis for GRN's absence in SGs. Together, the results help uncover potential modulatory mechanisms by which extracellular GRNs, formed during chronic inflammatory conditions, could internalize, and modulate cytoplasmic TDP-43 inclusions in proteinopathies.
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Affiliation(s)
- Anukool A Bhopatkar
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg MS 39406
| | - Shailendra Dhakal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg MS 39406
| | - Hannah G Abernathy
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg MS 39406
| | - Sarah E Morgan
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg MS 39406
| | - Vijay Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg MS 39406;; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg MS 39406;.
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16
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De Rossi P, Lewis AJ, Furrer J, De Vos L, Demeter T, Zbinden A, Zhong W, Wiersma VI, Scialo C, Weber J, Guo Z, Scaramuzza S, Di Fabrizio M, Böing C, Castaño‐Díez D, Al‐Amoudi A, Pérez‐Berlanga M, Lashley T, Stahlberg H, Polymenidou M. FTLD-TDP assemblies seed neoaggregates with subtype-specific features via a prion-like cascade. EMBO Rep 2021; 22:e53877. [PMID: 34806807 PMCID: PMC8647015 DOI: 10.15252/embr.202153877] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Morphologically distinct TDP-43 aggregates occur in clinically different FTLD-TDP subtypes, yet the mechanism of their emergence and contribution to clinical heterogeneity are poorly understood. Several lines of evidence suggest that pathological TDP-43 follows a prion-like cascade, but the molecular determinants of this process remain unknown. We use advanced microscopy techniques to compare the seeding properties of pathological FTLD-TDP-A and FTLD-TDP-C aggregates. Upon inoculation of patient-derived aggregates in cells, FTLD-TDP-A seeds amplify in a template-dependent fashion, triggering neoaggregation more efficiently than those extracted from FTLD-TDP-C patients, correlating with the respective disease progression rates. Neoaggregates are sequentially phosphorylated with N-to-C directionality and with subtype-specific timelines. The resulting FTLD-TDP-A neoaggregates are large and contain densely packed fibrils, reminiscent of the pure compacted fibrils present within cytoplasmic inclusions in postmortem brains. In contrast, FTLD-TDP-C dystrophic neurites show less dense fibrils mixed with cellular components, and their respective neoaggregates are small, amorphous protein accumulations. These cellular seeding models replicate aspects of the patient pathological diversity and will be a useful tool in the quest for subtype-specific therapeutics.
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Affiliation(s)
- Pierre De Rossi
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Amanda J Lewis
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
| | - Johanna Furrer
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Laura De Vos
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Tomas Demeter
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Aurélie Zbinden
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Weijia Zhong
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Vera I Wiersma
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Carlo Scialo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Julien Weber
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Zhongning Guo
- Department of Quantitative BiomedicineUniversity of ZurichZurichSwitzerland
| | - Stefano Scaramuzza
- C‐CINABiozentrumUniversity of BaselBaselSwitzerland
- BioEM LabBiozentrumUniversity of BaselBaselSwitzerland
| | - Marta Di Fabrizio
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
| | | | | | | | | | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological diseasesDepartment of Movement DisordersUCL Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
| | - Henning Stahlberg
- Laboratory of Biological Electron MicroscopyInstitute of Physics, SB, EPFLDepartment of Fundamental MicrobiologyFaculty of Biology and MedicineUNILLausanneSwitzerland
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17
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Chien HM, Lee CC, Huang JJT. The Different Faces of the TDP-43 Low-Complexity Domain: The Formation of Liquid Droplets and Amyloid Fibrils. Int J Mol Sci 2021; 22:ijms22158213. [PMID: 34360978 PMCID: PMC8348237 DOI: 10.3390/ijms22158213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) is a nucleic acid-binding protein that is involved in transcription and translation regulation, non-coding RNA processing, and stress granule assembly. Aside from its multiple functions, it is also known as the signature protein in the hallmark inclusions of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) patients. TDP-43 is built of four domains, but its low-complexity domain (LCD) has become an intense research focus that brings to light its possible role in TDP-43 functions and involvement in the pathogenesis of these neurodegenerative diseases. Recent endeavors have further uncovered the distinct biophysical properties of TDP-43 under various circumstances. In this review, we summarize the multiple structural and biochemical properties of LCD in either promoting the liquid droplets or inducing fibrillar aggregates. We also revisit the roles of the LCD in paraspeckles, stress granules, and cytoplasmic inclusions to date.
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Affiliation(s)
- Hung-Ming Chien
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
- Department of Chemistry, National Taiwan University, Taipei City 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei City 115, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
- Department of Applied Chemistry, National Chiayi University, Chiayi City 600, Taiwan
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei City 115, Taiwan
- Correspondence: ; Tel.: +886-2-5572-8652
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18
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Rai SK, Savastano A, Singh P, Mukhopadhyay S, Zweckstetter M. Liquid-liquid phase separation of tau: From molecular biophysics to physiology and disease. Protein Sci 2021; 30:1294-1314. [PMID: 33930220 PMCID: PMC8197432 DOI: 10.1002/pro.4093] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022]
Abstract
Biomolecular condensation via liquid-liquid phase separation (LLPS) of intrinsically disordered proteins/regions (IDPs/IDRs), with and without nucleic acids, has drawn widespread interest due to the rapidly unfolding role of phase-separated condensates in a diverse range of cellular functions and human diseases. Biomolecular condensates form via transient and multivalent intermolecular forces that sequester proteins and nucleic acids into liquid-like membrane-less compartments. However, aberrant phase transitions into gel-like or solid-like aggregates might play an important role in neurodegenerative and other diseases. Tau, a microtubule-associated neuronal IDP, is involved in microtubule stabilization, regulates axonal outgrowth and transport in neurons. A growing body of evidence indicates that tau can accomplish some of its cellular activities via LLPS. However, liquid-to-solid transition resulting in the abnormal aggregation of tau is associated with neurodegenerative diseases. The physical chemistry of tau is crucial for governing its propensity for biomolecular condensation which is governed by various intermolecular and intramolecular interactions leading to simple one-component and complex multi-component condensates. In this review, we aim at capturing the current scientific state in unveiling the intriguing molecular mechanism of phase separation of tau. We particularly focus on the amalgamation of existing and emerging biophysical tools that offer unique spatiotemporal resolutions on a wide range of length- and time-scales. We also discuss the link between quantitative biophysical measurements and novel biological insights into biomolecular condensation of tau. We believe that this account will provide a broad and multidisciplinary view of phase separation of tau and its association with physiology and disease.
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Affiliation(s)
- Sandeep K. Rai
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical SciencesIndian Institute of Science Education and Research (IISER)MohaliIndia
| | - Adriana Savastano
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Priyanka Singh
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical SciencesIndian Institute of Science Education and Research (IISER)MohaliIndia
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Department of Biological Sciences, and Department of Chemical SciencesIndian Institute of Science Education and Research (IISER)MohaliIndia
| | - Markus Zweckstetter
- Research group Translational Structural BiologyGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- Department for NMR‐based Structural BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
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19
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Wang XM, Zeng P, Fang YY, Zhang T, Tian Q. Progranulin in neurodegenerative dementia. J Neurochem 2021; 158:119-137. [PMID: 33930186 DOI: 10.1111/jnc.15378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/28/2021] [Accepted: 04/16/2021] [Indexed: 01/21/2023]
Abstract
Long-term or severe lack of protective factors is important in the pathogenesis of neurodegenerative dementia. Progranulin (PGRN), a neurotrophic factor expressed mainly in neurons and microglia, has various neuroprotective effects such as anti-inflammatory effects, promoting neuron survival and neurite growth, and participating in normal lysosomal function. Mutations in the PGRN gene (GRN) have been found in several neurodegenerative dementias, including frontotemporal lobar degeneration (FTLD) and Alzheimer's disease (AD). Herein, PGRN deficiency and PGRN hydrolytic products (GRNs) in the pathological changes related to dementia, including aggregation of tau and TAR DNA-binding protein 43 (TDP-43), amyloid-β (Aβ) overproduction, neuroinflammation, lysosomal dysfunction, neuronal death, and synaptic deficit have been summarized. Furthermore, as some therapeutic strategies targeting PGRN have been developed in various models, we highlighted PGRN as a potential anti-neurodegeneration target in dementia.
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Affiliation(s)
- Xiao-Ming Wang
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Key Laboratory of Neurological Disease of National Education Ministry, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zeng
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Key Laboratory of Neurological Disease of National Education Ministry, Huazhong University of Science and Technology, Wuhan, China
| | - Ying-Yan Fang
- Hubei Key Laboratory for Kidney Disease Pathogenesis and Intervention, Hubei Polytechnic University School of Medicine, Huangshi, China
| | - Teng Zhang
- Department of Neurology, Shanxian Central Hospital, The Affiliated Huxi Hospital of Jining Medical College, Heze, China
| | - Qing Tian
- Department of Pathology and Pathophysiology, School of Basic Medicine, Tongji Medical College, Key Laboratory of Neurological Disease of National Education Ministry, Huazhong University of Science and Technology, Wuhan, China
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20
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Shuster SO, Lee JC. Tryptophan Probes of TDP-43 C-Terminal Domain Amyloid Formation. J Phys Chem B 2021; 125:3781-3789. [PMID: 33835818 DOI: 10.1021/acs.jpcb.1c00767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aggregated TAR DNA-binding protein 43 (TDP-43) forms the cytoplasmic hallmarks associated with patients suffering from amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin. Under normal conditions, TDP-43 is a 414-amino acid protein; however, aggregates are enriched with N-terminal truncations which contain residues 267-414, known as the C-terminal domain of TDP-43 (TDP-43CTD). To gain residue-specific information on the aggregation process of TDP-43CTD, we created three single-Trp containing mutants (W385F/W412F, W334F/W412F, and W334F/W385F) by substituting two of the three native Trp residues with Phe, yielding fluorescent probes at W334, W385, and W412, respectively. Aggregation kinetics, secondary structure, and fibril morphology were compared to the wild-type protein using thioflavin-T fluorescence, Raman spectroscopy, and transmission electron microscopy, respectively. While only W334 is determined to be in the proteinase-K resistant core, all three sites are sensitive reporters of aggregation, revealing site-specific differences. Interestingly, W334 exhibited unusual multistep Trp kinetics, pinpointing a distinctive role for W334 and its nearby region during aggregation. This behavior is retained even upon seeding, suggesting the observed spectral change is related to fibril growth. This work provides new insights into the aggregation mechanism of TDP-43CTD and exemplifies the advantages of Trp as a site-specific environmentally sensitive fluorescent probe.
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Affiliation(s)
- Sydney O Shuster
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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21
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Dhakal S, Wyant CE, George HE, Morgan SE, Rangachari V. Prion-like C-Terminal Domain of TDP-43 and α-Synuclein Interact Synergistically to Generate Neurotoxic Hybrid Fibrils. J Mol Biol 2021; 433:166953. [PMID: 33771571 DOI: 10.1016/j.jmb.2021.166953] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]
Abstract
Aberrant aggregation and amyloid formation of tar DNA binding protein (TDP-43) and α-synuclein (αS) underlie frontotemporal dementia (FTD) and Parkinson's disease (PD), respectively. Amyloid inclusions of TDP-43 and αS are also commonly co-observed in amyotrophic lateral sclerosis (ALS), dementia with Lewy bodies (DLB) and Alzheimer disease (AD). Emerging evidence from cellular and animal models show colocalization of the TDP-43 and αS aggregates, raising the possibility of direct interactions and co-aggregation between the two proteins. In this report, we set out to answer this question by investigating the interactions between αS and prion-like pathogenic C-terminal domain of TDP-43 (TDP-43 PrLD). PrLD is an aggregation-prone fragment generated both by alternative splicing as well as aberrant proteolytic cleavage of full length TDP-43. Our results indicate that two proteins interact in a synergistic manner to augment each other's aggregation towards hybrid fibrils. While monomers, oligomers and sonicated fibrils of αS seed TDP-43 PrLD monomers, TDP-43 PrLD fibrils failed to seed αS monomers indicating selectivity in interactions. Furthermore, αS modulates liquid droplets formed by TDP-43 PrLD and RNA to promote insoluble amyloid aggregates. Importantly, the cross-seeded hybrid aggregates show greater cytotoxicity as compared to the individual homotypic aggregates suggesting that the interactions between the two proteins have a discernable impact on cellular functions. Together, these results bring forth insights into TDP-43 PrLD - αS interactions that could help explain clinical and pathological presentations in patients with co-morbidities involving the two proteins.
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Affiliation(s)
- Shailendra Dhakal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Courtney E Wyant
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Hannah E George
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sarah E Morgan
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA.
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22
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Li J, Zhang Y, Chen X, Ma L, Li P, Yu H. Protein phase separation and its role in chromatin organization and diseases. Biomed Pharmacother 2021; 138:111520. [PMID: 33765580 DOI: 10.1016/j.biopha.2021.111520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/04/2021] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
In the physical sciences, solid, liquid, and gas are the most familiar phase states, whose essence is their existence reflecting the different spatial distribution of molecular components. The biological molecules in the living cell also have differences in spatial distribution. The molecules organized in the form of membrane-bound organelles are well recognized. However, the biomolecules organized in membraneless compartments called biomolecular condensates remain elusive. The liquid-liquid phase separation (LLPS), as a new emerging scientific breakthrough, describes the biomolecules assembled in special distribution and appeared as membraneless condensates in the form of a new "phase" compared with the surrounding liquid milieu. LLPS provides an important theoretical basis for explaining the composition of biological molecules and related biological reactions. Mounting evidence has emerged recently that phase-separated condensates participate in various biological activities. This article reviews the occurrence of LLPS and underlying regulatory mechanisms for understanding how multivalent molecules drive phase transitions to form the biomolecular condensates. And, it also summarizes recent major progress in elucidating the roles of LLPS in chromatin organization and provides clues for the development of new innovative therapeutic strategies for related diseases.
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Affiliation(s)
- Jiaqi Li
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Yao Zhang
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Xi Chen
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Lijuan Ma
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haijie Yu
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China.
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Zbinden A, Pérez-Berlanga M, De Rossi P, Polymenidou M. Phase Separation and Neurodegenerative Diseases: A Disturbance in the Force. Dev Cell 2021; 55:45-68. [PMID: 33049211 DOI: 10.1016/j.devcel.2020.09.014] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
Protein aggregation is the main hallmark of neurodegenerative diseases. Many proteins found in pathological inclusions are known to undergo liquid-liquid phase separation, a reversible process of molecular self-assembly. Emerging evidence supports the hypothesis that aberrant phase separation behavior may serve as a trigger of protein aggregation in neurodegeneration, and efforts to understand and control the underlying mechanisms are underway. Here, we review similarities and differences among four main proteins, α-synuclein, FUS, tau, and TDP-43, which are found aggregated in different diseases and were independently shown to phase separate. We discuss future directions in the field that will help shed light on the molecular mechanisms of aggregation and neurodegeneration.
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Affiliation(s)
- Aurélie Zbinden
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Manuela Pérez-Berlanga
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pierre De Rossi
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Magdalini Polymenidou
- Department of Quantitative Biomedicine, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Bhopatkar AA, Rangachari V. Are granulins copper sequestering proteins? Proteins 2020; 89:450-461. [PMID: 33252789 DOI: 10.1002/prot.26031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
Granulins (GRN 1-7) are short (~6 kDa), cysteine-rich proteins that are generated upon the proteolytic processing of progranulin (PGRN). These peptides, along with their precursor, have been implicated in multiple pathophysiological roles, especially in neurodegenerative diseases. Previously we showed that GRN-3 and GRN-5 are fully disordered in the reduced form implicating redox sensitive attributes to the proteins. Redox-based modulations are often carried out by metalloproteins in mitigating oxidative stress and maintaining metal-homeostasis within cells. To probe whether GRNs play a role in metal sequestration, we tested the metal binding propensity of the reduced forms of GRNs -3 and - 5 under neutral and acidic pH mimicking cytosolic and lysosomal conditions, respectively. We found, at neutral pH, both GRNs selectively bind Cu and no other divalent metal cations, with a greater specificity for Cu(I). Binding of Cu did not result in a disorder-to-order structural transition but partly triggered the multimerization of GRNs via uncoordinated cystines at both pH conditions. Overall, the results indicate that GRNs -3 and - 5 have surprisingly strong affinity for Cu in the pM range, comparable to other known copper sequestering proteins. The results also hint at a potential of GRNs to reduce Cu(II) to Cu(I), a process that has significance in mitigating Cu-induced ROS cytotoxicity in cells. Together, this report uncovers metal-coordinating property of GRNs for the first time, which may have profound significance in their structure and pathophysiological functions.
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Affiliation(s)
- Anukool A Bhopatkar
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and, University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Vijayaraghavan Rangachari
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA
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25
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Chaplot K, Jarvela TS, Lindberg I. Secreted Chaperones in Neurodegeneration. Front Aging Neurosci 2020; 12:268. [PMID: 33192447 PMCID: PMC7481362 DOI: 10.3389/fnagi.2020.00268] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis, or proteostasis, is a combination of cellular processes that govern protein quality control, namely, protein translation, folding, processing, and degradation. Disruptions in these processes can lead to protein misfolding and aggregation. Proteostatic disruption can lead to cellular changes such as endoplasmic reticulum or oxidative stress; organelle dysfunction; and, if continued, to cell death. A majority of neurodegenerative diseases involve the pathologic aggregation of proteins that subverts normal neuronal function. While prior reviews of neuronal proteostasis in neurodegenerative processes have focused on cytoplasmic chaperones, there is increasing evidence that chaperones secreted both by neurons and other brain cells in the extracellular - including transsynaptic - space play important roles in neuronal proteostasis. In this review, we will introduce various secreted chaperones involved in neurodegeneration. We begin with clusterin and discuss its identification in various protein aggregates, and the use of increased cerebrospinal fluid (CSF) clusterin as a potential biomarker and as a potential therapeutic. Our next secreted chaperone is progranulin; polymorphisms in this gene represent a known genetic risk factor for frontotemporal lobar degeneration, and progranulin overexpression has been found to be effective in reducing Alzheimer's- and Parkinson's-like neurodegenerative phenotypes in mouse models. We move on to BRICHOS domain-containing proteins, a family of proteins containing highly potent anti-amyloidogenic activity; we summarize studies describing the biochemical mechanisms by which recombinant BRICHOS protein might serve as a therapeutic agent. The next section of the review is devoted to the secreted chaperones 7B2 and proSAAS, small neuronal proteins which are packaged together with neuropeptides and released during synaptic activity. Since proteins can be secreted by both classical secretory and non-classical mechanisms, we also review the small heat shock proteins (sHsps) that can be secreted from the cytoplasm to the extracellular environment and provide evidence for their involvement in extracellular proteostasis and neuroprotection. Our goal in this review focusing on extracellular chaperones in neurodegenerative disease is to summarize the most recent literature relating to neurodegeneration for each secreted chaperone; to identify any common mechanisms; and to point out areas of similarity as well as differences between the secreted chaperones identified to date.
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Affiliation(s)
| | | | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
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