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Lang R, Hodgson RE, Shelkovnikova TA. TDP-43 in nuclear condensates: where, how, and why. Biochem Soc Trans 2024; 52:1809-1825. [PMID: 38958608 DOI: 10.1042/bst20231447] [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: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
TDP-43 is an abundant and ubiquitously expressed nuclear protein that becomes dysfunctional in a spectrum of neurodegenerative diseases. TDP-43's ability to phase separate and form/enter biomolecular condensates of varying size and composition is critical for its functionality. Despite the high density of phase-separated assemblies in the nucleus and the nuclear abundance of TDP-43, our understanding of the condensate-TDP-43 relationship in this cellular compartment is only emerging. Recent studies have also suggested that misregulation of nuclear TDP-43 condensation is an early event in the neurodegenerative disease amyotrophic lateral sclerosis. This review aims to draw attention to the nuclear facet of functional and aberrant TDP-43 condensation. We will summarise the current knowledge on how TDP-43 containing nuclear condensates form and function and how their homeostasis is affected in disease.
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Affiliation(s)
- Ruaridh Lang
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN) and Neuroscience Institute, University of Sheffield, Sheffield, U.K
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2
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Gatch AJ, Ding F. TDP-43 Promotes Amyloid-Beta Toxicity by Delaying Fibril Maturation via Direct Molecular Interaction. ACS Chem Neurosci 2024; 15:2936-2953. [PMID: 39073874 PMCID: PMC11323227 DOI: 10.1021/acschemneuro.4c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024] Open
Abstract
Amyloid-β (Aβ) is a peptide that undergoes self-assembly into amyloid fibrils, which compose the hallmark plaques observed in Alzheimer's disease (AD). TAR DNA-binding protein 43 (TDP-43) is a protein with mislocalization and aggregation implicated in amyotrophic lateral sclerosis and other neurodegenerative diseases. Recent work suggests that TDP-43 may interact with Aβ, inhibiting the formation of amyloid fibrils and worsening AD pathology, but the molecular details of their interaction remain unknown. Using all-atom discrete molecular dynamics simulations, we systematically investigated the direct molecular interaction between Aβ and TDP-43. We found that Aβ monomers were able to bind near the flexible nuclear localization sequence of the N-terminal domain (NTD) of TDP-43, adopting β-sheet rich conformations that were promoted by the interaction. Furthermore, Aβ associated with the nucleic acid binding interface of the tandem RNA recognition motifs of TDP-43 via electrostatic interactions. Using the computational peptide array method, we found the strongest C-terminal domain interaction with Aβ to be within the amyloidogenic core region of TDP-43. With experimental evidence suggesting that the NTD is necessary for inhibiting Aβ fibril growth, we also simulated the NTD with an Aβ40 fibril seed. We found that the NTD was able to strongly bind the elongation surface of the fibril seed via extensive hydrogen bonding and could also diffuse along the lateral surface via electrostatic interactions. Our results suggest that TDP-43 binding to the elongation surface, thereby sterically blocking Aβ monomer addition, is responsible for the experimentally observed inhibition of fibril growth. We conclude that TDP-43 may promote Aβ toxicity by stabilizing the oligomeric state and kinetically delaying fibril maturation.
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Affiliation(s)
- Adam J. Gatch
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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3
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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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4
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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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5
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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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6
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Doke AA, Jha SK. Electrostatics Choreographs the Aggregation Dynamics of Full-Length TDP-43 via a Monomeric Amyloid Precursor. Biochemistry 2024; 63:1553-1568. [PMID: 38820318 DOI: 10.1021/acs.biochem.4c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
TDP-43 is a ubiquitously expressed, multidomain functional protein that is distinctively known to form aggregates in many fatal neurodegenerative disorders. However, the information for arresting TDP-43 aggregation is missing due to a lack of understanding of the molecular mechanism of the aggregation and structural properties of TDP-43. TDP-43 is inherently prone to aggregation and has minimal protein solubility. Multiple studies have been performed on the smaller parts of TDP-43 or the full-length protein attached to a large solubilization tag. However, the presence of co-solutes or solubilization tags is observed to interfere with the molecular properties and aggregation mechanism of full-length TDP-43. Notably, this study populated and characterized the native, dimeric state of TDP-43 without the interference of co-solutes or protein modifications. We observed that the electrostatics of the local environment is capable of the partial unfolding and monomerization of the native dimeric state of TDP-43 into an amyloidogenic molten globule. By employing the tools of thermodynamics and kinetics, we reveal the structural characteristics and temporal order of the early intermediates and transition states during the transition of the molten globule to β-rich, amyloid-like aggregates of TDP-43, which is governed by the electrostatics of the environment. The current advanced understanding of the nature of native and early aggregation-prone intermediates, early steps, and the influence of electrostatics in TDP-43 aggregation is essential for drug design.
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Affiliation(s)
- Abhilasha A Doke
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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7
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Schneider TR, Stöckli L, Felbecker A, Nirmalraj PN. Protein fibril aggregation on red blood cells: a potential biomarker to distinguish neurodegenerative diseases from healthy aging. Brain Commun 2024; 6:fcae180. [PMID: 38873003 PMCID: PMC11170662 DOI: 10.1093/braincomms/fcae180] [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: 07/21/2023] [Revised: 04/19/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Neurodegenerative diseases like Alzheimer's disease are characterized by the accumulation of misfolded proteins into fibrils in the brain. Atomic force microscopy is a nanoscale imaging technique that can be used to resolve and quantify protein aggregates from oligomers to fibrils. Recently, we characterized protein fibrillar aggregates adsorbed on the surface of red blood cells with atomic force microscopy from patients with neurocognitive disorders, suggesting a novel Alzheimer's disease biomarker. However, the age association of fibril deposits on red blood cells has not yet been studied in detail in healthy adults. Here, we used atomic force microscopy to visualize and quantify fibril coverage on red blood cells in 50 healthy adults and 37 memory clinic patients. Fibrillar protein deposits sporadically appeared in healthy individuals but were much more prevalent in patients with neurodegenerative disease, especially those with Alzheimer's disease as confirmed by positive CSF amyloid beta 1-42/1-40 ratios. The prevalence of fibrils on the red blood cell surface did not significantly correlate with age in either healthy individuals or Alzheimer's disease patients. The overlap in fibril prevalence on red blood cells between Alzheimer's disease and amyloid-negative patients suggests that fibril deposition on red blood cells could occur in various neurodegenerative diseases. Quantifying red blood cell protein fibril morphology and prevalence on red blood cells could serve as a sensitive biomarker for neurodegeneration, distinguishing between healthy individuals and those with neurodegenerative diseases. Future studies that combine atomic force microscopy with immunofluorescence techniques in larger-scale studies could further identify the chemical nature of these fibrils, paving the way for a comprehensive, non-invasive biomarker platform for neurodegenerative diseases.
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Affiliation(s)
| | - Luisa Stöckli
- Department of Neurology, Cantonal Hospital St. Gallen, St. Gallen CH-9007, Switzerland
| | - Ansgar Felbecker
- Department of Neurology, Cantonal Hospital St. Gallen, St. Gallen CH-9007, Switzerland
| | - Peter Niraj Nirmalraj
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf CH-8600, Switzerland
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8
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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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9
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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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10
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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11
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Pokrishevsky E, DuVal MG, McAlary L, Louadi S, Pozzi S, Roman A, Plotkin SS, Dijkstra A, Julien JP, Allison WT, Cashman NR. Tryptophan residues in TDP-43 and SOD1 modulate the cross-seeding and toxicity of SOD1. J Biol Chem 2024; 300:107207. [PMID: 38522514 PMCID: PMC11087967 DOI: 10.1016/j.jbc.2024.107207] [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: 10/02/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease of motor neurons. Neuronal superoxide dismutase-1 (SOD1) inclusion bodies are characteristic of familial ALS with SOD1 mutations, while a hallmark of sporadic ALS is inclusions containing aggregated WT TAR DNA-binding protein 43 (TDP-43). We show here that co-expression of mutant or WT TDP-43 with SOD1 leads to misfolding of endogenous SOD1 and aggregation of SOD1 reporter protein SOD1G85R-GFP in human cell cultures and promotes synergistic axonopathy in zebrafish. Intriguingly, this pathological interaction is modulated by natively solvent-exposed tryptophans in SOD1 (tryptophan-32) and TDP-43 RNA-recognition motif RRM1 (tryptophan-172), in concert with natively sequestered TDP-43 N-terminal domain tryptophan-68. TDP-43 RRM1 intrabodies reduce WT SOD1 misfolding in human cell cultures, via blocking tryptophan-172. Tryptophan-68 becomes antibody-accessible in aggregated TDP-43 in sporadic ALS motor neurons and cell culture. 5-fluorouridine inhibits TDP-43-induced G85R-GFP SOD1 aggregation in human cell cultures and ameliorates axonopathy in zebrafish, via its interaction with SOD1 tryptophan-32. Collectively, our results establish a novel and potentially druggable tryptophan-mediated mechanism whereby two principal ALS disease effector proteins might directly interact in disease.
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Affiliation(s)
- Edward Pokrishevsky
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michéle G DuVal
- Department of Biological Sciences, Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Alberta, Canada
| | - Luke McAlary
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada; Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah Louadi
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Silvia Pozzi
- Department of Psychiatry and Neuroscience, University of Laval, Québec, Quebec, Canada; CERVO Brain Research Center, Québec, Quebec, Canada
| | - Andrei Roman
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anke Dijkstra
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | - Jean-Pierre Julien
- Department of Psychiatry and Neuroscience, University of Laval, Québec, Quebec, Canada; CERVO Brain Research Center, Québec, Quebec, Canada
| | - W Ted Allison
- Department of Biological Sciences, Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, Alberta, Canada.
| | - Neil R Cashman
- Department of Medicine, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada.
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12
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Mumford TR, Rae D, Brackhahn E, Idris A, Gonzalez-Martinez D, Pal AA, Chung MC, Guan J, Rhoades E, Bugaj LJ. Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter. Cell Syst 2024; 15:166-179.e7. [PMID: 38335954 PMCID: PMC10947474 DOI: 10.1016/j.cels.2024.01.005] [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: 08/22/2022] [Revised: 11/06/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Protein clustering plays numerous roles in cell physiology and disease. However, protein oligomers can be difficult to detect because they are often too small to appear as puncta in conventional fluorescence microscopy. Here, we describe a fluorescent reporter strategy that detects protein clusters with high sensitivity called CluMPS (clusters magnified by phase separation). A CluMPS reporter detects and visually amplifies even small clusters of a binding partner, generating large, quantifiable fluorescence condensates. We use computational modeling and optogenetic clustering to demonstrate that CluMPS can detect small oligomers and behaves rationally according to key system parameters. CluMPS detected small aggregates of pathological proteins where the corresponding GFP fusions appeared diffuse. CluMPS also detected and tracked clusters of unmodified and tagged endogenous proteins, and orthogonal CluMPS probes could be multiplexed in cells. CluMPS provides a powerful yet straightforward approach to observe higher-order protein assembly in its native cellular context. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Thomas R Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Diarmid Rae
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Brackhahn
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abbas Idris
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ayush Aditya Pal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Chung
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
| | - Juan Guan
- Department of Physics, University of Florida, Gainesville, FL 32611, USA; Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Yang L, Jasiqi Y, Lashuel H. Recombinant Full-Length TDP-43 Oligomers Retain Their Ability to Bind RNAs, Are Not Toxic, and Do Not Seed TDP-43 Aggregation in Vitro. ACS Chem Neurosci 2024; 15:193-204. [PMID: 38116987 PMCID: PMC10767740 DOI: 10.1021/acschemneuro.3c00691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
TAR DNA-binding protein with 43 kD (TDP-43) is a partially disordered protein that misfolds and accumulates in the brains of patients affected by several neurodegenerative diseases. TDP-43 oligomers have been reported to form due to aberrant misfolding or self-assembly of TDP-43 monomers. However, very little is known about the molecular and structural basis of TDP-43 oligomerization and the toxic properties of TDP-43 oligomers due to several reasons, including the lack of conditions available for isolating native TDP-43 oligomers or producing pure TDP-43 oligomers in sufficient quantities for biophysical, cellular, and in vivo studies. To address these challenges, we developed new protocols to generate different stable forms of unmodified and small-molecule-induced TDP-43 oligomers. Our results showed that co-incubation of TDP-43 with small molecules, such as epigallocatechin gallate (EGCG), dopamine, and 4-hydroxynonenal (4-HNE), increased the production yield of TDP-43 stable oligomers, which could be purified by size-exclusion chromatography. Interestingly, despite significant differences in the morphology and size distribution of the TDP-43 oligomer preparations revealed by transmission electron microscopy (TEM) and dynamic light scattering (DLS), they all retained the ability to bind to nucleotide DNA. Besides, circular dichroism (CD) analysis of these oligomers did not show much difference in the secondary structure composition. Surprisingly, none of these oligomer preparations could seed the aggregation of TDP-43 core peptide 279-360. Finally, we showed that all four types of TDP-43 oligomers exert very mild cytotoxicity to primary neurons. Collectively, our results suggest that functional TDP-43 oligomers can be selectively stabilized by small-molecule compounds. This strategy may offer a new approach to halt TDP-43 aggregation in various proteinopathies.
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Affiliation(s)
- Lixin Yang
- Laboratory of Molecular and
Chemical Biology of Neurodegeneration, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yllza Jasiqi
- Laboratory of Molecular and
Chemical Biology of Neurodegeneration, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Hilal Lashuel
- Laboratory of Molecular and
Chemical Biology of Neurodegeneration, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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14
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Liu X, Duan S, Jin Y, Walker E, Tsao M, Jang JH, Chen Z, Singh AK, Cantrell KL, Ingolfsson HI, Buratto SK, Bowers MT. Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43 307-319 Aggregation. ACS Chem Neurosci 2023; 14:4395-4408. [PMID: 38050862 DOI: 10.1021/acschemneuro.3c00582] [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: 12/07/2023] Open
Abstract
Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43307-319, but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43307-319 monomer. The JPS-designed molecules can insert themselves between the β-strands in the hexameric cylindrin structure of TDP-43307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43307-319 oligomers on an atomistic scale are proposed.
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Affiliation(s)
- Xikun Liu
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Shuya Duan
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yingying Jin
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ethan Walker
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Michelle Tsao
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joshua H Jang
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Ziying Chen
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ambuj K Singh
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kristi Lazar Cantrell
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Helgi I Ingolfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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15
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Babazadeh A, Rayner SL, Lee A, Chung RS. TDP-43 as a therapeutic target in neurodegenerative diseases: Focusing on motor neuron disease and frontotemporal dementia. Ageing Res Rev 2023; 92:102085. [PMID: 37813308 DOI: 10.1016/j.arr.2023.102085] [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: 07/13/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
A common feature of adult-onset neurodegenerative diseases is the presence of characteristic pathological accumulations of specific proteins. These pathological protein depositions can vary in their protein composition, cell-type distribution, and intracellular (or extracellular) location. For example, abnormal cytoplasmic protein deposits which consist of the TDP-43 protein are found within motor neurons in patients with amyotrophic lateral sclerosis (ALS, a common form of motor neuron disease) and frontotemporal dementia (FTD). The presence of these insoluble intracellular TDP-43 inclusions suggests that restoring TDP-43 homeostasis represents a potential therapeutical strategy, which has been demonstrated in alleviating neurodegenerative symptoms in cell and animal models of ALS/FTD. We have reviewed the mechanisms that lead to disrupted TDP-43 homeostasis and discussed how small molecule-based therapies could be applied in modulating these mechanisms. This review covers recent advancements and challenges in small molecule-based therapies that could be used to clear pathological forms of TDP-43 through various protein homeostasis mechanisms and advance the way towards finding effective therapeutical drug discoveries for neurodegenerative diseases characterized by TDP-43 proteinopathies, especially ALS and FTD. We also consider the wider insight of these therapeutic strategies for other neurodegenerative diseases.
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Affiliation(s)
- Afshin Babazadeh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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16
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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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17
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Minogue G, Kawles A, Zouridakis A, Keszycki R, Macomber A, Lubbat V, Gill N, Mao Q, Flanagan ME, Zhang H, Castellani R, Bigio EH, Mesulam MM, Geula C, Gefen T. Distinct Patterns of Hippocampal Pathology in Alzheimer's Disease with Transactive Response DNA-binding Protein 43. Ann Neurol 2023; 94:1036-1047. [PMID: 37592884 PMCID: PMC10872839 DOI: 10.1002/ana.26762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 07/31/2023] [Accepted: 08/05/2023] [Indexed: 08/19/2023]
Abstract
OBJECTIVE Age-related dementia syndromes are often not related to a single pathophysiological process, leading to multiple neuropathologies found at autopsy. An amnestic dementia syndrome can be associated with Alzheimer's disease (AD) with comorbid transactive response DNA-binding protein 43 (TDP-43) pathology (AD/TDP). Here, we investigated neuronal integrity and pathological burden of TDP-43 and tau, along the well-charted trisynaptic hippocampal circuit (dentate gyrus [DG], CA3, and CA1) in participants with amnestic dementia due to AD/TDP, amnestic dementia due to AD alone, or non-amnestic dementia due to TDP-43 proteinopathy associated with frontotemporal lobar degeneration (FTLD-TDP). METHODS A total of 48 extensively characterized cases (14 AD, 16 AD/TDP, 18 FTLD-TDP) were analyzed using digital HALO software (Indica Labs, Albuquerque, NM, USA) to quantify pathological burden and neuronal loss. RESULTS In AD/TDP and FTLD-TDP, TDP-43 immunoreactivity was greatest in the DG. Tau immunoreactivity was significantly greater in DG and CA3 in AD/TDP compared with pure AD. All clinical groups showed the highest amounts of neurons in DG, followed by CA3, then CA1. The AD and AD/TDP groups showed lower neuronal counts compared with the FTLD-TDP group across all hippocampal subregions consistent with the salience of the amnestic phenotype. INTERPRETATION We conclude that AD/TDP can be distinguished from AD and FTLD-TDP based on differential regional distributions of hippocampal tau and TDP-43. Findings suggest that tau aggregation in AD/TDP might be enhanced by TDP-43. ANN NEUROL 2023;94:1036-1047.
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Affiliation(s)
- Grace Minogue
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Allegra Kawles
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Antonia Zouridakis
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Rachel Keszycki
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Alyssa Macomber
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Vivienne Lubbat
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Nathan Gill
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Qinwen Mao
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Margaret E. Flanagan
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Hui Zhang
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Rudolph Castellani
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Eileen H. Bigio
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - M.-Marsel Mesulam
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Tamar Gefen
- Mesulam Center for Cognitive Neurology and Alzheimer’s Disease, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL
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18
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Ingólfsson HI, Rizuan A, Liu X, Mohanty P, Souza PCT, Marrink SJ, Bowers MT, Mittal J, Berry J. Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation. Biophys J 2023; 122:4370-4381. [PMID: 37853696 PMCID: PMC10720261 DOI: 10.1016/j.bpj.2023.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/27/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023] Open
Abstract
The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent C⍺ model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.
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Affiliation(s)
- Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.
| | - Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas
| | - Xikun Liu
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California; Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, Lyon, France; Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M College of Engineering, College Station, Texas; Department of Chemistry, Texas A&M University, College Station, Texas; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas
| | - Joel Berry
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
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19
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Ortiz GG, Ramírez-Jirano J, Arizaga RL, Delgado-Lara DLC, Torres-Sánchez ED. Frontotemporal-TDP and LATE Neurocognitive Disorders: A Pathophysiological and Genetic Approach. Brain Sci 2023; 13:1474. [PMID: 37891841 PMCID: PMC10605418 DOI: 10.3390/brainsci13101474] [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: 09/15/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Frontotemporal lobar degeneration (FTLD) belongs to a heterogeneous group of highly complex neurodegenerative diseases and represents the second cause of presenile dementia in individuals under 65. Frontotemporal-TDP is a subgroup of frontotemporal dementia characterized by the aggregation of abnormal protein deposits, predominantly transactive response DNA-binding protein 43 (TDP-43), in the frontal and temporal brain regions. These deposits lead to progressive degeneration of neurons resulting in cognitive and behavioral impairments. Limbic age-related encephalopathy (LATE) pertains to age-related cognitive decline primarily affecting the limbic system, which is crucial for memory, emotions, and learning. However, distinct, emerging research suggests a potential overlap in pathogenic processes, with some cases of limbic encephalopathy displaying TDP-43 pathology. Genetic factors play a pivotal role in both disorders. Mutations in various genes, such as progranulin (GRN) and chromosome 9 open reading frame 72 (C9orf72), have been identified as causative in frontotemporal-TDP. Similarly, specific genetic variants have been associated with an increased risk of developing LATE. Understanding these genetic links provides crucial insights into disease mechanisms and the potential for targeted therapies.
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Affiliation(s)
- Genaro Gabriel Ortiz
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico;
- Postgraduate Gerontology Program, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Javier Ramírez-Jirano
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute, IMSS, Guadalajara 44340, Jalisco, Mexico;
| | - Raul L. Arizaga
- Public Health Department, School of Medicine, University of Buenos Aires, Buenos Aires C1121ABG, Argentina;
| | - Daniela L. C. Delgado-Lara
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico;
- Departamento Académico de Formación Universitaria, Ciencias de la Salud, Universidad Autónoma de Guadalajara, Zapopan 45129, Jalisco, Mexico
| | - Erandis D. Torres-Sánchez
- Department of Medical and Life Sciences, University Center of la Cienega, University of Guadalajara, Ocotlan 47820, Jalisco, Mexico
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20
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Tomé SO, Tsaka G, Ronisz A, Ospitalieri S, Gawor K, Gomes LA, Otto M, von Arnim CAF, Van Damme P, Van Den Bosch L, Ghebremedhin E, Laureyssen C, Sleegers K, Vandenberghe R, Rousseau F, Schymkowitz J, Thal DR. TDP-43 pathology is associated with increased tau burdens and seeding. Mol Neurodegener 2023; 18:71. [PMID: 37777806 PMCID: PMC10544192 DOI: 10.1186/s13024-023-00653-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Most Alzheimer's Disease (AD) cases also exhibit limbic predominant age-related TDP-43 encephalopathy neuropathological changes (LATE-NC), besides amyloid-β plaques and neurofibrillary tangles (NFTs) containing hyperphosphorylated tau (p-tau). LATE-NC is characterized by cytoplasmic aggregates positive for pathological TDP-43 and is associated with more severe clinical outcomes in AD, compared to AD cases lacking TDP-43 pathology TDP-43: AD(LATE-NC-). Accumulating evidence suggests that TDP-43 and p-tau interact and exhibit pathological synergy during AD pathogenesis. However, it is not yet fully understood how the presence of TDP-43 affects p-tau aggregation in symptomatic AD. METHODS In this study, we investigated the impact of TDP-43 proteinopathy on p-tau pathology with different approaches: histologically, in a human post-mortem cohort (n = 98), as well as functionally using a tau biosensor cell line and TDP-43A315T transgenic mice. RESULTS We found that AD cases with comorbid LATE-NC, AD(LATE-NC+), have increased burdens of pretangles and/or NFTs as well as increased brain levels of p-tau199, compared to AD(LATE-NC-) cases and controls. The burden of TDP-43 pathology was also correlated with the Braak NFT stages. A tau biosensor cell line treated with sarkosyl-insoluble, brain-derived homogenates from AD(LATE-NC+) cases displayed exacerbated p-tau seeding, compared to control and AD(LATE-NC-)-treated cells. Consistently, TDP-43A315T mice injected with AD(LATE-NC+)-derived extracts also exhibited a more severe hippocampal seeding, compared to the remaining experimental groups, albeit no TDP-43 aggregation was observed. CONCLUSIONS Our findings extend the current knowledge by supporting a functional synergy between TDP-43 and p-tau. We further demonstrate that TDP-43 pathology worsens p-tau aggregation in an indirect manner and increases its seeding potential, probably by increasing p-tau levels. This may ultimately contribute to tau-driven neurotoxicity and cell death. Because most AD cases present with comorbid LATE-NC, this study has an impact on the understanding of TDP-43 and tau pathogenesis in AD and LATE, which account for the majority of dementia cases worldwide. Moreover, it highlights the need for the development of a biomarker that detects TDP-43 during life, in order to properly stratify AD and LATE patients.
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Affiliation(s)
- Sandra O Tomé
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, Leuven, Belgium.
| | - Grigoria Tsaka
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Alicja Ronisz
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Simona Ospitalieri
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Klara Gawor
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Luis Aragão Gomes
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
- Department of Neurology, University of Halle, Halle, Germany
| | - Christine A F von Arnim
- Department of Neurology, University of Ulm, Ulm, Germany
- Department of Geriatrics, University Medical Center Göttingen, Göttingen, Germany
| | - Philip Van Damme
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Laboratory for Neurobiology - VIB-KU Leuven, Leuven, Belgium
- Department of Neurology, UZ Leuven, Leuven, Belgium
| | - Ludo Van Den Bosch
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Laboratory for Neurobiology - VIB-KU Leuven, Leuven, Belgium
| | - Estifanos Ghebremedhin
- Institute for Clinical Neuroanatomy - Johann Wolfgang Goethe University, Frankfurt Am Main, Germany
| | - Celeste Laureyssen
- Complex Genetics of Alzheimer's Disease Group, VIB-University of Antwerp Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB-University of Antwerp Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Rik Vandenberghe
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Department of Neurology, UZ Leuven, Leuven, Belgium
- Laboratory of Experimental Neurology - Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Dietmar Rudolf Thal
- Laboratory of Neuropathology - Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Department of Pathology, UZ Leuven, Leuven, Belgium
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21
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Kulichikhin KY, Malikova OA, Zobnina AE, Zalutskaya NM, Rubel AA. Interaction of Proteins Involved in Neuronal Proteinopathies. Life (Basel) 2023; 13:1954. [PMID: 37895336 PMCID: PMC10608209 DOI: 10.3390/life13101954] [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: 08/15/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Proteinopathy is characterized by the accumulation of aggregates of a specific protein in a target organ, tissue, or cell. The aggregation of the same protein can cause different pathologies as single protein can adopt various amyloidogenic, disease-specific conformations. The conformation governs the interaction of amyloid aggregates with other proteins that are prone to misfolding and, thus, determines disease-specific spectrum of concomitant pathologies. In this regard, a detailed description of amyloid protein conformation as well as spectrum of its interaction with other proteins become a key point for drafting of precise description of the disease. The majority of clinical cases of neuronal proteinopathies is caused by the aggregation of rather limited range of amyloidogenic proteins. Here, we provided the characterization of pathologies, related to the aggregation of amyloid β peptide, tau protein, α-synuclein, TDP-43, and amylin, giving a short description of pathologies themselves, recent advances in elucidation of misfolded protein conformation, with emphasis on those protein aggregates extracted from biological samples, what is known about the interaction of this proteins, and the influence of this interaction on the progression of underlying disease and comorbidities.
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Affiliation(s)
- Konstantin Y. Kulichikhin
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
| | - Oksana A. Malikova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
| | - Anastasia E. Zobnina
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
| | - Natalia M. Zalutskaya
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, 192019 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
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22
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Jamerlan AM, Shim KH, Youn YC, Teunissen C, An SSA, Scheltens P, Kim S. Increased oligomeric TDP-43 in the plasma of Korean frontotemporal dementia patients with semantic dementia. Alzheimers Dement 2023; 19:4020-4027. [PMID: 37200243 DOI: 10.1002/alz.13127] [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: 02/21/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/20/2023]
Abstract
INTRODUCTION Semantic dementia (SD) is a progressive neurodegenerative disease associated with impaired vocabulary that progresses to memory impairment. Post-mortem immunohistochemical analysis is the current reliable method of differentiating TDP-43 deposits in cortical tissue; no means of antemortem diagnosis exists in biofluids, let alone in plasma. METHODS Here the multimer detection system (MDS) was used to quantify the oligomeric TDP-43 (o-TDP-43) concentrations in plasma of Korean SD patients (n = 16, 6 male, 10 female, ages 59-87). The o-TDP-43 concentrations were compared with the total TDP-43 (t-TDP-43) concentrations quantified through conventional enzyme-linked immunosorbent assay (ELISA). RESULTS AND DISCUSSION Only MDS showed a significant increase in o-TDP-43 concentrations in the plasma of patients with SD compared to other neurodegenerative disorders and normal controls (p < 0.05). Based on these results, o-TDP-43 concentrations through the application of MDS may be a useful plasma biomarker in SD-FTD (frontotemporal dementia) diagnosis.
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Affiliation(s)
- Angelo M Jamerlan
- Department of Bionano Technology, Bionano Research Institute, Gachon University, Gyeonggi-do, Republic of Korea
| | - Kyu Hwan Shim
- Department of Bionano Technology, Bionano Research Institute, Gachon University, Gyeonggi-do, Republic of Korea
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University Hospital, Seoul, Republic of Korea
| | - Charlotte Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Seong Soo A An
- Department of Bionano Technology, Bionano Research Institute, Gachon University, Gyeonggi-do, Republic of Korea
| | - Philip Scheltens
- Department of Neurology & Alzheimer Center, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - SangYun Kim
- Department of Neurology, Seoul National University Bundang Hospital & Seoul National University College of Medicine, Gyeonggi-do, Republic of Korea
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23
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [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: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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24
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Behera A, Sa N, Pradhan SP, Swain S, Sahu PK. Metal Nanoparticles in Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:791-810. [PMID: 37662608 PMCID: PMC10473155 DOI: 10.3233/adr-220112] [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: 12/26/2022] [Accepted: 06/21/2023] [Indexed: 09/05/2023] Open
Abstract
Nanotechnology has emerged in different fields of biomedical application, including lifestyle diseases like diabetes, hypertension, and chronic kidney disease, neurodegenerative diseases like Alzheimer's disease (AD), Parkinson's disease, and different types of cancers. Metal nanoparticles are one of the most used drug delivery systems due to the benefits of their enhanced physicochemical properties as compared to bulk metals. Neurodegenerative diseases are the second most cause affecting mortality worldwide after cancer. Hence, they require the most specific and targeted drug delivery systems for maximum therapeutic benefits. Metal nanoparticles are the preferred drug delivery system, possessing greater blood-brain barrier permeability, biocompatibility, and enhanced bioavailability. But some metal nanoparticles exhibit neurotoxic activity owing to their shape, size, surface charge, or surface modification. This review article has discussed the pathophysiology of AD. The neuroprotective mechanism of gold, silver, selenium, ruthenium, cerium oxide, zinc oxide, and iron oxide nanoparticles are discussed. Again, the neurotoxic mechanisms of gold, iron oxide, titanium dioxide, and cobalt oxide are also included. The neuroprotective and neurotoxic effects of nanoparticles targeted for treating AD are discussed elaborately. The review also focusses on the biocompatibility of metal nanoparticles for targeting the brain in treating AD. The clinical trials and the requirement to develop new drug delivery systems are critically analyzed. This review can show a path for the researchers involved in the brain-targeted drug delivery for AD.
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Affiliation(s)
- Anindita Behera
- School of Pharmaceutical Sciences, Siksha’ O’Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Nishigandha Sa
- School of Pharmaceutical Sciences, Siksha’ O’Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | | | - Sunsita Swain
- School of Pharmaceutical Sciences, Siksha’ O’Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Pratap Kumar Sahu
- School of Pharmaceutical Sciences, Siksha’ O’Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
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25
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Zaman M, Fu Y, Chen PC, Sun H, Yang S, Wu Z, Wang Z, Poudel S, Serrano GE, Beach TG, Li L, Wang X, Peng J. Dissecting Detergent-Insoluble Proteome in Alzheimer's Disease by TMTc-Corrected Quantitative Mass Spectrometry. Mol Cell Proteomics 2023; 22:100608. [PMID: 37356496 PMCID: PMC10392608 DOI: 10.1016/j.mcpro.2023.100608] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023] Open
Abstract
Protein aggregation of amyloid-β peptides and tau are pathological hallmarks of Alzheimer's disease (AD), which are often resistant to detergent extraction and thus enriched in the insoluble proteome. However, additional proteins that coaccumulate in the detergent-insoluble AD brain proteome remain understudied. Here, we comprehensively characterized key proteins and pathways in the detergent-insoluble proteome from human AD brain samples using differential extraction, tandem mass tag (TMT) labeling, and two-dimensional LC-tandem mass spectrometry. To improve quantification accuracy of the TMT method, we developed a complement TMT-based strategy to correct for ratio compression. Through the meta-analysis of two independent detergent-insoluble AD proteome datasets (8914 and 8917 proteins), we identified 190 differentially expressed proteins in AD compared with control brains, highlighting the pathways of amyloid cascade, RNA splicing, endocytosis/exocytosis, protein degradation, and synaptic activity. To differentiate the truly detergent-insoluble proteins from copurified background during protein extraction, we analyzed the fold of enrichment for each protein by comparing the detergent-insoluble proteome with the whole proteome from the same AD samples. Among the 190 differentially expressed proteins, 84 (51%) proteins of the upregulated proteins (n = 165) were enriched in the insoluble proteome, whereas all downregulated proteins (n = 25) were not enriched, indicating that they were copurified components. The vast majority of these enriched 84 proteins harbor low-complexity regions in their sequences, including amyloid-β, Tau, TARDBP/TAR DNA-binding protein 43, SNRNP70/U1-70K, MDK, PTN, NTN1, NTN3, and SMOC1. Moreover, many of the enriched proteins in AD were validated in the detergent-insoluble proteome by five steps of differential extraction, proteomic analysis, or immunoblotting. Our study reveals a resource list of proteins and pathways that are exclusively present in the detergent-insoluble proteome, providing novel molecular insights to the formation of protein pathology in AD.
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Affiliation(s)
- Masihuz Zaman
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yingxue Fu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ping-Chung Chen
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Huan Sun
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shu Yang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zhiping Wu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zhen Wang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Ling Li
- Department of Biology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
| | - Junmin Peng
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA; Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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26
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Hurtle BT, Xie L, Donnelly CJ. Disrupting pathologic phase transitions in neurodegeneration. J Clin Invest 2023; 133:e168549. [PMID: 37395272 DOI: 10.1172/jci168549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Solid-like protein deposits found in aged and diseased human brains have revealed a relationship between insoluble protein accumulations and the resulting deficits in neurologic function. Clinically diverse neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis, exhibit unique and disease-specific biochemical protein signatures and abnormal protein depositions that often correlate with disease pathogenesis. Recent evidence indicates that many pathologic proteins assemble into liquid-like protein phases through the highly coordinated process of liquid-liquid phase separation. Over the last decade, biomolecular phase transitions have emerged as a fundamental mechanism of cellular organization. Liquid-like condensates organize functionally related biomolecules within the cell, and many neuropathology-associated proteins reside within these dynamic structures. Thus, examining biomolecular phase transitions enhances our understanding of the molecular mechanisms mediating toxicity across diverse neurodegenerative diseases. This Review explores the known mechanisms contributing to aberrant protein phase transitions in neurodegenerative diseases, focusing on tau and TDP-43 proteinopathies and outlining potential therapeutic strategies to regulate these pathologic events.
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Affiliation(s)
- Bryan T Hurtle
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Longxin Xie
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Christopher J Donnelly
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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27
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Mesulam MM, Gefen T, Flanagan M, Castellani R, Jamshidi P, Barbieri E, Sridhar J, Kawles A, Weintraub S, Geula C, Rogalski E. Frontotemporal Degeneration with Transactive Response DNA-Binding Protein Type C at the Anterior Temporal Lobe. Ann Neurol 2023; 94:1-12. [PMID: 37183762 PMCID: PMC10330481 DOI: 10.1002/ana.26677] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/06/2023] [Indexed: 05/16/2023]
Abstract
The anatomical distribution of most neurodegenerative diseases shows considerable interindividual variations. In contrast, frontotemporal lobar degeneration with transactive response DNA-binding protein type C (TDP-C) shows a consistent predilection for the anterior temporal lobe (ATL). The relatively selective atrophy of ATL in TDP-C patients has highlighted the importance of this region for complex cognitive and behavioral functions. This review includes observations on 28 TDP-C patients, 18 with semantic primary progressive aphasia and 10 with other syndromes. Longitudinal imaging allowed the delineation of progression trajectories. At post-mortem examination, the pathognomonic feature of TDP-C consisted of long, thick neurites found predominantly in superficial cortical layers. These neurites may represent dystrophic apical dendrites of layer III and V pyramidal neurons that are known to play pivotal roles in complex cortical computations. Other types of frontotemporal lobar degeneration TDP, such as TDP-A and TDP-B, are not associated with long dystrophic neurites in the cerebral cortex, and do not show similar predilection patterns for ATL. Research is beginning to identify molecular, structural, and immunological differences between pathological TDP-43 in TDP-C versus TDP-A and B. Parallel investigations based on proteomics, somatic mutations, and genome-wide association studies are detecting molecular features that could conceivably mediate the selective vulnerability of ATL to TDP-C. Future work will focus on characterizing the distinctive features of the abnormal TDP-C neurites, the mechanisms of neurotoxicity, initial cellular targets within the ATL, trajectory of spread, and the nature of ATL-specific markers that modulate vulnerability to TDP-C. ANN NEUROL 2023;94:1-12.
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Affiliation(s)
- Marek-Marsel Mesulam
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tamar Gefen
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Psychiatry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Margaret Flanagan
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rudolph Castellani
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pouya Jamshidi
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elena Barbieri
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jaiashre Sridhar
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Allegra Kawles
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Psychiatry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sandra Weintraub
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Psychiatry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emily Rogalski
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Psychiatry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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28
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Arnold FJ, Nguyen AD, Bedlack RS, Bennett CL, La Spada AR. Intercellular transmission of pathogenic proteins in ALS: Exploring the pathogenic wave. Neurobiol Dis 2023:106218. [PMID: 37394036 DOI: 10.1016/j.nbd.2023.106218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023] Open
Abstract
In patients with amyotrophic lateral sclerosis (ALS), disease symptoms and pathology typically spread in a predictable spatiotemporal pattern beginning at a focal site of onset and progressing along defined neuroanatomical tracts. Like other neurodegenerative diseases, ALS is characterized by the presence of protein aggregates in postmortem patient tissue. Cytoplasmic, ubiquitin-positive aggregates of TDP-43 are observed in approximately 97% of sporadic and familial ALS patients, while SOD1 inclusions are likely specific to cases of SOD1-ALS. Additionally, the most common subtype of familial ALS, caused by a hexanucleotide repeat expansion in the first intron of the C9orf72 gene (C9-ALS), is further characterized by the presence of aggregated dipeptide repeat proteins (DPRs). As we will describe, cell-to-cell propagation of these pathological proteins tightly correlates with the contiguous spread of disease. While TDP-43 and SOD1 are capable of seeding protein misfolding and aggregation in a prion-like manner, C9orf72 DPRs appear to induce (and transmit) a 'disease state' more generally. Multiple mechanisms of intercellular transport have been described for all of these proteins, including anterograde and retrograde axonal transport, extracellular vesicle secretion, and macropinocytosis. In addition to neuron-to-neuron transmission, transmission of pathological proteins occurs between neurons and glia. Given that the spread of ALS disease pathology corresponds with the spread of symptoms in patients, the various mechanisms by which ALS-associated protein aggregates propagate through the central nervous system should be closely examined.
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Affiliation(s)
- F J Arnold
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - A D Nguyen
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - R S Bedlack
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - C L Bennett
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - A R La Spada
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; Departments of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California, Irvine, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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29
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Kumar ST, Nazarov S, Porta S, Maharjan N, Cendrowska U, Kabani M, Finamore F, Xu Y, Lee VMY, Lashuel HA. Seeding the aggregation of TDP-43 requires post-fibrillization proteolytic cleavage. Nat Neurosci 2023:10.1038/s41593-023-01341-4. [PMID: 37248338 DOI: 10.1038/s41593-023-01341-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 04/18/2023] [Indexed: 05/31/2023]
Abstract
Despite the strong evidence linking the transactive response DNA-binding protein 43 (TDP-43) aggregation to the pathogenesis of frontotemporal lobar degeneration with TDP-43, amyotrophic lateral sclerosis and several neurodegenerative diseases, our knowledge of the sequence and structural determinants of its aggregation and neurotoxicity remains incomplete. Herein, we present a new method for producing recombinant full-length TDP-43 filaments that exhibit sequence and morphological features similar to those of brain-derived TDP-43 filaments. We show that TDP-43 filaments contain a β-sheet-rich helical amyloid core that is fully buried by the flanking structured domains of the protein. We demonstrate that the proteolytic cleavage of TDP-43 filaments and exposure of this amyloid core are necessary for propagating TDP-43 pathology and enhancing the seeding of brain-derived TDP-43 aggregates. Only TDP-43 filaments with exposed amyloid core efficiently seeded the aggregation of endogenous TDP-43 in cells. These findings suggest that inhibiting the enzymes mediating cleavage of TDP-43 aggregates represents a viable disease-modifying strategy to slow the progression of amyotrophic lateral sclerosis and other TDP-43 proteinopathies.
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Affiliation(s)
- Senthil T Kumar
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Sergey Nazarov
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Sílvia Porta
- Center for Neurodegenerative Disease Research (CNDR), Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Niran Maharjan
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Urszula Cendrowska
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Malek Kabani
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Francesco Finamore
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland
| | - Yan Xu
- Center for Neurodegenerative Disease Research (CNDR), Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research (CNDR), Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, EPFL, Lausanne, Switzerland.
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30
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Evangelista BA, Cahalan SR, Ragusa JV, Mordant A, Necarsulmer JC, Perna RJ, Ajit T, White K, Barker NK, Tian X, Cohen S, Meeker R, Herring LE, Cohen TJ. Tandem detergent-extraction and immunoprecipitation of proteinopathy: Scalable enrichment of ALS-associated TDP-43 aggregates. iScience 2023; 26:106645. [PMID: 37182104 PMCID: PMC10173608 DOI: 10.1016/j.isci.2023.106645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
Transactive response DNA-binding protein of 43 kDa (TDP-43) is a highly conserved, ubiquitously expressed nucleic acid-binding protein that regulates DNA/RNA metabolism. Genetics and neuropathology studies have linked TDP-43 to several neuromuscular and neurological disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Under pathological conditions, TDP-43 mislocalizes to the cytoplasm where it forms insoluble, hyper-phosphorylated aggregates during disease progression. Here, we optimized a scalable in vitro immuno-purification strategy referred to as tandem detergent-extraction and immunoprecipitation of proteinopathy (TDiP) to isolate TDP-43 aggregates that recapitulate those identified in postmortem ALS tissue. Moreover, we demonstrate that these purified aggregates can be utilized in biochemical, proteomics, and live-cell assays. This platform offers a rapid, accessible, and streamlined approach to study ALS disease mechanisms, while overcoming many limitations that have hampered TDP-43 disease modeling and therapeutic drug discovery efforts.
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Affiliation(s)
- Baggio A. Evangelista
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon R. Cahalan
- Medical Student Training in Aging Research, Center for Aging and Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joey V. Ragusa
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angie Mordant
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie C. Necarsulmer
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert J. Perna
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tejazaditya Ajit
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kristen White
- Microscopy Services Laboratory, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie K. Barker
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xu Tian
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rick Meeker
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura E. Herring
- Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Todd J. Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Tseng YL, Lu PC, Lee CC, He RY, Huang YA, Tseng YC, Cheng TJR, Huang JJT, Fang JM. Degradation of neurodegenerative disease-associated TDP-43 aggregates and oligomers via a proteolysis-targeting chimera. J Biomed Sci 2023; 30:27. [PMID: 37101169 PMCID: PMC10131537 DOI: 10.1186/s12929-023-00921-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) associated with TAR DNA-binding protein 43 (TDP-43) aggregation has been considered as a lethal and progressive motor neuron disease. Recent studies have shown that both C-terminal TDP-43 (C-TDP-43) aggregates and oligomers were neurotoxic and pathologic agents in ALS and frontotemporal lobar degeneration (FTLD). However, misfolding protein has long been considered as an undruggable target by applying conventional inhibitors, agonists, or antagonists. To provide this unmet medical need, we aim to degrade these misfolding proteins by designing a series of proteolysis targeting chimeras (PROTACs) against C-TDP-43. METHODS By applying filter trap assay, western blotting, and microscopy imaging, the degradation efficiency of C-TDP-43 aggregates was studied in Neuro-2a cells overexpressing eGFP-C-TDP-43 or mCherry-C-TDP-43. The cell viability was characterized by alarmarBlue assay. The beneficial and disaggregating effects of TDP-43 PROTAC were examined with the YFP-C-TDP-43 transgenic C. elegans by motility assay and confocal microscopy. The impact of TDP-43 PROTAC on C-TDP-43 oligomeric intermediates was monitored by fluorescence lifetime imaging microscopy and size exclusion chromatography in the Neuro-2a cells co-expressing eGFP-C-TDP-43 and mCherry-C-TDP-43. RESULTS Four PROTACs with different linker lengths were synthesized and characterized. Among these chimeras, PROTAC 2 decreased C-TDP-43 aggregates and relieved C-TDP-43-induced cytotoxicity in Neuro-2a cells without affecting endogenous TDP-43. We showed that PROTAC 2 bound to C-TDP-43 aggregates and E3 ligase to initiate ubiquitination and proteolytic degradation. By applying advanced microscopy, it was further shown that PROTAC 2 decreased the compactness and population of C-TDP-43 oligomers. In addition to cellular model, PROTAC 2 also improved the motility of transgenic C. elegans by reducing the C-TDP-43 aggregates in the nervous system. CONCLUSIONS Our study demonstrated the dual-targeting capacity of the newly-designed PROTAC 2 against both C-TDP-43 aggregates and oligomers to reduce their neurotoxicity, which shed light on the potential drug development for ALS as well as other neurodegenerative diseases.
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Affiliation(s)
- Yu-Ling Tseng
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Po-Chao Lu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department and Graduate Institute of Pharmacology, National Taiwan University, Taipei, 100, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yin-Chen Tseng
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
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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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Lin NH, Goh A, Lin SH, Chuang KA, Chang CH, Li MH, Lu CH, Chen WY, Wei PH, Pan IH, Perng MD, Wen SF. Neuroprotective Effects of a Multi-Herbal Extract on Axonal and Synaptic Disruption in Vitro and Cognitive Impairment in Vivo. J Alzheimers Dis Rep 2023; 7:51-76. [PMID: 36777330 PMCID: PMC9912829 DOI: 10.3233/adr-220056] [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: 08/04/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023] Open
Abstract
Background Alzheimer's disease (AD) is a multifactorial disorder characterized by cognitive decline. Current available therapeutics for AD have limited clinical benefit. Therefore, preventive therapies for interrupting the development of AD are critically needed. Molecules targeting multifunction to interact with various pathlogical components have been considered to improve the therapeutic efficiency of AD. In particular, herbal medicines with multiplicity of actions produce cognitive benefits on AD. Bugu-M is a multi-herbal extract composed of Ganoderma lucidum (Antler form), Nelumbo nucifera Gaertn., Ziziphus jujuba Mill., and Dimocarpus longan, with the ability of its various components to confer resilience to cognitive deficits. Objective To evaluate the potential of Bugu-M on amyloid-β (Aβ) toxicity and its in vitro mechanisms and on in vivo cognitive function. Methods We illustrated the effect of Bugu-M on Aβ25-35-evoked toxicity as well as its possible mechanisms to diminish the pathogenesis of AD in rat cortical neurons. For cognitive function studies, 2-month-old female 3×Tg-AD mice were administered 400 mg/kg Bugu-M for 30 days. Behavioral tests were performed to assess the efficacy of Bugu-M on cognitive impairment. Results In primary cortical neuronal cultures, Bugu-M mitigated Aβ-evoked toxicity by reducing cytoskeletal aberrations and axonal disruption, restoring presynaptic and postsynaptic protein expression, suppressing mitochondrial damage and apoptotic signaling, and reserving neurogenic and neurotrophic factors. Importantly, 30-day administration of Bugu-M effectively prevented development of cognitive impairment in 3-month-old female 3×Tg-AD mice. Conclusion Bugu-M might be beneficial in delaying the progression of AD, and thus warrants consideration for its preventive potential for AD.
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Affiliation(s)
- Ni-Hsuan Lin
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Angela Goh
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Shyh-Horng Lin
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Kai-An Chuang
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Chih-Hsuan Chang
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Ming-Han Li
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Chu-Hsun Lu
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Wen-Yin Chen
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Pei-Hsuan Wei
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - I-Hong Pan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Ming-Der Perng
- Institute of Molecular Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan,
School of Medicine, College of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan,Correspondence to: Shu-Fang Wen, Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, 321, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan. Tel.: +886 35743946; E-mail: and Ming-Der Perng, College of Life Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan. Tel.: +886 35742024; E-mail:
| | - Shu-Fang Wen
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan,Correspondence to: Shu-Fang Wen, Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, 321, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan. Tel.: +886 35743946; E-mail: and Ming-Der Perng, College of Life Sciences, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan. Tel.: +886 35742024; E-mail:
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Tsoi PS, Quan MD, Ferreon JC, Ferreon ACM. Aggregation of Disordered Proteins Associated with Neurodegeneration. Int J Mol Sci 2023; 24:3380. [PMID: 36834792 PMCID: PMC9966039 DOI: 10.3390/ijms24043380] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Cellular deposition of protein aggregates, one of the hallmarks of neurodegeneration, disrupts cellular functions and leads to neuronal death. Mutations, posttranslational modifications, and truncations are common molecular underpinnings in the formation of aberrant protein conformations that seed aggregation. The major proteins involved in neurodegeneration include amyloid beta (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, and TAR DNA-binding protein (TDP-43) in amyotrophic lateral sclerosis (ALS). These proteins are described as intrinsically disordered and possess enhanced ability to partition into biomolecular condensates. In this review, we discuss the role of protein misfolding and aggregation in neurodegenerative diseases, specifically highlighting implications of changes to the primary/secondary (mutations, posttranslational modifications, and truncations) and the quaternary/supramolecular (oligomerization and condensation) structural landscapes for the four aforementioned proteins. Understanding these aggregation mechanisms provides insights into neurodegenerative diseases and their common underlying molecular pathology.
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Affiliation(s)
| | | | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
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35
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Angeloni C, Malaguti M, Prata C, Freschi M, Barbalace MC, Hrelia S. Mechanisms Underlying Neurodegenerative Disorders and Potential Neuroprotective Activity of Agrifood By-Products. Antioxidants (Basel) 2022; 12:antiox12010094. [PMID: 36670956 PMCID: PMC9854890 DOI: 10.3390/antiox12010094] [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: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
Neurodegenerative diseases, characterized by progressive loss in selected areas of the nervous system, are becoming increasingly prevalent worldwide due to an aging population. Despite their diverse clinical manifestations, neurodegenerative diseases are multifactorial disorders with standard features and mechanisms such as abnormal protein aggregation, mitochondrial dysfunction, oxidative stress and inflammation. As there are no effective treatments to counteract neurodegenerative diseases, increasing interest has been directed to the potential neuroprotective activities of plant-derived compounds found abundantly in food and in agrifood by-products. Food waste has an extremely negative impact on the environment, and recycling is needed to promote their disposal and overcome this problem. Many studies have been carried out to develop green and effective strategies to extract bioactive compounds from food by-products, such as peel, leaves, seeds, bran, kernel, pomace, and oil cake, and to investigate their biological activity. In this review, we focused on the potential neuroprotective activity of agrifood wastes obtained by common products widely produced and consumed in Italy, such as grapes, coffee, tomatoes, olives, chestnuts, onions, apples, and pomegranates.
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Affiliation(s)
- Cristina Angeloni
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Marco Malaguti
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
- Correspondence: (M.M.); (C.P.)
| | - Cecilia Prata
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
- Correspondence: (M.M.); (C.P.)
| | - Michela Freschi
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Maria Cristina Barbalace
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
| | - Silvana Hrelia
- Department for Life Quality Studies, Alma Mater Studiorum–University of Bologna, Corso D’Augusto 237, 47921 Rimini, Italy
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Pillai M, Jha SK. Multistep molecular mechanism of amyloid-like aggregation of nucleic acid-binding domain of TDP-43. Proteins 2022; 91:649-664. [PMID: 36530161 DOI: 10.1002/prot.26455] [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: 05/02/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
TDP-43 protein is associated with many neurodegenerative diseases and has been shown to adopt various oligomeric and fibrillar states. However, a detailed kinetic understanding of the structural transformation of the native form of the protein to the fibrillar state is missing. In this study, we delineate the temporal sequence of structural events during the amyloid-like assembly of the functional nucleic acid-binding domain of TDP-43. We kinetically mapped the aggregation process using multiple probes such as tryptophan and thioflavin T (ThT) fluorescence, circular dichroism (CD), and dynamic light scattering (DLS) targeting different structural events. Our data reveal that aggregation occurs in four distinct steps-very fast, fast, slow, and very slow. The "very fast" change results in partially unfolded forms that undergo conformational conversion, oligomerization and bind to ThT in the "fast step" to form higher order intermediates (HOI). The temporal sequence of the formation of ThT binding sites and conformational conversion depends upon the protein concentration. The HOI further undergoes structural rearrangement to form protofibrils in the "slow" step, which, consequently, assembles in the "very slow" step to form an amyloid-like assembly. The spectroscopic properties of the amyloid-like assembly across the protein concentration remain similar. Additionally, we observe no lag phase across protein concentration for all the probes studied, suggesting that the aggregation process follows a linear polymerization reaction. Overall, our study demonstrates that the amyloid-like assembly forms in multiple steps, which is also supported by the temperature dependence of the kinetics.
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Affiliation(s)
- Meenakshi Pillai
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Romano R, De Luca M, Del Fiore VS, Pecoraro M, Lattante S, Sabatelli M, La Bella V, Bucci C. Allele-specific silencing as therapy for familial amyotrophic lateral sclerosis caused by the p.G376D TARDBP mutation. Brain Commun 2022; 4:fcac315. [PMID: 36751500 PMCID: PMC9897181 DOI: 10.1093/braincomms/fcac315] [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: 02/22/2022] [Revised: 08/25/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Amyotrophic lateral sclerosis is a neurodegenerative disease characterized by the degeneration of motor neurons. There is no treatment for this disease that affects the ability to move, eat, speak and finally breathe, causing death. In an Italian family, a heterozygous pathogenic missense variant has been previously discovered in Exon 6 of the gene TARDBP encoding the TAR DNA-binding protein 43 protein. Here, we developed a potential therapeutic tool based on allele-specific small interfering RNAs for familial amyotrophic lateral sclerosis with the heterozygous missense mutation c.1127G>A. We designed a small interfering RNA that was able to diminish specifically the expression of the exogenous Green Fluorescent Protein (TAR DNA-binding protein 43G376D mutant protein) in HEK-293T cells but not that of the Green Fluorescent Protein (TAR DNA-binding protein 43 wild-type). Similarly, this small interfering RNA silenced the mutated allele in fibroblasts derived from patients with amyotrophic lateral sclerosis but did not silence the wild-type gene in control fibroblasts. In addition, we established that silencing the mutated allele was able to strongly reduce the pathological cellular phenotypes induced by TAR DNA-binding protein 43G376D expression, such as the presence of cytoplasmic aggregates. Thus, we have identified a small interfering RNA that could be used to silence specifically the mutated allele to try a targeted therapy for patients carrying the p.G376D TAR DNA-binding protein 43 mutation.
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Affiliation(s)
- Roberta Romano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Via Provinciale Lecce-Monteroni n.165, 73100 Lecce, Italy
| | - Maria De Luca
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Via Provinciale Lecce-Monteroni n.165, 73100 Lecce, Italy
| | - Victoria Stefania Del Fiore
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), Via Provinciale Lecce-Monteroni n.165, 73100 Lecce, Italy
| | - Martina Pecoraro
- ALS Clinical Research Center, P Giaccone University Hospital and Department of Biomedicine, Neuroscience and advanced Diagnostic (BIND), University of Palermo, via Gaetano La Loggia n° 1, 90129 Palermo, Italy
| | - Serena Lattante
- Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy,Unit of Medical Genetics, Department of Laboratory and Infectious Disease Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Mario Sabatelli
- Adult NEMO Clinical Center, Unit of Neurology, Department of Aging, Neurological, Orthopedic and Head-Neck Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Section of Neurology, Department of Neuroscience, Faculty of Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Center, P Giaccone University Hospital and Department of Biomedicine, Neuroscience and advanced Diagnostic (BIND), University of Palermo, via Gaetano La Loggia n° 1, 90129 Palermo, Italy
| | - Cecilia Bucci
- Correspondence to: Cecilia Bucci Department of Biological and Environmental Sciences and Technologies (DiSTeBA) Via Provinciale Lecce-Monteroni n.165 73100 Lecce, Italy E-mail:
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Cho HJ, Schulz P, Venkataraman L, Caselli RJ, Sierks MR. Sex-Specific Multiparameter Blood Test for the Early Diagnosis of Alzheimer's Disease. Int J Mol Sci 2022; 23:ijms232415670. [PMID: 36555310 PMCID: PMC9779188 DOI: 10.3390/ijms232415670] [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: 10/21/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Blood-based biomarkers are needed for the early diagnosis of Alzheimer's disease (AD). We analyzed longitudinal human plasma samples from AD and control cases to identify biomarkers for the early diagnosis of AD. Plasma samples were grouped based on clinical diagnosis at the time of collection: AD, mild cognitive impairment (MCI), and pre-symptomatic (preMCI). Samples were analyzed by ELISA using a panel of reagents against nine different AD-related amyloid-β (Aβ), tau, or TDP-43 variants. Receiver operating characteristic (ROC) curves of different biomarker panels for different diagnostic sample groups were determined. Analysis of all of the samples gave a sensitivity of 92% and specificity of 76% for the diagnosis of AD. Early-stage diagnosis of AD, utilizing only the preMCI and MCI samples, identified 88% of AD cases. Using sex-biased biomarker panels, early diagnosis of AD cases improved to 96%. Using the sex-biased panels, we also identified 6 of the 25 control group cases as being at high risk of AD, which is consistent with what is expected given the advanced age of the control cases. Specific AD-associated protein variants are effective blood-based biomarkers for the early diagnosis of AD. Notably, significant differences were observed in biomarker profiles for the early detection of male and female AD cases.
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Affiliation(s)
- Hyung Joon Cho
- Department of Internal Medicine, The University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Philip Schulz
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Lalitha Venkataraman
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | | | - Michael R. Sierks
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
- Correspondence: ; Tel.: +1-480-965-2828; Fax: +1-480-727-9321
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39
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Staderini T, Bigi A, Mongiello D, Cecchi C, Chiti F. Biophysical characterization of full-length TAR DNA-binding protein (TDP-43) phase separation. Protein Sci 2022; 31:e4509. [PMID: 36371546 PMCID: PMC9703588 DOI: 10.1002/pro.4509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/17/2022] [Accepted: 11/05/2022] [Indexed: 11/15/2022]
Abstract
Amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin-positive inclusions are associated with deposition of cytosolic inclusion bodies of TAR DNA-binding protein 43 (TDP-43) in brain and motor neurons. We induced phase separation of purified full-length TDP-43 devoid of large tags using a solution-jump method, and monitored it with an array of biophysical techniques. The tetramethylrhodamine-5-maleimide- or Alexa488-labeled protein formed rapidly (<1 min) apparently round, homogeneous and 0.5-1.0 μm wide assemblies, when imaged using confocal fluorescence, bright-field, and stimulated emission depletion microscopy. The assemblies, however, had limited internal diffusion, as assessed with fluorescence recovery after photobleaching, and did not coalesce, but rather clustered into irregular bunches, unlike those formed by the C-terminal domain. They were enriched with α-helical structure, with minor contributions of β-sheet/random structure, had a red-shifted tryptophan fluorescence and did not bind thioflavin T. By monitoring with turbidimetry both the formation of the spherical species and their further clustering under different experimental conditions, we carried out a multiparametric analysis of the two phenomena. In particular, both processes were found to be promoted by high protein concentrations, salts, crowding agents, weakly by reducing agents, as the pH approached a value of 6.0 from either side (corresponding to the TDP-43 isoionic point), and as the temperature approached a value of 31°C from either side. Important differences were found with respect to the TDP-43 C-terminal domain. Our multiparametric results also provide explanations to some of the solubility data obtained on full-length TDP-43 that were difficult to explain following the multiparametric analysis acquired on the C-terminal domain.
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Affiliation(s)
- Tommaso Staderini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”University of FlorenceFlorenceItaly
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”University of FlorenceFlorenceItaly
| | - Daniele Mongiello
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”University of FlorenceFlorenceItaly
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”University of FlorenceFlorenceItaly
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”University of FlorenceFlorenceItaly
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40
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Different states and the associated fates of biomolecular condensates. Essays Biochem 2022; 66:849-862. [PMID: 36350032 DOI: 10.1042/ebc20220054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/20/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Abstract
Biomolecular condensates are functional assemblies, which can enrich intrinsically disordered proteins (IDPs) and/or RNAs at concentrations that are orders of magnitude higher than the bulk. In their native functional state, these structures can exist in multiple physical states including liquid-droplet phase, hydrogels, and solid assemblies. On the other hand, an aberrant transition between these physical states can result in loss-of-function or a gain-of-toxic-function. A prime example of such an aberrant transition is droplet aging—a phenomenon where some condensates may progressively transition into less dynamic material states at biologically relevant timescales. In this essay, we review structural and viscoelastic roots of aberrant liquid–solid transitions. Also, we highlight the different checkpoints and experimentally tunable handles, both active (ATP-dependent enzymes, post-translational modifications) and passive (colocalization of RNA molecules), that could alter the material state of assemblies.
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41
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Tamaki Y, Urushitani M. Molecular Dissection of TDP-43 as a Leading Cause of ALS/FTLD. Int J Mol Sci 2022; 23:ijms232012508. [PMID: 36293362 PMCID: PMC9604209 DOI: 10.3390/ijms232012508] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
TAR DNA binding protein 43 (TDP-43) is a DNA/RNA binding protein involved in pivotal cellular functions, especially in RNA metabolism. Hyperphosphorylated and ubiquitinated TDP-43-positive neuronal cytoplasmic inclusions are identified in the brain and spinal cord in most cases of amyotrophic lateral sclerosis (ALS) and a substantial proportion of frontotemporal lobar degeneration (FTLD) cases. TDP-43 dysfunctions and cytoplasmic aggregation seem to be the central pathogenicity in ALS and FTLD. Therefore, unraveling both the physiological and pathological mechanisms of TDP-43 may enable the exploration of novel therapeutic strategies. This review highlights the current understanding of TDP-43 biology and pathology, describing the cellular processes involved in the pathogeneses of ALS and FTLD, such as post-translational modifications, RNA metabolism, liquid–liquid phase separation, proteolysis, and the potential prion-like propagation propensity of the TDP-43 inclusions.
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Affiliation(s)
- Yoshitaka Tamaki
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Makoto Urushitani
- Department of Neurology, Shiga University of Medical Science, Otsu 520-2192, Japan
- Correspondence:
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42
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Chiang WC, Fang YS, Lye YS, Weng TY, Ganesan K, Huang SH, Chang LY, Chou SC, Chen YR. Hyperphosphorylation-Mimetic TDP-43 Drives Amyloid Formation and Possesses Neuronal Toxicity at the Oligomeric Stage. ACS Chem Neurosci 2022; 13:2599-2612. [PMID: 36007056 DOI: 10.1021/acschemneuro.1c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
TDP-43 proteinopathies cover a range of neurodegenerative diseases, including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Hyperphosphorylated TDP-43 was found within the inclusion bodies in disease lesions; however, the role of hyperphosphorylation and the toxic species are still ambiguous. To characterize the hyperphosphorylation effect of TDP-43, here, we employed five serine mutations implicated in the diseases at serine locations 379, 403, 404, 409, and 410 in the C-terminus to aspartate (S5D) and to alanine (S5A). We systematically characterized the conformation, liquid-liquid phase separation, oligomerization, and fibrillization of TDP-43 variants. Results revealed that the recombinant TDP-43 variants readily formed structurally similar spherical oligomers, as evidenced by circular dichroism spectroscopy, fluorescence spectroscopy, the TDP-43 oligomer-specific antibody assay, dynamic light scattering, and transmission electron microscopy. After incubation, only the phosphor-mimic S5D TDP-43 formed thioflavin-positive amyloid fibrils, whereas wild-type and S5A TDP-43 formed amorphous aggregates. We also examined membrane disruption, the cytotoxicity of human neuroblastoma, and the synaptic loss of primary neurons induced by oligomers and large aggregates of TDP-43. The results showed that all oligomeric TDP-43 variants were toxic regardless of hyperphosphorylation, but the fibrils and amorphous aggregates were not. Overall, our results demonstrated the hyperphosphorylation effect on fibril formation and the toxicity attributed from TDP-43 oligomers. This study facilitates the understanding and therapeutic development for TDP-43 proteinopathies.
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Affiliation(s)
- Wan-Chin Chiang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan
| | - Yu-Sheng Fang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Kuang-Fu Rd., Sec. 2., Hsinchu 30013, Taiwan
| | - Yuh Shen Lye
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Yu Weng
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan
| | - Kiruthika Ganesan
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan
| | - Shih-Han Huang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan
| | - Lan-Yun Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan
| | - Shih-Chieh Chou
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 11529, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Kuang-Fu Rd., Sec. 2., Hsinchu 30013, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei 11529, Taiwan
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43
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Ahmad A, Uversky VN, Khan RH. Aberrant liquid-liquid phase separation and amyloid aggregation of proteins related to neurodegenerative diseases. Int J Biol Macromol 2022; 220:703-720. [PMID: 35998851 DOI: 10.1016/j.ijbiomac.2022.08.132] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/05/2022]
Abstract
Recent evidence has shown that the processes of liquid-liquid phase separation (LLPS) or liquid-liquid phase transitions (LLPTs) are a crucial and prevalent phenomenon that underlies the biogenesis of numerous membrane-less organelles (MLOs) and biomolecular condensates within the cells. Findings show that processes associated with LLPS play an essential role in physiology and disease. In this review, we discuss the physical and biomolecular factors that contribute to the development of LLPS, the associated functions, as well as their consequences for cell physiology and neurological disorders. Additionally, the finding of mis-regulated proteins, which have long been linked to aggregates in neuropathology, are also known to induce LLPS/LLPTs, prompting a lot of interest in understanding the connection between aberrant phase separation and disorder conditions. Moreover, the methods used in recent and ongoing studies in this field are also explored, as is the possibility that these findings will encourage new lines of inquiry into the molecular causes of neurodegenerative diseases.
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Affiliation(s)
- Azeem Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P. 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P. 202002, India.
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44
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Doke AA, Jha SK. Effect of In Vitro Solvation Conditions on Inter- and Intramolecular Assembly of Full-Length TDP-43. J Phys Chem B 2022; 126:4799-4813. [PMID: 35758053 DOI: 10.1021/acs.jpcb.2c02203] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular stress is a major cause of neurodegenerative diseases. In particular, in amyotrophic lateral sclerosis (ALS), around 90% of the cases are believed to occur due to aggregation and misfolding of TDP-43 protein in neurons due to aging and chronic environmental stress. However, the physicochemical basis of how TDP-43 senses the change in solvation conditions during stress and misfolds remains very poorly understood. We show here that the full-length human TDP-43 can exist in equilibrium with multiple structural states. The equilibrium between these states is highly sensitive to changes in solvation conditions. We show that upon thermal and pH stress, amyloidogenic oligomers can form amyloid-like fibrils. However, the internal structure of the fibril depends upon the physicochemical nature of stress. Our results present a physical basis of the effect of solvation conditions on inter- and intramolecular assembly formation of TDP-43 and reconcile why the nature and the internal structure of the aggregated form have been found to be different when extracted from the brain of different ALS patients.
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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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45
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Zacco E, Kantelberg O, Milanetti E, Armaos A, Panei FP, Gregory J, Jeacock K, Clarke DJ, Chandran S, Ruocco G, Gustincich S, Horrocks MH, Pastore A, Tartaglia GG. Probing TDP-43 condensation using an in silico designed aptamer. Nat Commun 2022; 13:3306. [PMID: 35739092 PMCID: PMC9226187 DOI: 10.1038/s41467-022-30944-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On the pathway to forming insoluble inclusions, TDP-43 adopts a heterogeneous population of assemblies, many smaller than the diffraction-limit of light. We demonstrated that our aptamers bind TDP-43 and used the tightest interactor, Apt-1, as a probe to visualize TDP-43 condensates with super-resolution microscopy. At a resolution of 10 nanometers, we tracked TDP-43 oligomers undetectable by standard approaches. In cells, Apt-1 interacts with both diffuse and condensed forms of TDP-43, indicating that Apt-1 can be exploited to follow TDP-43 phase transition. The de novo generation of aptamers and their use for microscopy opens a new page to study protein condensation.
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Affiliation(s)
- Elsa Zacco
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Owen Kantelberg
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Francesco Paolo Panei
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Jenna Gregory
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Stefano Gustincich
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
- Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy.
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46
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Hu J, Zhao Y, Li Y. Rationally designed amyloid inhibitors based on amyloid-related structural studies. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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47
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C9orf72 Hexanucleotide Repeat Expansion-Related Neuropathology Is Attenuated by Nasal Rifampicin in Mice. Biomedicines 2022; 10:biomedicines10051080. [PMID: 35625816 PMCID: PMC9138602 DOI: 10.3390/biomedicines10051080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
The non-coding GGGGCC hexanucleotide repeat expansion (HRE) in C9orf72 gene is a dominant cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). This intronic mutation elicits the formation of nuclear and cytoplasmic inclusions containing RNA, RNA-binding proteins, and HRE-derived dipeptide repeat proteins (DPRs), leading to neurodegeneration via the gain-of-toxic function or loss-of-function of relevant proteins. Using C9-500 mice harboring ~500 repeats of the GGGGCC sequence in human C9orf72 gene, we investigated the effects of rifampicin against HRE-related pathological phenotypes. Rifampicin was administered intranasally to 4.5- to 5-month-old mice for 1 month, and their cognitive function and neuropathology were assessed by the Morris water maze test and immunohistochemical staining. Rifampicin treatment reduced the formation of RNA foci and cytoplasmic inclusions containing DPRs or phosphorylated TDP-43, and furthermore, the levels of phosphorylated double-strand RNA-dependent protein kinase (PKR) that regulates repeat-associated non-ATG (RAN) translation. Synapse loss in the hippocampus and neuronal loss and microglial activation in the prefrontal and motor cortices were also attenuated, and mouse memory was significantly improved. Our findings suggest a therapeutic potential of nasal rifampicin in the prevention of C9orf72-linked neurodegenerative disorders.
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48
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Jiedu-Yizhi Formula Improves Cognitive Impairment in an A β 25-35-Induced Rat Model of Alzheimer's Disease by Inhibiting Pyroptosis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6091671. [PMID: 35341145 PMCID: PMC8942661 DOI: 10.1155/2022/6091671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/19/2022] [Indexed: 12/28/2022]
Abstract
Jiedu-Yizhi formula (JDYZF) is prescribed for the treatment of Alzheimer's disease (AD) and was created by Jixue Ren, a master of traditional Chinese medicine, based on the "marrow deficiency and toxin damage" theory. In our clinic, this formula has been used for the treatment of AD for many years and has achieved good results. However, the mechanism by which JDYZF improves cognitive impairment has not been determined. In this study, we confirmed that orally administered JDYZF reversed the cognitive deficits in an Aβ 25-35-induced rat model, increased the number of neurons in the hippocampal CA1 area, improved their structure, decreased the deposition of β-amyloid (Aβ), reduced the expression of proteins related to the NLRP3/Caspase-1/GSDMD and LPS/Caspase-11/GSDMD pyroptosis pathways, and reduced the levels of interleukin 1β (IL-1β) and IL-18, thereby inhibiting the inflammatory response. In addition, JDYZF exerted no hepatotoxicity in rats. In short, these results provide scientific support for the clinical use of JDYZF to improve the cognitive function of patients with AD.
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49
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Lye YS, Chen YR. TAR DNA-binding protein 43 oligomers in physiology and pathology. IUBMB Life 2022; 74:794-811. [PMID: 35229461 DOI: 10.1002/iub.2603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA/DNA-binding protein involved in RNA regulation and diseases. In 2006, TDP-43 inclusions were found in the disease lesions of several neurodegenerative diseases. It is the pathological hallmark in both amyotrophic lateral sclerosis and frontotemporal lobar dementia. It also presents in a large portion of patients with Alzheimer's disease. TDP-43 is prone to aggregate; however, the role of TDP-43 oligomers remains poorly understood in both physiological and pathological conditions. In this review, we emphasize the role of oligomeric TDP-43 in both physiological and pathological conditions and discuss the potential mechanisms of oligomer formation. Finally, we suggest therapeutic strategies against the TDP-43 oligomers in neurodegenerative diseases.
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Affiliation(s)
- Yuh Shen Lye
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
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50
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Structure-Based Analysis of Protein Cluster Size for Super-Resolution Microscopy in the Nervous System. Biomedicines 2022; 10:biomedicines10020295. [PMID: 35203503 PMCID: PMC8869149 DOI: 10.3390/biomedicines10020295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023] Open
Abstract
To overcome the diffraction limit and resolve target structures in greater detail, far-field super-resolution techniques such as stochastic optical reconstruction microscopy (STORM) have been developed, and different STORM algorithms have been developed to deal with the various problems that arise. In particular, the effect of the local structure is an important issue. For objects with closely correlated distributions, simple Gaussian-based localization algorithms often used in STORM imaging misinterpret overlapping point spread functions (PSFs) as one, which limits the ability of super-resolution imaging to resolve nanoscale local structures and leads to inaccurate length measurements. The STORM super-resolution images of biological specimens from the cluster-forming proteins in the nervous system were reconstructed for localization-based analysis. Generally, the localization of each fluorophore was determined by two-dimensional Gaussian function fitting. Further, the physical shape of the cluster structure information was incorporated into the size parameter of the localization structure analysis in order to generate structure-based fitting algorithms. In the present study, we proposed a novel, structure-based, super-resolution image analysis method: structure-based analysis (SBA), which combines a structural function and a super-resolution localization algorithm. Using SBA, we estimated the size of fluorescent beads, inclusion proteins, and subtle synaptic structures in both wide-field and STORM images. The results show that SBA has a comparable and often superior performance to the commonly used full width at half maximum (FWHM) parameter. We demonstrated that SBA is able to estimate molecular cluster sizes in far-field super-resolution STORM images, and that SBA was comparable and often superior to FWHM. We also certified that SBA provides size estimations that corroborate previously published electron microscopy data.
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