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Cóppola-Segovia V, Reggiori F. Molecular Insights into Aggrephagy: Their Cellular Functions in the Context of Neurodegenerative Diseases. J Mol Biol 2024; 436:168493. [PMID: 38360089 DOI: 10.1016/j.jmb.2024.168493] [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: 12/19/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Protein homeostasis or proteostasis is an equilibrium of biosynthetic production, folding and transport of proteins, and their timely and efficient degradation. Proteostasis is guaranteed by a network of protein quality control systems aimed at maintaining the proteome function and avoiding accumulation of potentially cytotoxic proteins. Terminal unfolded and dysfunctional proteins can be directly turned over by the ubiquitin-proteasome system (UPS) or first amassed into aggregates prior to degradation. Aggregates can also be disposed into lysosomes by a selective type of autophagy known as aggrephagy, which relies on a set of so-called selective autophagy receptors (SARs) and adaptor proteins. Failure in eliminating aggregates, also due to defects in aggrephagy, can have devastating effects as underscored by several neurodegenerative diseases or proteinopathies, which are characterized by the accumulation of aggregates mostly formed by a specific disease-associated, aggregate-prone protein depending on the clinical pathology. Despite its medical relevance, however, the process of aggrephagy is far from being understood. Here we review the findings that have helped in assigning a possible function to specific SARs and adaptor proteins in aggrephagy in the context of proteinopathies, and also highlight the interplay between aggrephagy and the pathogenesis of proteinopathies.
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Affiliation(s)
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark.
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2
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Hipp MS, Hartl FU. Interplay of Proteostasis Capacity and Protein Aggregation: Implications for Cellular Function and Disease. J Mol Biol 2024; 436:168615. [PMID: 38759929 DOI: 10.1016/j.jmb.2024.168615] [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: 02/08/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Eukaryotic cells are equipped with an intricate proteostasis network (PN), comprising nearly 3,000 components dedicated to preserving proteome integrity and sustaining protein homeostasis. This protective system is particularly important under conditions of external and intrinsic cell stress, where inherently dynamic proteins may unfold and lose functionality. A decline in proteostasis capacity is associated with the aging process, resulting in a reduced folding efficiency of newly synthesized proteins and a deficit in the cellular capacity to degrade misfolded proteins. A critical consequence of PN insufficiency is the accumulation of cytotoxic protein aggregates that underlie various age-related neurodegenerative conditions and other pathologies. By interfering with specific proteostasis components, toxic aggregates place an excessive burden on the PN's ability to maintain proteome integrity. This initiates a feed-forward loop, wherein the generation of misfolded and aggregated proteins ultimately leads to proteostasis collapse and cellular demise.
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Affiliation(s)
- Mark S Hipp
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan, 1, 9713 AV Groningen, the Netherlands; Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, the Netherlands; School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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3
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Ferrari L, Bauer B, Qiu Y, Schuschnig M, Klotz S, Anrather D, Juretschke T, Beli P, Gelpi E, Martens S. Tau fibrils evade autophagy by excessive p62 coating and TAX1BP1 exclusion. SCIENCE ADVANCES 2024; 10:eadm8449. [PMID: 38865459 PMCID: PMC11168460 DOI: 10.1126/sciadv.adm8449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
The accumulation of protein aggregates is a hallmark of many diseases, including Alzheimer's disease. As a major pillar of the proteostasis network, autophagy mediates the degradation of protein aggregates. The autophagy cargo receptor p62 recognizes ubiquitin on proteins and cooperates with TAX1BP1 to recruit the autophagy machinery. Paradoxically, protein aggregates are not degraded in various diseases despite p62 association. Here, we reconstituted the recognition by the autophagy receptors of physiological and pathological Tau forms. Monomeric Tau recruits p62 and TAX1BP1 via the sequential actions of the chaperone and ubiquitylation machineries. In contrast, Tau fibrils from Alzheimer's disease brains are recognized by p62 but fail to recruit TAX1BP1. This failure is due to the masking of fibrils ubiquitin moieties by p62. Tau fibrils are resistant to deubiquitylation, and, thus, this nonproductive interaction of p62 with the fibrils is irreversible. Our results shed light on the mechanism underlying autophagy evasion by protein aggregates and their consequent accumulation in disease.
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Affiliation(s)
- Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Bernd Bauer
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Yue Qiu
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Martina Schuschnig
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sigrid Klotz
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Dorothea Anrather
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | | | - Petra Beli
- Institute of Molecular Biology, 55128 Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Ellen Gelpi
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
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4
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Rose K, Jepson T, Shukla S, Maya-Romero A, Kampmann M, Xu K, Hurley JH. Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes. Proc Natl Acad Sci U S A 2024; 121:e2315690121. [PMID: 38781206 PMCID: PMC11145263 DOI: 10.1073/pnas.2315690121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes and neurons, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification, and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Live cell imaging and STORM superresolution microscopy further show that the nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.
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Affiliation(s)
- Kevin Rose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Tyler Jepson
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
| | - Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Alex Maya-Romero
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94158
| | - Ke Xu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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5
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Phan JM, Creekmore BC, Nguyen AT, Bershadskaya DD, Darwich NF, Mann CN, Lee EB. VCP activator reverses nuclear proteostasis defects and enhances TDP-43 aggregate clearance in multisystem proteinopathy models. J Clin Invest 2024; 134:e169039. [PMID: 38787785 PMCID: PMC11257039 DOI: 10.1172/jci169039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Pathogenic variants in valosin-containing protein (VCP) cause multisystem proteinopathy (MSP), a disease characterized by multiple clinical phenotypes including inclusion body myopathy, Paget's disease of the bone, and frontotemporal dementia (FTD). How such diverse phenotypes are driven by pathogenic VCP variants is not known. We found that these diseases exhibit a common pathologic feature: ubiquitinated intranuclear inclusions affecting myocytes, osteoclasts, and neurons. Moreover, knock-in cell lines harboring MSP variants show a reduction in nuclear VCP. Given that MSP is associated with neuronal intranuclear inclusions comprised of TDP-43 protein, we developed a cellular model whereby proteostatic stress results in the formation of insoluble intranuclear TDP-43 aggregates. Consistent with a loss of nuclear VCP function, cells harboring MSP variants or cells treated with VCP inhibitor exhibited decreased clearance of insoluble intranuclear TDP-43 aggregates. Moreover, we identified 4 compounds that activate VCP primarily by increasing D2 ATPase activity, where pharmacologic VCP activation appears to enhance clearance of insoluble intranuclear TDP-43 aggregate. Our findings suggest that VCP function is important for nuclear protein homeostasis, that impaired nuclear proteostasis may contribute to MSP, and that VCP activation may be a potential therapeutic by virtue of enhancing the clearance of intranuclear protein aggregates.
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6
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Batra S, Vaquer-Alicea JI, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM, Kolay S, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP regulates early tau seed amplification via specific cofactors. RESEARCH SQUARE 2024:rs.3.rs-4307848. [PMID: 38826306 PMCID: PMC11142303 DOI: 10.21203/rs.3.rs-4307848/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu happens within hours, implicating a machinery with unknown players that controls this process in the acute phase. Methods We used proximity labeling to identify factors that control seed amplification within 5h of seed exposure. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity 5h after seeded intracellular tau aggregation. Valosin containing protein (VCP/p97) was the top hit. VCP harbors dominant mutations that underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We used immortalized cells and human neurons to study the effects of VCP on tau seeding. We exposed cells to fibrils or brain homogenates in cell culture media and measured effects on uptake and induction of intracellular tau aggregation following various genetic and chemical manipulations of VCP. Results VCP knockdown reduced tau seeding. Chemical inhibitors had opposing effects on aggregation in HEK293T tau biosensor cells and human neurons alike: ML-240 increased seeding efficiency, whereas NMS-873 decreased it. The inhibitors were effective only when administered within 8h of seed exposure, indicating a role for VCP early in seed processing. We screened 30 VCP co-factors in HEK293T biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. By contrast, reduction of FAF2 increased tau seeding. Conclusions Divergent effects on tau seeding of chemical inhibitors and cofactor reduction indicate that VCP regulates this process. This is consistent with a dedicated cytoplasmic processing complex based on VCP that directs seeds acutely towards degradation vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Clarissa Valdez
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Skyler P Taylor
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Victor A Manon
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Anthony R Vega
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Omar M Kashmer
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Sourav Kolay
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Andrew Lemoff
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Nigel J Cairns
- University of Exeter Faculty of Health and Life Sciences
| | - Charles L White
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Marc I Diamond
- UT Southwestern: The University of Texas Southwestern Medical Center
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7
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Zhao DY, Bäuerlein FJB, Saha I, Hartl FU, Baumeister W, Wilfling F. Autophagy preferentially degrades non-fibrillar polyQ aggregates. Mol Cell 2024; 84:1980-1994.e8. [PMID: 38759629 DOI: 10.1016/j.molcel.2024.04.018] [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: 08/08/2023] [Revised: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease (HD). Huntingtin (Htt), the disease protein of HD, forms amyloid-like fibrils by liquid-to-solid phase transition. Macroautophagy has been proposed to clear polyQ aggregates, but the efficiency of aggrephagy is limited. Here, we used cryo-electron tomography to visualize the interactions of autophagosomes with polyQ aggregates in cultured cells in situ. We found that an amorphous aggregate phase exists next to the radially organized polyQ fibrils. Autophagosomes preferentially engulfed this amorphous material, mediated by interactions between the autophagy receptor p62/SQSTM1 and the non-fibrillar aggregate surface. In contrast, amyloid fibrils excluded p62 and evaded clearance, resulting in trapping of autophagic structures. These results suggest that the limited efficiency of autophagy in clearing polyQ aggregates is due to the inability of autophagosomes to interact productively with the non-deformable, fibrillar disease aggregates.
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Affiliation(s)
- Dorothy Y Zhao
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Felix J B Bäuerlein
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; University Medical Center Göttingen, Institute of Neuropathology, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Itika Saha
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - F Ulrich Hartl
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Florian Wilfling
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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8
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Longhini AP, DuBose A, Lobo S, Vijayan V, Bai Y, Rivera EK, Sala-Jarque J, Nikitina A, Carrettiero DC, Unger MT, Sclafani OR, Fu V, Beckett ER, Vigers M, Buée L, Landrieu I, Shell S, Shea JE, Han S, Kosik KS. Precision proteoform design for 4R tau isoform selective templated aggregation. Proc Natl Acad Sci U S A 2024; 121:e2320456121. [PMID: 38568974 PMCID: PMC11009657 DOI: 10.1073/pnas.2320456121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024] Open
Abstract
Prion-like spread of disease-specific tau conformers is a hallmark of all tauopathies. A 19-residue probe peptide containing a P301L mutation and spanning the R2/R3 splice junction of tau folds and stacks into seeding-competent fibrils and induces aggregation of 4R, but not 3R tau. These tau peptide fibrils propagate aggregated intracellular tau over multiple generations, have a high β-sheet content, a colocalized lipid signal, and adopt a well-defined U-shaped fold found in 4R tauopathy brain-derived fibrils. Fully atomistic replica exchange molecular dynamics (MD) simulations were used to compute the free energy landscapes of the conformational ensemble of the peptide monomers. These identified an aggregation-prohibiting β-hairpin structure and an aggregation-competent U-fold unique to 4R tauopathy fibrils. Guided by MD simulations, we identified that the N-terminal-flanking residues to PHF6, which slightly vary between 4R and 3R isoforms, modulate seeding. Strikingly, when a single amino acid switch at position 305 replaced the serine of 4R tau with a lysine from the corresponding position in the first repeat of 3R tau, the seeding induced by the 19-residue peptide was markedly reduced. Conversely, a 4R tau mimic with three repeats, prepared by replacing those amino acids in the first repeat with those amino acids uniquely present in the second repeat, recovered aggregation when exposed to the 19-residue peptide. These peptide fibrils function as partial prions to recruit naive 4R tau-ten times the length of the peptide-and serve as a critical template for 4R tauopathy propagation. These results hint at opportunities for tau isoform-specific therapeutic interventions.
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Affiliation(s)
- Andrew P. Longhini
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Austin DuBose
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
| | - Samuel Lobo
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA93106
| | - Vishnu Vijayan
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
| | - Yeran Bai
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
- Photothermal Spectroscopy Corp., Santa Barbara, CA93101
| | - Erica Keane Rivera
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Julia Sala-Jarque
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Arina Nikitina
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Daniel C. Carrettiero
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, São Paulo09600-000, Brazil
| | - Matthew T. Unger
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Olivia R. Sclafani
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Valerie Fu
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Emily R. Beckett
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
| | - Michael Vigers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, Lille Neuroscience & CognitionLilleF-59000, France
- Laboratoire d'Excellence Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease, Alzheimer & Tauopathies Team, LilleF-59000, France
| | - Isabelle Landrieu
- Center National de la Recherche Scientifique Équipe de Recherche 9002–Integrative Structural Biology, LilleF-59000, France
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1167–Risk Factors and Molecular Determinants of Aging-Related DiseasesLilleF-59000, France
| | - Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA93106
| | - Joan E. Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Physics, University of California Santa Barbara, Santa Barbara, CA93106
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA93106
| | - Kenneth S. Kosik
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA93106
- Department of Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA93106
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9
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Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ. Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.10.544439. [PMID: 38617345 PMCID: PMC11014469 DOI: 10.1101/2023.06.10.544439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.
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Affiliation(s)
- Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Justin A. Sanders
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Gennifer Merrihew
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Edward D. Parker
- Vision Core Lab, Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Kathleen L. Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | | | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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10
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Morderer D, Wren MC, Liu F, Kouri N, Maistrenko A, Khalil B, Pobitzer N, Salemi M, Phinney BS, Dickson DW, Murray ME, Rossoll W. Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.585597. [PMID: 38585836 PMCID: PMC10996607 DOI: 10.1101/2024.03.25.585597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Tauopathies represent a diverse group of neurodegenerative disorders characterized by the abnormal aggregation of the microtubule-associated protein tau. Despite extensive research, the precise mechanisms underlying the complexity of different types of tau pathology remain incompletely understood. Here we describe an approach for proteomic profiling of aggregate-associated proteomes on slides with formalin-fixed, paraffin-embedded (FFPE) tissue that utilizes proximity labelling upon high preservation of aggregate morphology, which permits the profiling of pathological aggregates regardless of their size. To comprehensively investigate the common and unique protein interactors associated with the variety of tau lesions present across different human tauopathies, Alzheimer's disease (AD), corticobasal degeneration (CBD), Pick's disease (PiD), and progressive supranuclear palsy (PSP), were selected to represent the major tauopathy diseases. Implementation of our widely applicable Probe-dependent Proximity Profiling (ProPPr) strategy, using the AT8 antibody, permitted identification and quantification of proteins associated with phospho-tau lesions in well-characterized human post-mortem tissue. The analysis revealed both common and disease-specific proteins associated with phospho-tau aggregates, highlighting potential targets for therapeutic intervention and biomarker development. Candidate validation through high-resolution co-immunofluorescence of distinct aggregates across disease and control cases, confirmed the association of retromer complex protein VPS35 with phospho-tau lesions across the studied tauopathies. Furthermore, we discovered disease-specific associations of proteins including ferritin light chain (FTL) and the neuropeptide precursor VGF within distinct pathological lesions. Notably, examination of FTL-positive microglia in CBD astrocytic plaques indicate a potential role for microglial involvement in the pathogenesis of these tau lesions. Our findings provide valuable insights into the proteomic landscape of tauopathies, shedding light on the molecular mechanisms underlying tau pathology. This first comprehensive characterization of tau-associated proteomes across different tauopathies enhances our understanding of disease heterogeneity and provides a resource for future functional investigation, as well as development of targeted therapies and diagnostic biomarkers.
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11
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Creekmore BC, Watanabe R, Lee EB. Neurodegenerative Disease Tauopathies. ANNUAL REVIEW OF PATHOLOGY 2024; 19:345-370. [PMID: 37832941 PMCID: PMC11009985 DOI: 10.1146/annurev-pathmechdis-051222-120750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Tauopathies are a diverse group of progressive and fatal neurodegenerative diseases characterized by aberrant tau inclusions in the central nervous system. Tau protein forms pathologic fibrillar aggregates that are typically closely associated with neuronal cell death, leading to varied clinical phenotypes including dementia, movement disorders, and motor neuron disease. In this review, we describe the clinicopathologic features of tauopathies and highlight recent advances in understanding the mechanisms that lead to spread of pathologic aggregates through interconnected neuronal pathways. The cell-to-cell propagation of tauopathy is then linked to posttranslational modifications, tau fibril structural variants, and the breakdown of cellular protein quality control.
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Affiliation(s)
- Benjamin C Creekmore
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Ryohei Watanabe
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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12
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Diamond MI. Travels with tau prions. Cytoskeleton (Hoboken) 2024; 81:83-88. [PMID: 37950616 DOI: 10.1002/cm.21806] [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: 07/28/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/13/2023]
Abstract
Tau was originally identified as a microtubule associated protein, and subsequently recognized to constitute the fibrillar assemblies found in Alzheimer disease and related neurodegenerative tauopathies. Point mutations in the microtubule associated protein tau (MAPT) gene cause dominantly inherited tauopathies, and most predispose it to aggregate. This indicates tau aggregation underlies pathogenesis of tauopathies. Our work has suggested that tau functions as a prion, forming unique intracellular pathological assemblies that subsequently move to other cells, inducing further aggregation that underlies disease progression. Remarkably, in simple cells tau forms stably propagating aggregates of distinct conformation, termed strains. Each strain induces a unique and, in some cases, transmissible, neuropathological phenotype upon inoculation into a mouse model. After binding heparan sulfate proteoglycans on the plasma membrane, tau assemblies enter cells via macropinocytosis. From within a vesicle, if not trafficked to the endolysosomal system, tau subsequently enters the cytoplasm, where it becomes a template for its own replication, apparently after processing by valosin containing protein. The smallest seed unit is a stable monomer, which suggests that initial folding events in tau presage subsequent pathological aggregation. The study of tau prions has raised important questions about basic cell biological processes that underlie their replication and propagation, with implications for therapy of tauopathies.
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Affiliation(s)
- Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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13
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Wentink A, Rosenzweig R. Protein disaggregation machineries in the human cytosol. Curr Opin Struct Biol 2023; 83:102735. [PMID: 38000128 DOI: 10.1016/j.sbi.2023.102735] [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: 08/10/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023]
Abstract
Proteins carry out the vast majority of functions in cells, but can only do so when properly folded. Following stress or mutation, proteins can lose their proper fold, resulting in misfolding, inactivity, and aggregation-posing a threat to cellular health. In order to counteract protein aggregation, cells have evolved a remarkable subset of molecular chaperones, called protein disaggregases, which collaboratively possess the ability to forcibly untangle protein aggregates. Here, we review the different chaperone disaggregation machineries present in the human cytosol and their mechanisms of action. Understanding, how these disaggregases function, is both universally and clinically important, as protein aggregation has been linked to multiple, debilitating neurodegenerative diseases.
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Affiliation(s)
- Anne Wentink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands.
| | - Rina Rosenzweig
- Chemical and Structural Biology Department, Weizmann Institute of Science, Rehovot, 761000, Israel.
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14
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Longhini AP, DuBose A, Lobo S, Vijayan V, Bai Y, Rivera EK, Sala-Jarque J, Nikitina A, Carrettiero DC, Unger M, Sclafani O, Fu V, Vigers M, Buee L, Landrieu I, Shell S, Shea JE, Han S, Kosik KS. Precision Proteoform Design for 4R Tau Isoform Selective Templated Aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555649. [PMID: 37693456 PMCID: PMC10491155 DOI: 10.1101/2023.08.31.555649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Prion-like spread of disease-specific tau conformers is a hallmark of all tauopathies. A 19-residue probe peptide containing a P301L mutation and spanning the R2/R3 splice junction of tau, folds and stacks into seeding-competent fibrils and induces aggregation of 4R, but not 3R tau. These tau peptide fibrils propagate aggregated intracellular tau over multiple generations, have a high β-sheet content, a colocalized lipid signal, and adopt a well-defined U-shaped fold found in 4R tauopathy brain-derived fibrils. Fully atomistic replica exchange molecular dynamics (MD) simulations were used to compute the free energy landscapes of the conformational ensemble of the peptide monomers. These identified an aggregation-prohibiting β-hairpin structure and an aggregation-competent U-fold unique to 4R tauopathy fibrils. Guided by MD simulations, we identified that the N-terminal-flanking residues to PHF6, which slightly vary between 4R and 3R isoforms, modulate seeding. Strikingly, when a single amino acid switch at position 305 replaced the serine of 4R tau with a lysine from the corresponding position in the first repeat of 3R tau, the seeding induced by the 19-residue peptide was markedly reduced. Conversely, a 4R tau mimic with three repeats, prepared by replacing those amino acids in the first repeat with those amino acids uniquely present in the second repeat, recovered aggregation when exposed to the 19-residue peptide. These peptide fibrils function as partial prions to recruit naïve 4R tau-ten times the length of the peptide-and serve as a critical template for 4R tauopathy propagation. These results hint at opportunities for tau isoform-specific therapeutic interventions.
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Affiliation(s)
- Andrew P. Longhini
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Austin DuBose
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Samuel Lobo
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Vishnu Vijayan
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Yeran Bai
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Photothermal Spectroscopy Corp., Santa Barbara, CA 93101, USA
| | - Erica Keane Rivera
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Julia Sala-Jarque
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Arina Nikitina
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Daniel C. Carrettiero
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, Brazil
| | - Matthew Unger
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Olivia Sclafani
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Valerie Fu
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Michael Vigers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
| | - Luc Buee
- Univ. Lille, Inserm, CHU Lille, LilNCog – Lille Neuroscience & Cognition, F-59000 Lille, France
- LabEx DISTALZ, Alzheimer & Tauopathies Team, F-59000 Lille, France
| | - Isabelle Landrieu
- CNRS EMR9002 – BSI - Integrative Structural Biology F-59000 Lille, France
| | - Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Joan E. Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France. Department of Physics, University of California, Santa Barbara, Santa Barbara, CA
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Lead Contacts
| | - Kenneth S. Kosik
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
- Molecular, Cell and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Lead Contacts
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15
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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16
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Braxton JR, Southworth DR. Structural insights of the p97/VCP AAA+ ATPase: How adapter interactions coordinate diverse cellular functionality. J Biol Chem 2023; 299:105182. [PMID: 37611827 PMCID: PMC10641518 DOI: 10.1016/j.jbc.2023.105182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
p97/valosin-containing protein is an essential eukaryotic AAA+ ATPase with diverse functions including protein homeostasis, membrane remodeling, and chromatin regulation. Dysregulation of p97 function causes severe neurodegenerative disease and is associated with cancer, making this protein a significant therapeutic target. p97 extracts polypeptide substrates from macromolecular assemblies by hydrolysis-driven translocation through its central pore. Growing evidence indicates that this activity is highly coordinated by "adapter" partner proteins, of which more than 30 have been identified and are commonly described to facilitate translocation through substrate recruitment or modification. In so doing, these adapters enable critical p97-dependent functions such as extraction of misfolded proteins from the endoplasmic reticulum or mitochondria, and are likely the reason for the extreme functional diversity of p97 relative to other AAA+ translocases. Here, we review the known functions of adapter proteins and highlight recent structural and biochemical advances that have begun to reveal the diverse molecular bases for adapter-mediated regulation of p97 function. These studies suggest that the range of mechanisms by which p97 activity is controlled is vastly underexplored with significant advances possible for understanding p97 regulation by the most known adapters.
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Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA; Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA.
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17
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Venediktov AA, Bushueva OY, Kudryavtseva VA, Kuzmin EA, Moiseeva AV, Baldycheva A, Meglinski I, Piavchenko GA. Closest horizons of Hsp70 engagement to manage neurodegeneration. Front Mol Neurosci 2023; 16:1230436. [PMID: 37795273 PMCID: PMC10546621 DOI: 10.3389/fnmol.2023.1230436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/18/2023] [Indexed: 10/06/2023] Open
Abstract
Our review seeks to elucidate the current state-of-the-art in studies of 70-kilodalton-weighed heat shock proteins (Hsp70) in neurodegenerative diseases (NDs). The family has already been shown to play a crucial role in pathological aggregation for a wide spectrum of brain pathologies. However, a slender boundary between a big body of fundamental data and its implementation has only recently been crossed. Currently, we are witnessing an anticipated advancement in the domain with dozens of studies published every month. In this review, we briefly summarize scattered results regarding the role of Hsp70 in the most common NDs including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). We also bridge translational studies and clinical trials to portray the output for medical practice. Available options to regulate Hsp70 activity in NDs are outlined, too.
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Affiliation(s)
- Artem A. Venediktov
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Olga Yu Bushueva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russia
| | - Varvara A. Kudryavtseva
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Egor A. Kuzmin
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Aleksandra V. Moiseeva
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anna Baldycheva
- STEMM Laboratory, University of Exeter, Exeter, United Kingdom
| | - Igor Meglinski
- Department of Physics, University of Oulu, Oulu, Finland
- College of Engineering and Physical Sciences, Aston University, Birmingham, United Kingdom
| | - Gennadii A. Piavchenko
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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18
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Batra S, Vaquer-Alicea J, Manon VA, Kashmer OM, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP increases or decreases tau seeding using specific cofactors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555637. [PMID: 37693404 PMCID: PMC10491269 DOI: 10.1101/2023.08.30.555637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu can happen within hours. A cellular machinery might regulate this process, but potential players are unknown. Methods We used proximity labeling to identify factors that control seed amplification. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity upon seeded intracellular tau aggregation. We identified valosin containing protein (VCP/p97) 5h after seeding. Mutations in VCP underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We utilized tau biosensors, a cellular model for tau aggregation, to study the effects of VCP on tau seeding. Results VCP knockdown reduced tau seeding. However, distinct chemical inhibitors of VCP and the proteasome had opposing effects on aggregation, but only when given <8h of seed exposure. ML-240 increased seeding efficiency ~40x, whereas NMS-873 decreased seeding efficiency by 50%, and MG132 increased seeding ~10x. We screened VCP co-factors in HEK293 biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. Reduction of FAF2 and UBXN6 increased tau seeding. Conclusions VCP uses distinct cofactors to determine seed replication efficiency, consistent with a dedicated cytoplasmic processing complex that directs seeds towards dissolution vs. amplification.
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Affiliation(s)
- Sushobhna Batra
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jaime Vaquer-Alicea
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Victor A Manon
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Omar M Kashmer
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nigel J Cairns
- Department of Clinical and Biological Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Charles L White
- Department of Pathology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Neurology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
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19
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Rose K, Jepson T, Shukla S, Maya-Romero A, Kampmann M, Xu K, Hurley JH. Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555157. [PMID: 37693477 PMCID: PMC10491128 DOI: 10.1101/2023.08.28.555157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Using live cell and STORM, imaging, nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture, and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.
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Affiliation(s)
- Kevin Rose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Tyler Jepson
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
| | - Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Alex Maya-Romero
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Ke Xu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
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20
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Perez VA, Sanders DW, Mendoza-Oliva A, Stopschinski BE, Mullapudi V, White CL, Joachimiak LA, Diamond MI. DnaJC7 specifically regulates tau seeding. eLife 2023; 12:e86936. [PMID: 37387473 PMCID: PMC10473839 DOI: 10.7554/elife.86936] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/29/2023] [Indexed: 07/01/2023] Open
Abstract
Neurodegenerative tauopathies are caused by accumulation of toxic tau protein assemblies. This appears to involve template-based seeding events, whereby tau monomer changes conformation and is recruited to a growing aggregate. Several large families of chaperone proteins, including Hsp70s and J domain proteins (JDPs), cooperate to regulate the folding of intracellular proteins such as tau, but the factors that coordinate this activity are not well known. The JDP DnaJC7 binds tau and reduces its intracellular aggregation. However, it is unknown whether this is specific to DnaJC7 or if other JDPs might be similarly involved. We used proteomics within a cell model to determine that DnaJC7 co-purified with insoluble tau and colocalized with intracellular aggregates. We individually knocked out every possible JDP and tested the effect on intracellular aggregation and seeding. DnaJC7 knockout decreased aggregate clearance and increased intracellular tau seeding. This depended on the ability of the J domain (JD) of DnaJC7 to stimulate Hsp70 ATPase activity, as JD mutations that block this interaction abrogated the protective activity. Disease-associated mutations in the JD and substrate binding site of DnaJC7 also abolished its protective activity. DnaJC7 thus specifically regulates tau aggregation in cooperation with Hsp70.
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Affiliation(s)
- Valerie Ann Perez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - David W Sanders
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Barbara Elena Stopschinski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Charles L White
- Department of Pathology, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biochemistry, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical CenterDallasUnited States
- Department of Neurology, Peter O’Donnell Jr. Brain Institute, The University of Texas Southwestern Medical CenterDallasUnited States
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21
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Zhou M, Fang R, Colson L, Donovan KA, Hunkeler M, Song Y, Zhang C, Chen S, Lee DH, Bradshaw GA, Eisert R, Ye Y, Kalocsay M, Goldberg A, Fischer ES, Lu Y. HUWE1 Amplifies Ubiquitin Modifications to Broadly Stimulate Clearance of Proteins and Aggregates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542866. [PMID: 37398461 PMCID: PMC10312588 DOI: 10.1101/2023.05.30.542866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Selective breakdown of proteins and aggregates is crucial for maintaining normal cellular activities and is involved in the pathogenesis of diverse diseases. How the cell recognizes and tags these targets in different structural states for degradation by the proteasome and autophagy pathways has not been well understood. Here, we discovered that a HECT-family ubiquitin ligase HUWE1 is broadly required for the efficient degradation of soluble factors and for the clearance of protein aggregates/condensates. Underlying this capacity of HUWE1 is a novel Ubiquitin-Directed ubiquitin Ligase (UDL) activity which recognizes both soluble substrates and aggregates that carry a high density of ubiquitin chains and rapidly expand the ubiquitin modifications on these targets. Ubiquitin signal amplification by HUWE1 recruits the ubiquitin-dependent segregase p97/VCP to process these targets for subsequent degradation or clearance. HUWE1 controls the cytotoxicity of protein aggregates, mediates Targeted Protein Degradation and regulates cell-cycle transitions with its UDL activity.
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22
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Perez VA, Sanders DW, Mendoza-Oliva A, Stopschinski BE, Mullapudi V, White CL, Joachimiak LA, Diamond MI. DnaJC7 specifically regulates tau seeding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532880. [PMID: 36993367 PMCID: PMC10055123 DOI: 10.1101/2023.03.16.532880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neurodegenerative tauopathies are caused by accumulation of toxic tau protein assemblies. This appears to involve template-based seeding events, whereby tau monomer changes conformation and is recruited to a growing aggregate. Several large families of chaperone proteins, including Hsp70s and J domain proteins (JDPs) cooperate to regulate the folding of intracellular proteins such as tau, but the factors that coordinate this activity are not well known. The JDP DnaJC7 binds tau and reduces its intracellular aggregation. However, it is unknown whether this is specific to DnaJC7 or if other JDPs might be similarly involved. We used proteomics within a cell model to determine that DnaJC7 co-purified with insoluble tau and colocalized with intracellular aggregates. We individually knocked out every possible JDP and tested the effect on intracellular aggregation and seeding. DnaJC7 knockout decreased aggregate clearance and increased intracellular tau seeding. This depended on the ability of the J domain (JD) of DnaJC7 to bind to Hsp70, as JD mutations that block binding to Hsp70 abrogated the protective activity. Disease-associated mutations in the JD and substrate binding site of DnaJC7 also abrogated its protective activity. DnaJC7 thus specifically regulates tau aggregation in cooperation with Hsp70.
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Affiliation(s)
- Valerie A Perez
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - David W Sanders
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ayde Mendoza-Oliva
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Barbara E Stopschinski
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Vishruth Mullapudi
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles L White
- Department of Pathology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Biochemistry, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Neurology, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
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