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Zhou J, Chuang Y', Redding-Ochoa J, Zhang R, Platero AJ, Barrett AH, Troncoso JC, Worley PF, Zhang W. The autophagy adaptor TRIAD3A promotes tau fibrillation by nested phase separation. Nat Cell Biol 2024:10.1038/s41556-024-01461-4. [PMID: 39009640 DOI: 10.1038/s41556-024-01461-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Multiple neurodegenerative diseases are characterized by aberrant proteinaceous accumulations of tau. Here, we report a RING-in-between-RING-type E3 ligase, TRIAD3A, that functions as an autophagy adaptor for tau. TRIAD3A(RNF216) is an essential gene with mutations causing age-progressive neurodegeneration. Our studies reveal that TRIAD3A E3 ligase catalyses mixed K11/K63 polyubiquitin chains and self-assembles into liquid-liquid phase separated (LLPS) droplets. Tau is ubiquitinated and accumulates within TRIAD3A LLPS droplets and, via LC3 interacting regions, targets tau for autophagic degradation. Unexpectedly, tau sequestered within TRIAD3A droplets rapidly converts to fibrillar aggregates without the transitional liquid phase of tau. In vivo studies show that TRIAD3A decreases the accumulation of phosphorylated tau in a tauopathy mouse model, and a disease-associated mutation of TRIAD3A increases accumulation of phosphorylated tau, exacerbates gliosis and increases pathological tau spreading. In human Alzheimer disease brain, TRIAD3A co-localizes with tau amyloid in multiple histological forms, suggesting a role in tau proteostasis. TRIAD3A is an autophagic adaptor that utilizes E3 ligase and LLPS as a mechanism to capture cargo and appears especially relevant to neurodegenerative diseases.
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Affiliation(s)
- Jiechao Zhou
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yang 'an Chuang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Neuroscience and Brain Disease Center, China Medical University Hospital, Taichung, Taiwan, Republic of China
- Department of Psychology, Asia University, Taichung, Taiwan, Republic of China
| | - Javier Redding-Ochoa
- Division of Neuropathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rongzhen Zhang
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi City, People's Republic of China
| | - Alexander J Platero
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander H Barrett
- Division of Neuropathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan C Troncoso
- Division of Neuropathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Paul F Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Lumpkin CJ, Patel H, Potts GK, Chaurasia S, Gibilisco L, Srivastava GP, Lee JY, Brown NJ, Amarante P, Williams JD, Karran E, Townsend M, Woods D, Ravikumar B. Broad proteomics analysis of seeding-induced aggregation of α-synuclein in M83 neurons reveals remodeling of proteostasis mechanisms that might contribute to Parkinson's disease pathogenesis. Mol Brain 2024; 17:26. [PMID: 38778381 PMCID: PMC11110445 DOI: 10.1186/s13041-024-01099-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/11/2024] [Indexed: 05/25/2024] Open
Abstract
Aggregation of misfolded α-synuclein (α-syn) is a key characteristic feature of Parkinson's disease (PD) and related synucleinopathies. The nature of these aggregates and their contribution to cellular dysfunction is still not clearly elucidated. We employed mass spectrometry-based total and phospho-proteomics to characterize the underlying molecular and biological changes due to α-syn aggregation using the M83 mouse primary neuronal model of PD. We identified gross changes in the proteome that coincided with the formation of large Lewy body-like α-syn aggregates in these neurons. We used protein-protein interaction (PPI)-based network analysis to identify key protein clusters modulating specific biological pathways that may be dysregulated and identified several mechanisms that regulate protein homeostasis (proteostasis). The observed changes in the proteome may include both homeostatic compensation and dysregulation due to α-syn aggregation and a greater understanding of both processes and their role in α-syn-related proteostasis may lead to improved therapeutic options for patients with PD and related disorders.
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Affiliation(s)
- Casey J Lumpkin
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
- Laboratory of Aging and Infertility Research, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Hiral Patel
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Gregory K Potts
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Shilpi Chaurasia
- Excelra Knowledge Solutions Pvt Ltd, Uppal, Hyderabad, India, 500039
| | - Lauren Gibilisco
- Genomics Research Center, Computational Biology Neuroscience, AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Gyan P Srivastava
- Data & Statistical Sciences, AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA, 02139, USA
| | - Janice Y Lee
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Nathan J Brown
- Biotherapeutics, AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA
| | - Patricia Amarante
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Jon D Williams
- Discovery Research, AbbVie Inc, 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Eric Karran
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Matthew Townsend
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA
| | - Dori Woods
- Laboratory of Aging and Infertility Research, Department of Biology, Northeastern University, Boston, Massachusetts, USA.
| | - Brinda Ravikumar
- AbbVie, Cambridge Research Center, 200 Sidney Street Cambridge, Cambridge, MA, 02139, USA.
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3
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Sunna S, Bowen C, Zeng H, Rayaprolu S, Kumar P, Bagchi P, Dammer EB, Guo Q, Duong DM, Bitarafan S, Natu A, Wood L, Seyfried NT, Rangaraju S. Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines. Mol Cell Proteomics 2023; 22:100546. [PMID: 37061046 PMCID: PMC10205547 DOI: 10.1016/j.mcpro.2023.100546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics, in vivo proteomic labeling with proximity-dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without the need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole-cell proteome and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID labeled endolysosome, translation, vesicle, and signaling proteins in BV2 microglia and synaptic, neuron projection, and microtubule proteins in N2A neurons. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells and did not affect lipopolysaccharide-mediated cytokine production or resting cellular respiration in BV2 cells. MS analysis of the microglial biotin-labeled proteins captured the impact of lipopolysaccharide treatment (>500 differentially abundant proteins) including increased canonical proinflammatory proteins (Il1a, Irg1, and Oasl1) and decreased anti-inflammatory proteins (Arg1 and Mgl2).
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Christine Bowen
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Hollis Zeng
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Qi Guo
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Sara Bitarafan
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Aditya Natu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Levi Wood
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA.
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4
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Huang Z, Merrihew GE, Larson EB, Park J, Plubell D, Fox EJ, Montine KS, Latimer CS, Dirk Keene C, Zou JY, MacCoss MJ, Montine TJ. Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease. Nat Commun 2023; 14:2747. [PMID: 37173305 PMCID: PMC10182086 DOI: 10.1038/s41467-023-38376-x] [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: 10/09/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Resilience to Alzheimer's disease is an uncommon combination of high disease burden without dementia that offers valuable insights into limiting clinical impact. Here we assessed 43 research participants meeting stringent criteria, 11 healthy controls, 12 resilience to Alzheimer's disease and 20 Alzheimer's disease with dementia and analyzed matched isocortical regions, hippocampus, and caudate nucleus by mass spectrometry-based proteomics. Of 7115 differentially expressed soluble proteins, lower isocortical and hippocampal soluble Aβ levels is a significant feature of resilience when compared to healthy control and Alzheimer's disease dementia groups. Protein co-expression analysis reveals 181 densely-interacting proteins significantly associated with resilience that were enriched for actin filament-based processes, cellular detoxification, and wound healing in isocortex and hippocampus, further supported by four validation cohorts. Our results suggest that lowering soluble Aβ concentration may suppress severe cognitive impairment along the Alzheimer's disease continuum. The molecular basis of resilience likely holds important therapeutic insights.
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Affiliation(s)
- Zhi Huang
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gennifer E Merrihew
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Eric B Larson
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Edward J Fox
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Caitlin S Latimer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - James Y Zou
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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5
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Mukherjee S, Dubois C, Perez K, Varghese S, Birchall IE, Leckey M, Davydova N, McLean C, Nisbet RM, Roberts BR, Li QX, Masters CL, Streltsov VA. Quantitative proteomics of tau and Aβ in detergent fractions from Alzheimer's disease brains. J Neurochem 2023; 164:529-552. [PMID: 36271678 DOI: 10.1111/jnc.15713] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/16/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022]
Abstract
The two hallmarks of Alzheimer's disease (AD) are amyloid-β (Aβ) plaques and neurofibrillary tangles marked by phosphorylated tau. Increasing evidence suggests that aggregating Aβ drives tau accumulation, a process that involves synaptic degeneration leading to cognitive impairment. Conversely, there is a realization that non-fibrillar (oligomeric) forms of Aβ mediate toxicity in AD. Fibrillar (filamentous) aggregates of proteins across the spectrum of the primary and secondary tauopathies were the focus of recent structural studies with a filament structure-based nosologic classification, but less emphasis was given to non-filamentous co-aggregates of insoluble proteins in the fractions derived from post-mortem human brains. Here, we revisited sarkosyl-soluble and -insoluble extracts to characterize tau and Aβ species by quantitative targeted mass spectrometric proteomics, biochemical assays, and electron microscopy. AD brain sarkosyl-insoluble pellets were greatly enriched with Aβ42 at almost equimolar levels to N-terminal truncated microtubule-binding region (MTBR) isoforms of tau with multiple site-specific post-translational modifications (PTMs). MTBR R3 and R4 tau peptides were most abundant in the sarkosyl-insoluble materials with a 10-fold higher concentration than N-terminal tau peptides. This indicates that the major proportion of the enriched tau was the aggregation-prone N-terminal and proline-rich region (PRR) of truncated mixed 4R and 3R tau with more 4R than 3R isoforms. High concentration and occupancies of site-specific phosphorylation pT181 (~22%) and pT217 (~16%) (key biomarkers of AD) along with other PTMs in the PRR and MTBR indicated a regional susceptibility of PTMs in aggregated tau. Immunogold labelling revealed that tau may exist in globular non-filamentous form (N-terminal intact tau) co-localized with Aβ in the sarkosyl-insoluble pellets along with tau filaments (N-truncated MTBR tau). Our results suggest a model that Aβ and tau interact forming globular aggregates, from which filamentous tau and Aβ emerge. These characterizations contribute towards unravelling the sequence of events which lead to end-stage AD changes.
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Affiliation(s)
- Soumya Mukherjee
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Celine Dubois
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Keyla Perez
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shiji Varghese
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian E Birchall
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Miranda Leckey
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Natalia Davydova
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Lucas Heights, New South Wales, Australia
| | - Catriona McLean
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia.,Department of Anatomical Pathology, Alfred Hospital, Prahran, Victoria, Australia
| | - Rebecca M Nisbet
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Blaine R Roberts
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Qiao-Xin Li
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Victor A Streltsov
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
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PRIP: A Protein-RNA Interface Predictor Based on Semantics of Sequences. Life (Basel) 2022; 12:life12020307. [PMID: 35207594 PMCID: PMC8879494 DOI: 10.3390/life12020307] [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: 01/05/2022] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 01/08/2023] Open
Abstract
RNA–protein interactions play an indispensable role in many biological processes. Growing evidence has indicated that aberration of the RNA–protein interaction is associated with many serious human diseases. The precise and quick detection of RNA–protein interactions is crucial to finding new functions and to uncovering the mechanism of interactions. Although many methods have been presented to recognize RNA-binding sites, there is much room left for the improvement of predictive accuracy. We present a sequence semantics-based method (called PRIP) for predicting RNA-binding interfaces. The PRIP extracted semantic embedding by pre-training the Word2vec with the corpus. Extreme gradient boosting was employed to train a classifier. The PRIP obtained a SN of 0.73 over the five-fold cross validation and a SN of 0.67 over the independent test, outperforming the state-of-the-art methods. Compared with other methods, this PRIP learned the hidden relations between words in the context. The analysis of the semantics relationship implied that the semantics of some words were specific to RNA-binding interfaces. This method is helpful to explore the mechanism of RNA–protein interactions from a semantics point of view.
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McMillan PJ, Strovas TJ, Baum M, Mitchell BK, Eck RJ, Hendricks N, Wheeler JM, Latimer CS, Keene CD, Kraemer BC. Pathological tau drives ectopic nuclear speckle scaffold protein SRRM2 accumulation in neuron cytoplasm in Alzheimer's disease. Acta Neuropathol Commun 2021; 9:117. [PMID: 34187600 PMCID: PMC8243890 DOI: 10.1186/s40478-021-01219-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/19/2023] Open
Abstract
Several conserved nuclear RNA binding proteins (sut-1, sut-2, and parn-2) control tau aggregation and toxicity in C. elegans, mice, and human cells. MSUT2 protein normally resides in nuclear speckles, membraneless organelles composed of phase-separated RNAs and RNA-binding proteins that mediate critical steps in mRNA processing including mRNA splicing. We used human pathological tissue and transgenic mice to identify Alzheimer’s disease-specific cellular changes related to nuclear speckles. We observed that nuclear speckle constituent scaffold protein SRRM2 is mislocalized and accumulates in cytoplasmic lesions in AD brain tissue. Furthermore, progression of tauopathy in transgenic mice is accompanied by increasing mislocalization of SRRM2 from the neuronal nucleus to the soma. In AD brain tissue, SRRM2 mislocalization associates with increased severity of pathological tau deposition. These findings suggest potential mechanisms by which pathological tau impacts nuclear speckle function in diverse organisms ranging from C. elegans to mice to humans. Future translational studies aimed at restoring nuclear speckle homeostasis may provide novel candidate therapeutic targets for pharmacological intervention.
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