1
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Mercer RCC, Le NTT, Fraser DG, Houser MCQ, Beeler AB, Harris DA. Sigma Receptor Ligands Are Potent Antiprion Compounds that Act Independently of Sigma Receptor Binding. ACS Chem Neurosci 2024; 15:2265-2282. [PMID: 38743607 DOI: 10.1021/acschemneuro.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Prion diseases are invariably fatal neurodegenerative diseases of humans and other animals for which there are no effective treatment options. Previous work from our laboratory identified phenethylpiperidines as a novel class of anti-prion compounds. While working to identify the molecular target(s) of these molecules, we unexpectedly discovered ten novel antiprion compounds based on their known ability to bind to the sigma receptors, σ1R and σ2R, which are currently being tested as therapeutic or diagnostic targets for cancer and neuropsychiatric disorders. Surprisingly, however, knockout of the respective genes encoding σ1R and σ2R (Sigmar1 and Tmem97) in prion-infected N2a cells did not alter the antiprion activity of these compounds, demonstrating that these receptors are not the direct targets responsible for the antiprion effects of their ligands. Further investigation of the most potent molecules established that they are efficacious against multiple prion strains and protect against downstream prion-mediated synaptotoxicity. While the precise details of the mechanism of action of these molecules remain to be determined, the present work forms the basis for further investigation of these compounds in preclinical studies. Given the therapeutic utility of several of the tested compounds, including rimcazole and haloperidol for neuropsychiatric conditions, (+)-pentazocine for neuropathic pain, and the ongoing clinical trials of SA 4503 and ANAVEX2-73 for ischemic stroke and Alzheimer's disease, respectively, this work has immediate implications for the treatment of human prion disease.
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Affiliation(s)
- Robert C C Mercer
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Nhat T T Le
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Douglas G Fraser
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mei C Q Houser
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
| | - Aaron B Beeler
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - David A Harris
- Department of Biochemistry & Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts 02118, United States
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2
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Glynn C, Rodriguez JA, Hyman BT. The structural line between prion and "prion-like": Insights from prion protein and tau. Curr Opin Neurobiol 2024; 86:102857. [PMID: 38489865 PMCID: PMC11162956 DOI: 10.1016/j.conb.2024.102857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/15/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
The concept of 'prion-like' behavior has emerged in the study of diseases involving protein misfolding where fibrillar structures, called amyloids, self-propagate and induce disease in a fashion similar to prions. From a biological standpoint, in order to be considered 'prion-like,' a protein must traverse cells and tissues and further propagate via a templated conformational change. Since 2017, cryo-electron microscopy structures from patient-derived 'prion-like' amyloids, in particular tau, have been presented and revealed structural similarities shared across amyloids. Since 2021, cryo-EM structures from prions of known infectivity have been added to the ex vivo amyloid structure family. In this review, we discuss current proposals for the 'prion-like' mechanisms of spread for tau and prion protein as well as discuss different influencers on structures of aggregates from tauopathies and prion diseases. Lastly, we discuss some of the current hypotheses for what may distinguish structures that are 'prion-like' from transmissible prion structures.
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Affiliation(s)
- Calina Glynn
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, STROBE, NSF Science and Technology Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA.
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3
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Woerman AL, Bartz JC. Effect of host and strain factors on α-synuclein prion pathogenesis. Trends Neurosci 2024:S0166-2236(24)00084-5. [PMID: 38806297 DOI: 10.1016/j.tins.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/19/2024] [Accepted: 05/04/2024] [Indexed: 05/30/2024]
Abstract
Prion diseases are a group of neurodegenerative disorders caused by misfolding of proteins into pathogenic conformations that self-template to spread disease. Although this mechanism is largely associated with the prion protein (PrP) in classical prion diseases, a growing literature indicates that other proteins, including α-synuclein, rely on a similar disease mechanism. Notably, α-synuclein misfolds into distinct conformations, or strains, that cause discrete clinical disorders including multiple system atrophy (MSA) and Parkinson's disease (PD). Because the recognized similarities between PrP and α-synuclein are increasing, this review article draws from research on PrP to identify the host and strain factors that impact disease pathogenesis, predominantly in rodent models, and focuses on key considerations for future research on α-synuclein prions.
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Affiliation(s)
- Amanda L Woerman
- Department of Microbiology, Immunology, and Pathology, Prion Research Center, Colorado State University, Fort Collins, CO, USA.
| | - Jason C Bartz
- Department of Microbiology, Immunology, and Pathology, Prion Research Center, Colorado State University, Fort Collins, CO, USA; Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, USA.
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Abioye A, Akintade D, Mitchell J, Olorode S, Adejare A. Nonintuitive Immunogenicity and Plasticity of Alpha-Synuclein Conformers: A Paradigm for Smart Delivery of Neuro-Immunotherapeutics. Pharmaceutics 2024; 16:609. [PMID: 38794271 PMCID: PMC11124533 DOI: 10.3390/pharmaceutics16050609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the extensive research successes and continuous developments in modern medicine in terms of diagnosis, prevention, and treatment, the lack of clinically useful disease-modifying drugs or immunotherapeutic agents that can successfully treat or prevent neurodegenerative diseases is an ongoing challenge. To date, only one of the 244 drugs in clinical trials for the treatment of neurodegenerative diseases has been approved in the past decade, indicating a failure rate of 99.6%. In corollary, the approved monoclonal antibody did not demonstrate significant cognitive benefits. Thus, the prevalence of neurodegenerative diseases is increasing rapidly. Therefore, there is an urgent need for creative approaches to identifying and testing biomarkers for better diagnosis, prevention, and disease-modifying strategies for the treatment of neurodegenerative diseases. Overexpression of the endogenous α-synuclein has been identified as the driving force for the formation of the pathogenic α-synuclein (α-Syn) conformers, resulting in neuroinflammation, hypersensitivity, endogenous homeostatic responses, oxidative dysfunction, and degeneration of dopaminergic neurons in Parkinson's disease (PD). However, the conformational plasticity of α-Syn proffers that a certain level of α-Syn is essential for the survival of neurons. Thus, it exerts both neuroprotective and neurotoxic (regulatory) functions on neighboring neuronal cells. Furthermore, the aberrant metastable α-Syn conformers may be subtle and difficult to detect but may trigger cellular and molecular events including immune responses. It is well documented in literature that the misfolded α-Syn and its conformers that are released into the extracellular space from damaged or dead neurons trigger the innate and adaptive immune responses in PD. Thus, in this review, we discuss the nonintuitive plasticity and immunogenicity of the α-Syn conformers in the brain immune cells and their physiological and pathological consequences on the neuroimmune responses including neuroinflammation, homeostatic remodeling, and cell-specific interactions that promote neuroprotection in PD. We also critically reviewed the novel strategies for immunotherapeutic delivery interventions in PD pathogenesis including immunotherapeutic targets and potential nanoparticle-based smart drug delivery systems. It is envisioned that a greater understanding of the nonintuitive immunogenicity of aberrant α-Syn conformers in the brain's microenvironment would provide a platform for identifying valid therapeutic targets and developing smart brain delivery systems for clinically effective disease-modifying immunotherapeutics that can aid in the prevention and treatment of PD in the future.
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Affiliation(s)
- Amos Abioye
- College of Pharmacy and Health Sciences, Belmont University, Nashville, TN 37212, USA
| | - Damilare Akintade
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - James Mitchell
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - Simisade Olorode
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - Adeboye Adejare
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph’s University, Philadelphia, PA 19131, USA;
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5
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Zerr I, Ladogana A, Mead S, Hermann P, Forloni G, Appleby BS. Creutzfeldt-Jakob disease and other prion diseases. Nat Rev Dis Primers 2024; 10:14. [PMID: 38424082 DOI: 10.1038/s41572-024-00497-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Prion diseases share common clinical and pathological characteristics such as spongiform neuronal degeneration and deposition of an abnormal form of a host-derived protein, termed prion protein. The characteristic features of prion diseases are long incubation times, short clinical courses, extreme resistance of the transmissible agent to degradation and lack of nucleic acid involvement. Sporadic and genetic forms of prion diseases occur worldwide, of which genetic forms are associated with mutations in PRNP. Human to human transmission of these diseases has occurred due to iatrogenic exposure, and zoonotic forms of prion diseases are linked to bovine disease. Significant progress has been made in the diagnosis of these disorders. Clinical tools for diagnosis comprise brain imaging and cerebrospinal fluid tests. Aggregation assays for detection of the abnormally folded prion protein have a clear potential to diagnose the disease in peripherally accessible biofluids. After decades of therapeutic nihilism, new treatment strategies and clinical trials are on the horizon. Although prion diseases are relatively rare disorders, understanding their pathogenesis and mechanisms of prion protein misfolding has significantly enhanced the field in research of neurodegenerative diseases.
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Affiliation(s)
- Inga Zerr
- National Reference Center for CJD Surveillance, Department of Neurology, University Medical Center, Georg August University, Göttingen, Germany.
| | - Anna Ladogana
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| | - Simon Mead
- MRC Prion Unit at UCL, Institute of Prion Diseases, London, UK
| | - Peter Hermann
- National Reference Center for CJD Surveillance, Department of Neurology, University Medical Center, Georg August University, Göttingen, Germany
| | - Gianluigi Forloni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Brian S Appleby
- Departments of Neurology, Psychiatry and Pathology, Case Western Reserve University, Cleveland, OH, USA
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6
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Bridges LR. RNA as a component of scrapie fibrils. Sci Rep 2024; 14:5011. [PMID: 38424114 PMCID: PMC10904389 DOI: 10.1038/s41598-024-55278-0] [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: 11/02/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published and deposited in the electron microscopy data bank (EMDB). As noted by the primary authors, the fibrils contain a second component other than protein. The aim of the present study was to identify the nature of this second component in the published maps using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a structural role. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. A Y-shaped polymer consistent with RNA was found, in places forming a single chain and at one location forming a duplex, comprising two antiparallel chains, and raising the intriguing possibility of replicative behaviour. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a short tandem repeat. Fibrils from brains of patients with Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and other neurodegenerations also contain EDs and may be of a similar aetiology.
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Affiliation(s)
- Leslie R Bridges
- Neuropathology, Cellular Pathology, South West London Pathology, St George's Hospital, St George's University Hospitals NHS Foundation Trust, London, UK.
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.
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7
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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8
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Bocharova O, Makarava N, Pandit NP, Molesworth K, Baskakov IV. Multiple steps of prion strain adaptation to a new host. Front Neurosci 2024; 18:1329010. [PMID: 38362022 PMCID: PMC10867973 DOI: 10.3389/fnins.2024.1329010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
The transmission of prions across species is a critical aspect of their dissemination among mammalian hosts, including humans. This process often necessitates strain adaptation. In this study, we sought to investigate the mechanisms underlying prion adaptation while mitigating biases associated with the history of cross-species transmission of natural prion strains. To achieve this, we utilized the synthetic hamster prion strain S05. Propagation of S05 using mouse PrPC in Protein Misfolding Cyclic Amplification did not immediately overcome the species barrier. This finding underscores the involvement of factors beyond disparities in primary protein structures. Subsequently, we performed five serial passages to stabilize the incubation time to disease in mice. The levels of PrPSc increased with each passage, reaching a maximum at the third passage, and declining thereafter. This suggests that only the initial stage of adaptation is primarily driven by an acceleration in PrPSc replication. During the protracted adaptation to a new host, we observed significant alterations in the glycoform ratio and sialylation status of PrPSc N-glycans. These changes support the notion that qualitative modifications in PrPSc contribute to a more rapid disease progression. Furthermore, consistent with the decline in sialylation, a cue for "eat me" signaling, the newly adapted strain exhibited preferential colocalization with microglia. In contrast to PrPSc dynamics, the intensity of microglia activation continued to increase after the third passage in the new host. In summary, our study elucidates that the adaptation of a prion strain to a new host is a multi-step process driven by several factors.
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Affiliation(s)
- Olga Bocharova
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Narayan P. Pandit
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kara Molesworth
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Ilia V. Baskakov
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
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9
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Zhang W, Orrú CD, Foutz A, Ding M, Yuan J, Shah SZA, Zhang J, Kotobelli K, Gerasimenko M, Gilliland T, Chen W, Tang M, Cohen M, Safar J, Xu B, Hong DJ, Cui L, Hughson AG, Schonberger LB, Tatsuoka C, Chen SG, Greenlee JJ, Wang Z, Appleby BS, Caughey B, Zou WQ. Large-scale validation of skin prion seeding activity as a biomarker for diagnosis of prion diseases. Acta Neuropathol 2024; 147:17. [PMID: 38231266 DOI: 10.1007/s00401-023-02661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024]
Abstract
Definitive diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD) relies on the examination of brain tissues for the pathological prion protein (PrPSc). Our previous study revealed that PrPSc-seeding activity (PrPSc-SA) is detectable in skin of sCJD patients by an ultrasensitive PrPSc seed amplification assay (PrPSc-SAA) known as real-time quaking-induced conversion (RT-QuIC). A total of 875 skin samples were collected from 2 cohorts (1 and 2) at autopsy from 2-3 body areas of 339 cases with neuropathologically confirmed prion diseases and non-sCJD controls. The skin samples were analyzed for PrPSc-SA by RT-QuIC assay. The results were compared with demographic information, clinical manifestations, cerebrospinal fluid (CSF) PrPSc-SA, other laboratory tests, subtypes of prion diseases defined by the methionine (M) or valine (V) polymorphism at residue 129 of PrP, PrPSc types (#1 or #2), and gene mutations in deceased patients. RT-QuIC assays of the cohort #1 by two independent laboratories gave 87.3% or 91.3% sensitivity and 94.7% or 100% specificity, respectively. The cohort #2 showed sensitivity of 89.4% and specificity of 95.5%. RT-QuIC of CSF available from 212 cases gave 89.7% sensitivity and 94.1% specificity. The sensitivity of skin RT-QuIC was subtype dependent, being highest in sCJDVV1-2 subtype, followed by VV2, MV1-2, MV1, MV2, MM1, MM1-2, MM2, and VV1. The skin area next to the ear gave highest sensitivity, followed by lower back and apex of the head. Although no difference in brain PrPSc-SA was detected between the cases with false negative and true positive skin RT-QuIC results, the disease duration was significantly longer with the false negatives [12.0 ± 13.3 (months, SD) vs. 6.5 ± 6.4, p < 0.001]. Our study validates skin PrPSc-SA as a biomarker for the detection of prion diseases, which is influenced by the PrPSc types, PRNP 129 polymorphisms, dermatome sampled, and disease duration.
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Affiliation(s)
- Weiguanliu Zhang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Neurology, The First Hospital of Jilin University, Changchun, 130021, Jilin Province, China
| | - Christina D Orrú
- Laboratory of Persistent Viral Diseases, NIH/NIAID Rocky Mountain Laboratories, 903 S 4 St., Hamilton, MT, 59840, USA
| | - Aaron Foutz
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mingxuan Ding
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Neurology, The First Hospital of Jilin University, Changchun, 130021, Jilin Province, China
| | - Jue Yuan
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Syed Zahid Ali Shah
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jing Zhang
- Department of Population and Quantitative Health Science, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Keisi Kotobelli
- National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Maria Gerasimenko
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Tricia Gilliland
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Wei Chen
- National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Michelle Tang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Mark Cohen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jiri Safar
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Bin Xu
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC, 27707, USA
| | - Dao-Jun Hong
- Institute of Neurology and Department of Neurology, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Li Cui
- Department of Neurology, The First Hospital of Jilin University, Changchun, 130021, Jilin Province, China
| | - Andrew G Hughson
- Laboratory of Persistent Viral Diseases, NIH/NIAID Rocky Mountain Laboratories, 903 S 4 St., Hamilton, MT, 59840, USA
| | - Lawrence B Schonberger
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30329, USA
| | - Curtis Tatsuoka
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Shu G Chen
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Justin J Greenlee
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, 1920 Dayton Avenue, Ames, IA, 50010, USA
| | - Zerui Wang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Brian S Appleby
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Neurology, University Hospitals Cleveland Medical Center and Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, NIH/NIAID Rocky Mountain Laboratories, 903 S 4 St., Hamilton, MT, 59840, USA.
| | - Wen-Quan Zou
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- National Prion Disease Pathology Surveillance Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Institute of Neurology and Department of Neurology, Jiangxi Academy of Clinical Medical Sciences, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi Province, China.
- Department of Neurology, University Hospitals Cleveland Medical Center and Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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10
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Asarnow D, Becker VA, Bobe D, Dubbledam C, Johnston JD, Kopylov M, Lavoie NR, Li Q, Mattingly JM, Mendez JH, Paraan M, Turner J, Upadhye V, Walsh RM, Gupta M, Eng ET. Recent advances in infectious disease research using cryo-electron tomography. Front Mol Biosci 2024; 10:1296941. [PMID: 38288336 PMCID: PMC10822977 DOI: 10.3389/fmolb.2023.1296941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
With the increasing spread of infectious diseases worldwide, there is an urgent need for novel strategies to combat them. Cryogenic sample electron microscopy (cryo-EM) techniques, particularly electron tomography (cryo-ET), have revolutionized the field of infectious disease research by enabling multiscale observation of biological structures in a near-native state. This review highlights the recent advances in infectious disease research using cryo-ET and discusses the potential of this structural biology technique to help discover mechanisms of infection in native environments and guiding in the right direction for future drug discovery.
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Affiliation(s)
- Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Vada A. Becker
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
| | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Charlie Dubbledam
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jake D. Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Nathalie R. Lavoie
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, United States
| | - Qiuye Li
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Jacob M. Mattingly
- Department of Chemistry, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jack Turner
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Viraj Upadhye
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology and Harvard Medical School, Boston, MA, United States
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
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11
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Jones E, Hill E, Linehan J, Nazari T, Caulder A, Codner GF, Hutchison M, Mackenzie M, Farmer M, Coysh T, De Oliveira MW, Al-Doujaily H, Sandberg M, Viré E, Cunningham TJ, Asante EA, Brandner S, Collinge J, Mead S. Characterisation and prion transmission study in mice with genetic reduction of sporadic Creutzfeldt-Jakob disease risk gene Stx6. Neurobiol Dis 2024; 190:106363. [PMID: 37996040 PMCID: PMC7615600 DOI: 10.1016/j.nbd.2023.106363] [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: 08/16/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Sporadic Creutzfeldt-Jakob disease (sCJD), the most common human prion disease, is thought to occur when the cellular prion protein (PrPC) spontaneously misfolds and assembles into prion fibrils, culminating in fatal neurodegeneration. In a genome-wide association study of sCJD, we recently identified risk variants in and around the gene STX6, with evidence to suggest a causal increase of STX6 expression in disease-relevant brain regions. STX6 encodes syntaxin-6, a SNARE protein primarily involved in early endosome to trans-Golgi network retrograde transport. Here we developed and characterised a mouse model with genetic depletion of Stx6 and investigated a causal role of Stx6 expression in mouse prion disease through a classical prion transmission study, assessing the impact of homozygous and heterozygous syntaxin-6 knockout on disease incubation periods and prion-related neuropathology. Following inoculation with RML prions, incubation periods in Stx6-/- and Stx6+/- mice differed by 12 days relative to wildtype. Similarly, in Stx6-/- mice, disease incubation periods following inoculation with ME7 prions also differed by 12 days. Histopathological analysis revealed a modest increase in astrogliosis in ME7-inoculated Stx6-/- animals and a variable effect of Stx6 expression on microglia activation, however no differences in neuronal loss, spongiform change or PrP deposition were observed at endpoint. Importantly, Stx6-/- mice are viable and fertile with no gross impairments on a range of neurological, biochemical, histological and skeletal structure tests. Our results provide some support for a pathological role of Stx6 expression in prion disease, which warrants further investigation in the context of prion disease but also other neurodegenerative diseases considering syntaxin-6 appears to have pleiotropic risk effects in progressive supranuclear palsy and Alzheimer's disease.
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Affiliation(s)
- Emma Jones
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Elizabeth Hill
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Jacqueline Linehan
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Tamsin Nazari
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Adam Caulder
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Gemma F Codner
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Marie Hutchison
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Matthew Mackenzie
- Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Michael Farmer
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Thomas Coysh
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Michael Wiggins De Oliveira
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Huda Al-Doujaily
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Malin Sandberg
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Emmanuelle Viré
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Thomas J Cunningham
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Emmanuel A Asante
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Sebastian Brandner
- Division of Neuropathology and Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - John Collinge
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK
| | - Simon Mead
- Medical Research Council Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, London W1W 7FF, UK.
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12
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Mishra S. Emerging Trends in Cryo-EM-based Structural Studies of Neuropathological Amyloids. J Mol Biol 2023; 435:168361. [PMID: 37949311 DOI: 10.1016/j.jmb.2023.168361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tauopathies, synucleinopathies, Aβ amyloidosis, TDP-43 proteinopathies, and prion diseases- these neurodegenerative diseases have in common the formation of amyloid filaments rich in cross-β sheets. Cryo-electron microscopy now permits the visualization of amyloid assemblies at atomic resolution, ushering a wide range of structural studies on several of these poorly understood amyloidogenic proteins. Amyloids are polymorphic with minor modulations in reaction environment affecting the overall architecture of their assembly, making amyloids an extremely challenging venture for structure-based therapeutic intervention. In 2017, the first cryo-EM structure of tau filaments from an Alzheimer's disease-affected brain established that in vitro assemblies might not necessarily reflect the native amyloid fold. Since then, brain-derived amyloid structures for several proteins across many neurodegenerative diseases have uncovered the disease-relevant amyloid folds. It has now been shown for tauopathies, synucleinopathies and TDP-43 proteinopathies, that distinct amyloid folds of the same protein might be related to different diseases. Salient features of each of these brain-derived folds are discussed in detail. It was also recently observed that seeded aggregation does not necessarily replicate the brain-derived structural fold. Owing to high throughput structure determination, some of these native amyloid folds have also been successfully replicated in vitro. In vitro replication of disease-relevant filaments will aid development of imaging ligands and defibrillating drugs. Towards this direction, recent high-resolution structures of tau filaments with positron emission tomography tracers and a defibrillating drug are also discussed. This review summarizes and celebrates the recent advancements in structural understanding of neuropathological amyloid filaments using cryo-EM.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Biological Sciences Division, Indian Institute of Science, Bengaluru 560 012, Karnataka, India.
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13
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Tao J, Zeng Y, Dai B, Liu Y, Pan X, Wang LQ, Chen J, Zhou Y, Lu Z, Xie L, Liang Y. Excess PrP C inhibits muscle cell differentiation via miRNA-enhanced liquid-liquid phase separation implicated in myopathy. Nat Commun 2023; 14:8131. [PMID: 38065962 PMCID: PMC10709375 DOI: 10.1038/s41467-023-43826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The cellular prion protein (PrPC) is required for skeletal muscle function. Here, we report that a higher level of PrPC accumulates in the cytoplasm of the skeletal muscle of six myopathy patients compared to controls. PrPC inhibits skeletal muscle cell autophagy, and blocks myoblast differentiation. PrPC selectively binds to a subset of miRNAs during myoblast differentiation, and the colocalization of PrPC and miR-214-3p was observed in the skeletal muscle of six myopathy patients with excessive PrPC. We demonstrate that PrPC is overexpressed in skeletal muscle cells under pathological conditions, inhibits muscle cell differentiation by physically interacting with a subset of miRNAs, and selectively recruits these miRNAs into its phase-separated condensate in living myoblasts, which in turn enhances liquid-liquid phase separation of PrPC, promotes pathological aggregation of PrP, and results in the inhibition of autophagy-related protein 5-dependent autophagy and muscle bundle formation in myopathy patients characterized by incomplete muscle regeneration.
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Affiliation(s)
- Jing Tao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanping Zeng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Bin Dai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yin Liu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xiaohan Pan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Li-Qiang Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Wuhan University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jie Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuneng Lu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Liwei Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
- Wuhan University Shenzhen Research Institute, Shenzhen, 518057, China.
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14
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Legname G. Copper coordination modulates prion conversion and infectivity in mammalian prion proteins. Prion 2023; 17:1-6. [PMID: 36597284 PMCID: PMC9815218 DOI: 10.1080/19336896.2022.2163835] [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] [Indexed: 01/05/2023] Open
Abstract
In mammals the cellular form of the prion protein (PrPC) is a ubiquitous protein involved in many relevant functions in the central nervous system. In addition to its physiological functions PrPC plays a central role in a group of invariably fatal neurodegenerative disorders collectively called prion diseases. In fact, the protein is a substrate in a process in which it converts into an infectious and pathological form denoted as prion. The protein has a unique primary structure where the unstructured N-terminal moiety possesses characteristic sequences wherein histidines are able to coordinate metal ions, in particular copper ions. These sequences are called octarepeats for their characteristic length. Moreover, a non-octarepeat fifth-copper binding site is present where copper coordination seems to control infectivity. In this review, I will argue that these sequences may play a significant role in modulating prion conversion and replication.
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Affiliation(s)
- Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste, Italy,CONTACT Giuseppe Legname Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore Di Studi Avanzati (SISSA), Trieste34136, Italy
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15
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Soto P, Gloeb GM, Tsuchida KA, Charles AA, Greenwood NM, Hendrickson H. Insight into the conserved structural dynamics of the C-terminus of mammal PrPC identifies structural core and possible structural role of pharmacological chaperones. Prion 2023; 17:55-66. [PMID: 36892160 PMCID: PMC10012922 DOI: 10.1080/19336896.2023.2186674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Misfolding of the prion protein is central to prion disease aetiology. Although understanding the dynamics of the native fold helps to decipher the conformational conversion mechanism, a complete depiction of distal but coupled prion protein sites common across species is lacking. To fill this gap, we used normal mode analysis and network analysis to examine a collection of prion protein structures deposited on the protein data bank. Our study identified a core of conserved residues that sustains the connectivity across the C-terminus of the prion protein. We propose how a well-characterized pharmacological chaperone may stabilize the fold. Also, we provide insight into the effect on the native fold of initial misfolding pathways identified by others using kinetics studies.
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Affiliation(s)
- Patricia Soto
- Physics department, Creighton University, Omaha, NE, USA
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16
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Wu S, Edskes HK, Wickner RB. Human proteins curing yeast prions. Proc Natl Acad Sci U S A 2023; 120:e2314781120. [PMID: 37903258 PMCID: PMC10636303 DOI: 10.1073/pnas.2314781120] [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: 08/25/2023] [Accepted: 09/25/2023] [Indexed: 11/01/2023] Open
Abstract
Recognition that common human amyloidoses are prion diseases makes the use of the Saccharomyces cerevisiae prion model systems to screen for possible anti-prion components of increasing importance. [PSI+] and [URE3] are amyloid-based prions of Sup35p and Ure2p, respectively. Yeast has at least six anti-prion systems that together cure nearly all [PSI+] and [URE3] prions arising in their absence. We made a GAL-promoted bank of 14,913 human open reading frames in a yeast shuttle plasmid and isolated 20 genes whose expression cures [PSI+] or [URE3]. PRPF19 is an E3 ubiquitin ligase that cures [URE3] if its U-box is intact. DNAJA1 is a J protein that cures [PSI+] unless its interaction with Hsp70s is defective. Human Bag5 efficiently cures [URE3] and [PSI+]. Bag family proteins share a 110 to 130 residue "BAG domain"; Bag 1, 2, 3, 4, and 6 each have one BAG domain while Bag5 has five BAG domains. Two BAG domains are necessary for curing [PSI+], but one can suffice to cure [URE3]. Although most Bag proteins affect autophagy in mammalian cells, mutations blocking autophagy in yeast do not affect Bag5 curing of [PSI+] or [URE3]. Curing by Bag proteins depends on their interaction with Hsp70s, impairing their role, with Hsp104 and Sis1, in the amyloid filament cleavage necessary for prion propagation. Since Bag5 curing is reduced by overproduction of Sis1, we propose that Bag5 cures prions by blocking Sis1 access to Hsp70s in its role with Hsp104 in filament cleavage.
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Affiliation(s)
- Songsong Wu
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0830
| | - Herman K. Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0830
| | - Reed B. Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0830
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17
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Hara H, Miyata H, Chida J, Sakaguchi S. Strain-dependent role of copper in prion disease through binding to histidine residues in the N-terminal domain of prion protein. J Neurochem 2023; 167:394-409. [PMID: 37777338 DOI: 10.1111/jnc.15971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
The cellular prion protein, PrPC , is a copper-binding protein abundantly expressed in the brain, particularly by neurons, and its conformational conversion into the amyloidogenic isoform, PrPSc , plays a key pathogenic role in prion diseases. However, the role of copper binding to PrPC in prion diseases remains unclear. Here, we fed mice with a low-copper or regular diet and intracerebrally inoculated them with two different mouse-adapted RML scrapie and BSE prions. Mice with a low-copper diet developed disease significantly but only slightly later than those with a regular diet after inoculation with BSE prions, but not with RML prions, suggesting that copper could play a minor role in BSE prion pathogenesis, but not in RML prion pathogenesis. We then generated two lines of transgenic mice expressing mouse PrP with copper-binding histidine (His) residues in the N-terminal domain replaced with alanine residues, termed TgPrP(5H > A)-7342/Prnp0/0 and TgPrP(5H > A)-7524/Prnp0/0 mice, and similarly inoculated RML and BSE prions into them. Due to 2-fold higher expression of PrP(5H > A) than PrPC in wild-type (WT) mice, TgPrP(5H > A)-7524/Prnp0/0 mice were highly susceptible to these prions, compared to WT mice. However, TgPrP(5H > A)-7342/Prnp0/0 mice, which express PrP(5H > A) 1.2-fold as high as PrPC in WT mice, succumbed to disease slightly, but not significantly, later than WT mice after inoculation with RML prions, but significantly so after inoculation with BSE prions. Subsequent secondary inoculation experiments revealed that amino acid sequence differences between PrP(5H > A) and WT PrPSc created no prion transmission barrier to BSE prions. These results suggest that copper-binding His residues in PrPC are dispensable for RML prion pathogenesis but have a minor effect on BSE prion pathogenesis. Taken together, our current results suggest that copper could have a minor effect on prion pathogenesis in a strain-dependent manner through binding to His residues in the N-terminal domain of PrPC .
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Affiliation(s)
- Hideyuki Hara
- Division of Molecular Neurobiology, The Institute for Enzyme Research (KOSOKEN), Tokushima University, Tokushima, Japan
| | - Hironori Miyata
- Animal Research Center, School of Medicine, University of Occupational and Environmental Health, Yahatanishi, Kitakyushu, Japan
| | - Junji Chida
- Division of Molecular Neurobiology, The Institute for Enzyme Research (KOSOKEN), Tokushima University, Tokushima, Japan
| | - Suehiro Sakaguchi
- Division of Molecular Neurobiology, The Institute for Enzyme Research (KOSOKEN), Tokushima University, Tokushima, Japan
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18
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Bohl J, Moudjou M, Herzog L, Reine F, Sailer F, Klute H, Halgand F, Rest GVD, Boulard Y, Béringue V, Igel A, Rezaei H. The Smallest Infectious Substructure Encoding the Prion Strain Structural Determinant Revealed by Spontaneous Dissociation of Misfolded Prion Protein Assemblies. J Mol Biol 2023; 435:168280. [PMID: 37730082 DOI: 10.1016/j.jmb.2023.168280] [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: 03/21/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
It is commonly accepted that the prion replicative propensity and strain structural determinant (SSD) are encoded in the fold of PrPSc amyloid fibril assemblies. By exploring the quaternary structure dynamicity of several prion strains, we revealed that all mammalian prion assemblies exhibit the generic property of spontaneously generating two sets of discreet infectious tetrameric and dimeric species differing significantly by their specific infectivity. By using perturbation approaches such as dilution and ionic strength variation, we demonstrated that these two oligomeric species were highly dynamic and evolved differently in the presence of chaotropic agents. In general, our observations of seven different prion strains from three distinct species highlight the high dynamicity of PrPSc assemblies as a common and intrinsic property of mammalian prions. The existence of such small infectious PrPSc species harboring the SSD indicates that the prion infectivity and the SSD are not restricted only to the amyloid fold but can also be encoded in other alternative quaternary structures. Such diversity in the quaternary structure of prion assemblies tends to indicate that the structure of PrPSc can be divided into two independent folding domains: a domain encoding the strain structural determinant and a second domain whose fold determines the type of quaternary structure that could adopt PrPSc assemblies.
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Affiliation(s)
- Jan Bohl
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France; ICP, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Mohammed Moudjou
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Laetitia Herzog
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Fabienne Reine
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Fiona Sailer
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Hannah Klute
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | | | | | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Vincent Béringue
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France.
| | - Angelique Igel
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France.
| | - Human Rezaei
- Université Paris-Saclay, INRAe, UVSQ, VIM, 78350 Jouy-en-Josas, France.
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19
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Li XN, Gao Y, Li Y, Yin JX, Yi CW, Yuan HY, Huang JJ, Wang LQ, Chen J, Liang Y. Arg177 and Asp159 from dog prion protein slow liquid-liquid phase separation and inhibit amyloid formation of human prion protein. J Biol Chem 2023; 299:105329. [PMID: 37805139 PMCID: PMC10641668 DOI: 10.1016/j.jbc.2023.105329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 10/09/2023] Open
Abstract
Prion diseases are a group of transmissible neurodegenerative diseases primarily caused by the conformational conversion of prion protein (PrP) from α-helix-dominant cellular prion protein (PrPC) to β-sheet-rich pathological aggregated form of PrPSc in many mammalian species. Dogs exhibit resistance to prion diseases, but the mechanism behind the phenomenon remains poorly understood. Compared with human PrP and mouse PrP, dog PrP has two unique amino acid residues, Arg177 and Asp159. Because PrPC contains a low-complexity and intrinsically disordered region in its N-terminal domain, it undergoes liquid-liquid phase separation (LLPS) in vitro and forms protein condensates. However, little is known about whether these two unique residues modulate the formation of PrPC condensates. Here, using confocal microscopy, fluorescence recovery after photobleaching assays, thioflavin T binding assays, and transmission electron microscopy, we report that Arg177 and Asp159 from the dog PrP slow the LLPS of full-length human PrPC, shifting the equilibrium phase boundary to higher protein concentrations and inhibit amyloid formation of the human protein. In sharp contrast, His177 and Asn159 from the human PrP enhance the LLPS of full-length dog PrPC, shifting the equilibrium phase boundary to lower protein concentrations, and promote fibril formation of the canid protein. Collectively, these results demonstrate how LLPS and amyloid formation of PrP are inhibited by a single residue Arg177 or Asp159 associated with prion disease resistance, and how LLPS and fibril formation of PrP are promoted by a single residue His177 or Asn159. Therefore, Arg177/His177 and Asp159/Asn159 are key residues in modulating PrPC liquid-phase condensation.
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Affiliation(s)
- Xiang-Ning Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yuan Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yang Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jin-Xu Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Chuan-Wei Yi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Han-Ye Yuan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jun-Jie Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Li-Qiang Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Wuhan University Shenzhen Research Institute, Shenzhen, China
| | - Jie Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yi Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Wuhan University Shenzhen Research Institute, Shenzhen, China.
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20
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Bocharova O, Makarava N, Pandit NP, Molesworth K, Baskakov IV. Multiple steps of prion strain adaptation to a new host. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563743. [PMID: 37961127 PMCID: PMC10634783 DOI: 10.1101/2023.10.24.563743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The transmission of prions across species is a critical aspect of their dissemination among mammalian hosts, including humans. This process often necessitates strain adaptation. In this study, we sought to investigate the mechanisms underlying prion adaptation while mitigating biases associated with the history of cross-species transmission of natural prion strains. To achieve this, we utilized the synthetic hamster prion strain S05. Propagation of S05 using mouse PrPC in Protein Misfolding Cyclic Amplification did not immediately overcome the species barrier. This finding underscores the involvement of factors beyond disparities in primary protein structures. Subsequently, we performed five serial passages to stabilize the incubation time to disease in mice. The levels of PrPSc increased with each passage, reaching a maximum at the third passage, and declining thereafter. This suggests that only the initial stage of adaptation is primarily driven by an acceleration in PrPSc replication. During the protracted adaptation to a new host, we observed significant alterations in the glycoform ratio and sialylation status of PrPSc N-glycans. These changes support the notion that qualitative modifications in PrPSc contribute to a more rapid disease progression. Furthermore, consistent with the decline in sialylation, a cue for "eat me" signaling, the newly adapted strain exhibited preferential colocalization with microglia. In contrast to PrPSc dynamics, the intensity of microglia activation continued to increase after the third passage in the new host. In summary, our study elucidates that the adaptation of a prion strain to a new host is a multi-step process driven by several factors.
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Affiliation(s)
- Olga Bocharova
- Center for Biomedical Engineering and Technology, Baltimore, Maryland, USA
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Natallia Makarava
- Center for Biomedical Engineering and Technology, Baltimore, Maryland, USA
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Narayan P. Pandit
- Center for Biomedical Engineering and Technology, Baltimore, Maryland, USA
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kara Molesworth
- Center for Biomedical Engineering and Technology, Baltimore, Maryland, USA
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ilia V. Baskakov
- Center for Biomedical Engineering and Technology, Baltimore, Maryland, USA
- Department of Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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21
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Eraña H, Díaz-Domínguez CM, Charco JM, Vidal E, González-Miranda E, Pérez-Castro MA, Piñeiro P, López-Moreno R, Sampedro-Torres-Quevedo C, Fernández-Veiga L, Tasis-Galarza J, Lorenzo NL, Santini-Santiago A, Lázaro M, García-Martínez S, Gonçalves-Anjo N, San-Juan-Ansoleaga M, Galarza-Ahumada J, Fernández-Muñoz E, Giler S, Valle M, Telling GC, Geijó M, Requena JR, Castilla J. Understanding the key features of the spontaneous formation of bona fide prions through a novel methodology that enables their swift and consistent generation. Acta Neuropathol Commun 2023; 11:145. [PMID: 37679832 PMCID: PMC10486007 DOI: 10.1186/s40478-023-01640-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/20/2023] [Indexed: 09/09/2023] Open
Abstract
Among transmissible spongiform encephalopathies or prion diseases affecting humans, sporadic forms such as sporadic Creutzfeldt-Jakob disease are the vast majority. Unlike genetic or acquired forms of the disease, these idiopathic forms occur seemingly due to a random event of spontaneous misfolding of the cellular PrP (PrPC) into the pathogenic isoform (PrPSc). Currently, the molecular mechanisms that trigger and drive this event, which occurs in approximately one individual per million each year, remain completely unknown. Modelling this phenomenon in experimental settings is highly challenging due to its sporadic and rare occurrence. Previous attempts to model spontaneous prion misfolding in vitro have not been fully successful, as the spontaneous formation of prions is infrequent and stochastic, hindering the systematic study of the phenomenon. In this study, we present the first method that consistently induces spontaneous misfolding of recombinant PrP into bona fide prions within hours, providing unprecedented possibilities to investigate the mechanisms underlying sporadic prionopathies. By fine-tuning the Protein Misfolding Shaking Amplification method, which was initially developed to propagate recombinant prions, we have created a methodology that consistently produces spontaneously misfolded recombinant prions in 100% of the cases. Furthermore, this method gives rise to distinct strains and reveals the critical influence of charged surfaces in this process.
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Affiliation(s)
- Hasier Eraña
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
- ATLAS Molecular Pharma S. L. Bizkaia Technology Park, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III National Health Institute, 28029, Madrid, Spain
| | - Carlos M Díaz-Domínguez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III National Health Institute, 28029, Madrid, Spain
| | - Jorge M Charco
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
- ATLAS Molecular Pharma S. L. Bizkaia Technology Park, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III National Health Institute, 28029, Madrid, Spain
| | - Enric Vidal
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Ezequiel González-Miranda
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Miguel A Pérez-Castro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Patricia Piñeiro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Rafael López-Moreno
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Cristina Sampedro-Torres-Quevedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Leire Fernández-Veiga
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Juan Tasis-Galarza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Nuria L Lorenzo
- CIMUS Biomedical Research Institute and Department of Medical Sciences, University of Santiago de Compostela-IDIS, 15782, Santiago de Compostela, Spain
| | - Aileen Santini-Santiago
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Melisa Lázaro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Sandra García-Martínez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Nuno Gonçalves-Anjo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Maitena San-Juan-Ansoleaga
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Josu Galarza-Ahumada
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Eva Fernández-Muñoz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Samanta Giler
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Mikel Valle
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain
| | - Glenn C Telling
- Prion Research Center (PRC), Colorado State University, Fort Collins, CO, 80523, USA
| | - Mariví Geijó
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Spain
| | - Jesús R Requena
- CIMUS Biomedical Research Institute and Department of Medical Sciences, University of Santiago de Compostela-IDIS, 15782, Santiago de Compostela, Spain
| | - Joaquín Castilla
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160, Derio, Bizkaia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Carlos III National Health Institute, 28029, Madrid, Spain.
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain.
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22
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Schwind AM, Walsh DJ, Burke CM, Supattapone S. Phospholipid cofactor solubilization inhibits formation of native prions. J Neurochem 2023; 166:875-884. [PMID: 37551010 PMCID: PMC10528465 DOI: 10.1111/jnc.15930] [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: 05/03/2023] [Revised: 07/05/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Cofactor molecules are required to generate infectious mammalian prions in vitro. Mouse and hamster prions appear to have different cofactor preferences: Whereas both mouse and hamster prions can use phosphatidylethanolamine (PE) as a prion cofactor, only hamster prions can also use single-stranded RNA as an alternative cofactor. Here, we investigated the effect of detergent solubilization on rodent prion formation in vitro. We discovered that detergents that can solubilize PE (n-octylglucoside, n-octylgalactoside, and CHAPS) inhibit mouse prion formation in serial protein misfolding cyclic amplification (sPMCA) reactions using bank vole brain homogenate substrate, whereas detergents that are unable to solubilize PE (Triton X-100 and IPEGAL) have no effect. For all three PE-solubilizing detergents, inhibition of RML mouse prion formation was only observed above the critical micellar concentration (CMC). Two other mouse prion strains, Me7 and 301C, were also inhibited by the three PE-solubilizing detergents but not by Triton X-100 or IPEGAL. In contrast, none of the detergents inhibited hamster prion formation in parallel sPMCA reactions using the same bank vole brain homogenate substrate. In reconstituted sPMCA reactions using purified substrates, n-octylglucoside inhibited hamster prion formation when immunopurified bank vole PrPC substrate was supplemented with brain phospholipid but not with RNA. Interestingly, phospholipid cofactor solubilization had no effect in sPMCA reactions using bacterially expressed recombinant PrP substrate, indicating that the inhibitory effect of solubilization requires PrPC post-translational modifications. Overall, these in vitro results show that the ability of PE to facilitate the formation of native but not recombinant prions requires phospholipid bilayer integrity, suggesting that membrane structure may play an important role in prion formation in vivo.
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Affiliation(s)
- Abigail M. Schwind
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Daniel J. Walsh
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Cassandra M. Burke
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Surachai Supattapone
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
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23
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Gunnels T, Shikiya RA, York TC, Block AJ, Bartz JC. Evidence for preexisting prion substrain diversity in a biologically cloned prion strain. PLoS Pathog 2023; 19:e1011632. [PMID: 37669293 PMCID: PMC10503715 DOI: 10.1371/journal.ppat.1011632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/15/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Prion diseases are a group of inevitably fatal neurodegenerative disorders affecting numerous mammalian species, including Sapiens. Prions are composed of PrPSc, the disease specific conformation of the host encoded prion protein. Prion strains are operationally defined as a heritable phenotype of disease under controlled transmission conditions. Treatment of rodents with anti-prion drugs results in the emergence of drug-resistant prion strains and suggest that prion strains are comprised of a dominant strain and substrains. While much experimental evidence is consistent with this hypothesis, direct observation of substrains has not been observed. Here we show that replication of the dominant strain is required for suppression of a substrain. Based on this observation we reasoned that selective reduction of the dominant strain may allow for emergence of substrains. Using a combination of biochemical methods to selectively reduce drowsy (DY) PrPSc from biologically-cloned DY transmissible mink encephalopathy (TME)-infected brain resulted in the emergence of strains with different properties than DY TME. The selection methods did not occur during prion formation, suggesting the substrains identified preexisted in the DY TME-infected brain. We show that DY TME is biologically stable, even under conditions of serial passage at high titer that can lead to strain breakdown. Substrains therefore can exist under conditions where the dominant strain does not allow for substrain emergence suggesting that substrains are a common feature of prions. This observation has mechanistic implications for prion strain evolution, drug resistance and interspecies transmission.
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Affiliation(s)
- Tess Gunnels
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Ronald A. Shikiya
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Taylor C. York
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Alyssa J. Block
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
| | - Jason C. Bartz
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, Nebraska, United States of America
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24
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Bridges LR. Replicating RNA as a component of scrapie fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553578. [PMID: 37645951 PMCID: PMC10462133 DOI: 10.1101/2023.08.17.553578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published1-5 and deposited in the electron microscopy data bank (EMDB)6. This represents long-awaited near-atomic level structural evidence, widely expected to confirm the protein-only prion hypothesis7,8. Instead, the maps reveal a second component, other than protein. The aim of the present study was to identify the nature of this second component, in the published maps1-5, using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a role as guide and support in fibril construction. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. In one ED, there was evidence of a Y-shaped polymer forming two antiparallel chains, consistent with replicating RNA. Although the protein-only prion hypothesis7 is still popular, convincing counter-evidence for an essential role of RNA as a cofactor has amassed in the last 20 years8. The present findings go beyond this in providing evidence for RNA as the genetic element of scrapie. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a tandem repeat. This is against the protein-only prion hypothesis and in favour of a more orthodox agent, more akin to a virus. Fibrils from brains of patients with Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and other neurodegenerations also contain EDs9 and may be of a similar aetiology.
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Affiliation(s)
- Leslie R Bridges
- Neuropathology, Cellular Pathology, South West London Pathology, St George's Hospital, St George's University Hospitals NHS Foundation Trust, London, UK and Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
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25
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Kell DB, Pretorius E. Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases? Biochem J 2023; 480:1217-1240. [PMID: 37584410 DOI: 10.1042/bcj20230241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
It is now well established that the blood-clotting protein fibrinogen can polymerise into an anomalous form of fibrin that is amyloid in character; the resultant clots and microclots entrap many other molecules, stain with fluorogenic amyloid stains, are rather resistant to fibrinolysis, can block up microcapillaries, are implicated in a variety of diseases including Long COVID, and have been referred to as fibrinaloids. A necessary corollary of this anomalous polymerisation is the generation of novel epitopes in proteins that would normally be seen as 'self', and otherwise immunologically silent. The precise conformation of the resulting fibrinaloid clots (that, as with prions and classical amyloid proteins, can adopt multiple, stable conformations) must depend on the existing small molecules and metal ions that the fibrinogen may (and is some cases is known to) have bound before polymerisation. Any such novel epitopes, however, are likely to lead to the generation of autoantibodies. A convergent phenomenology, including distinct conformations and seeding of the anomalous form for initiation and propagation, is emerging to link knowledge in prions, prionoids, amyloids and now fibrinaloids. We here summarise the evidence for the above reasoning, which has substantial implications for our understanding of the genesis of autoimmunity (and the possible prevention thereof) based on the primary process of fibrinaloid formation.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
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26
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Concha-Marambio L, Wang F, Armijo E, Gorski D, Ramirez F, Scowcroft A, Pritzkow S, Soto C. Development of a methodology for large-scale production of prions for biological and structural studies. Front Mol Biosci 2023; 10:1184029. [PMID: 37635939 PMCID: PMC10449461 DOI: 10.3389/fmolb.2023.1184029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Prion diseases are a group of infectious neurodegenerative diseases produced by the conversion of the normal prion protein (PrPC) into the disease-associated form (PrPSc). Extensive evidence indicate that the main or sole component of the infectious agent is PrPSc, which can replicate in affected individuals in the absence of nucleic acids. However, the mechanism of PrPC-to-PrPSc conversion remains elusive, which has been attributed to the lack of sufficient structural information of infectious PrPSc and a reliable system to study prion replication in vitro. In this article we adapted the Protein Misfolding Cyclic Amplification (PMCA) technology for rapid and efficient generation of highly infectious prions in large-scale. Murine prions of the RML strain were efficiently propagated in volumes up to 1,000-fold larger than conventional PMCA. The large-scale PMCA (LS-PMCA) procedure enabled to produce highly infectious prions, which maintain the strain properties of the seed used to begin the reaction. LS-PMCA was shown to work with various species and strains of prions, including mouse RML and 301C strains, hamster Hyper prion, cervid CWD prions, including a rare Norwegian CWD prion, and human CJD prions. We further improved the LS-PMCA into a bioreactor format that can operate under industry-mimicking conditions for continuous and unlimited production of PrPSc without the need to keep adding brain-derived prions. In our estimation, this bioreactor can produce in 1d an amount of prions equivalent to that present in 25 infected animals at the terminal stage of the disease. Our LS-PMCA technology may provide a valuable tool to produce large quantities of well-defined and homogeneous infectious prions for biological and structural studies.
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Affiliation(s)
- Luis Concha-Marambio
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
- Amprion Inc., San Diego, CA, United States
| | - Fei Wang
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Enrique Armijo
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Damian Gorski
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Frank Ramirez
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Andrew Scowcroft
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Sandra Pritzkow
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Claudio Soto
- Department of Neurology, Mitchell Center for Alzheimer’s Disease and Related Brain Disorders, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
- Amprion Inc., San Diego, CA, United States
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27
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Shoup D, Priola SA. Full-length prion protein incorporated into prion aggregates is a marker for prion strain-specific destabilization of aggregate structure following cellular uptake. J Biochem 2023; 174:165-181. [PMID: 37099550 PMCID: PMC10506170 DOI: 10.1093/jb/mvad032] [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: 01/06/2023] [Revised: 03/30/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
Accumulation of insoluble aggregates of infectious, partially protease-resistant prion protein (PrPD) generated via the misfolding of protease sensitive prion protein (PrPC) into the same infectious conformer, is a hallmark of prion diseases. Aggregated PrPD is taken up and degraded by cells, a process likely involving changes in aggregate structure that can be monitored by accessibility of the N-terminus of full-length PrPD to cellular proteases. We therefore tracked the protease sensitivity of full-length PrPD before and after cellular uptake for two murine prion strains, 22L and 87V. For both strains, PrPD aggregates were less stable following cellular uptake with increased accessibility of the N-terminus to cellular proteases across most aggregate sizes. However, a limited size range of aggregates was able to better protect the N-termini of full-length PrPD, with the N-terminus of 22L-derived PrPD more protected than that of 87V. Interestingly, changes in aggregate structure were associated with minimal changes to the protease-resistant core of PrPD. Our data show that cells destabilize the aggregate quaternary structure protecting PrPD from proteases in a strain-dependent manner, with structural changes exposing protease sensitive PrPD having little effect on the protease-resistant core, and thus conformation, of aggregated PrPD.
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Affiliation(s)
- Daniel Shoup
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy & Infectious Diseases, National Institutes of Health, 903 S. 4th Str, Hamilton, MT 59840 USA
| | - Suzette A Priola
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy & Infectious Diseases, National Institutes of Health, 903 S. 4th Str, Hamilton, MT 59840 USA
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28
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L P Hosszu L, Sangar D, Batchelor M, Risse E, Hounslow AM, Collinge J, Waltho JP, Bieschke J. Loss of residues 119 - 136, including the first β-strand of human prion protein, generates an aggregation-competent partially "open" form. J Mol Biol 2023:168158. [PMID: 37244570 DOI: 10.1016/j.jmb.2023.168158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
In prion replication, the cellular form of prion protein (PrPC) must undergo a full conformational transition to its disease-associated fibrillar form. Transmembrane forms of PrP have been implicated in this structural conversion. The cooperative unfolding of a structural core in PrPC presents a substantial energy barrier to prion formation, with membrane insertion and detachment of parts of PrP presenting a plausible route to its reduction. Here, we examined the removal of residues 119 - 136 of PrP, a region which includes the first β-strand and a substantial portion of the conserved hydrophobic region of PrP, a region which associates with the ER membrane, on the structure, stability and self-association of the folded domain of PrPC. We see an "open" native-like conformer with increased solvent exposure which fibrilises more readily than the native state. These data suggest a stepwise folding transition, which is initiated by the conformational switch to this "open" form of PrPC.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Daljit Sangar
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Mark Batchelor
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Emmanuel Risse
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jan Bieschke
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK.
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29
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Manka SW, Wenborn A, Betts J, Joiner S, Saibil HR, Collinge J, Wadsworth JDF. A structural basis for prion strain diversity. Nat Chem Biol 2023; 19:607-613. [PMID: 36646960 PMCID: PMC10154210 DOI: 10.1038/s41589-022-01229-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/18/2022] [Indexed: 01/17/2023]
Abstract
Recent cryogenic electron microscopy (cryo-EM) studies of infectious, ex vivo, prion fibrils from hamster 263K and mouse RML prion strains revealed a similar, parallel in-register intermolecular β-sheet (PIRIBS) amyloid architecture. Rungs of the fibrils are composed of individual prion protein (PrP) monomers that fold to create distinct N-terminal and C-terminal lobes. However, disparity in the hamster/mouse PrP sequence precludes understanding of how divergent prion strains emerge from an identical PrP substrate. In this study, we determined the near-atomic resolution cryo-EM structure of infectious, ex vivo mouse prion fibrils from the ME7 prion strain and compared this with the RML fibril structure. This structural comparison of two biologically distinct mouse-adapted prion strains suggests defined folding subdomains of PrP rungs and the way in which they are interrelated, providing a structural definition of intra-species prion strain-specific conformations.
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Affiliation(s)
- Szymon W Manka
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK
| | - Adam Wenborn
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK
| | - Jemma Betts
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK
| | - Susan Joiner
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK
| | - Helen R Saibil
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
| | - John Collinge
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK.
| | - Jonathan D F Wadsworth
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, London, UK.
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Sun Y, Jack K, Ercolani T, Sangar D, Hosszu L, Collinge J, Bieschke J. Direct Observation of Competing Prion Protein Fibril Populations with Distinct Structures and Kinetics. ACS NANO 2023; 17:6575-6588. [PMID: 36802500 PMCID: PMC10100569 DOI: 10.1021/acsnano.2c12009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In prion diseases, fibrillar assemblies of misfolded prion protein (PrP) self-propagate by incorporating PrP monomers. These assemblies can evolve to adapt to changing environments and hosts, but the mechanism of prion evolution is poorly understood. We show that PrP fibrils exist as a population of competing conformers, which are selectively amplified under different conditions and can "mutate" during elongation. Prion replication therefore possesses the steps necessary for molecular evolution analogous to the quasispecies concept of genetic organisms. We monitored structure and growth of single PrP fibrils by total internal reflection and transient amyloid binding super-resolution microscopy and detected at least two main fibril populations, which emerged from seemingly homogeneous PrP seeds. All PrP fibrils elongated in a preferred direction by an intermittent "stop-and-go" mechanism, but each population possessed distinct elongation mechanisms that incorporated either unfolded or partially folded monomers. Elongation of RML and ME7 prion rods likewise exhibited distinct kinetic features. The discovery of polymorphic fibril populations growing in competition, which were previously hidden in ensemble measurements, suggests that prions and other amyloid replicating by prion-like mechanisms may represent quasispecies of structural isomorphs that can evolve to adapt to new hosts and conceivably could evade therapeutic intervention.
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Affiliation(s)
- Yuanzi Sun
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Kezia Jack
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Tiziana Ercolani
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Daljit Sangar
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Laszlo Hosszu
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - John Collinge
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Jan Bieschke
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
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31
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Arshad H, Patel Z, Amano G, Li LY, Al-Azzawi ZAM, Supattapone S, Schmitt-Ulms G, Watts JC. A single protective polymorphism in the prion protein blocks cross-species prion replication in cultured cells. J Neurochem 2023; 165:230-245. [PMID: 36511154 DOI: 10.1111/jnc.15739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022]
Abstract
The bank vole (BV) prion protein (PrP) can function as a universal acceptor of prions. However, the molecular details of BVPrP's promiscuity for replicating a diverse range of prion strains remain obscure. To develop a cultured cell paradigm capable of interrogating the unique properties of BVPrP, we generated monoclonal lines of CAD5 cells lacking endogenous PrP but stably expressing either hamster (Ha), mouse (Mo), or BVPrP (M109 or I109 polymorphic variants) and then challenged them with various strains of mouse or hamster prions. Cells expressing BVPrP were susceptible to both mouse and hamster prions, whereas cells expressing MoPrP or HaPrP could only be infected with species-matched prions. Propagation of mouse and hamster prions in cells expressing BVPrP resulted in strain adaptation in several instances, as evidenced by alterations in conformational stability, glycosylation, susceptibility to anti-prion small molecules, and the inability of BVPrP-adapted mouse prion strains to infect cells expressing MoPrP. Interestingly, cells expressing BVPrP containing the G127V prion gene variant, identified in individuals resistant to kuru, were unable to become infected with prions. Moreover, the G127V polymorphic variant impeded the spontaneous aggregation of recombinant BVPrP. These results demonstrate that BVPrP can facilitate cross-species prion replication in cultured cells and that a single amino acid change can override the prion-permissive nature of BVPrP. This cellular paradigm will be useful for dissecting the molecular features of BVPrP that allow it to function as a universal prion acceptor.
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Affiliation(s)
- Hamza Arshad
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Zeel Patel
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Genki Amano
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Le Yao Li
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Zaid A M Al-Azzawi
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Surachai Supattapone
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joel C Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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32
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Šulskis D, Šneiderienė G, Žiaunys M, Smirnovas V. The seeding barrier between human and Syrian hamster prion protein amyloid fibrils is determined by β2-α2 loop sequence elements. Int J Biol Macromol 2023; 238:124038. [PMID: 36921824 DOI: 10.1016/j.ijbiomac.2023.124038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023]
Abstract
Transmissive spongiform encephalopathies (TSE) are a group of neurodegenerative diseases caused by infectious protein particles, known as prions. Prions are formed from cellular prion proteins (PrP) and can be transmitted between different mammalian species. Subsequently, the host's PrPs are then converted to prions, followed by the onset of TSE. Interspecies prion infectivity is governed by the amino acid sequence differences of PrPs and prions' inability to replicate in a host is termed a species barrier. Here, we investigated the amino acid sequence determinants of species barrier between recombinant human (rHuPrP) and hamster (rShaPrP) prion protein amyloid fibrils. We discovered that a unidirectional species barrier between rShaPrP and rHuPrP amyloid fibrils exists. This barrier stems from the difference of amino acid sequences in the conserved β2-α2 loop region. Our results revealed that individual amino acids in the β2-α2 loop region are critical for overcoming the barrier between human and hamster prion protein amyloid fibrils in vitro. Furthermore, the barrier was only possible to observe through aggregation kinetics, as the secondary structure rHuPrP fibrils was not affected by the cross-seeding. Overall, we demonstrated the mechanistic pathway behind this interspecies barrier phenomenon, which increases our understanding of prion-related disease development.
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Affiliation(s)
- Darius Šulskis
- Amyloid Research Sector, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.
| | - Greta Šneiderienė
- Amyloid Research Sector, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Mantas Žiaunys
- Amyloid Research Sector, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Amyloid Research Sector, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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33
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Groveman BR, Race B, Foliaki ST, Williams K, Hughson AG, Baune C, Zanusso G, Haigh CL. Sporadic Creutzfeldt-Jakob disease infected human cerebral organoids retain the original human brain subtype features following transmission to humanized transgenic mice. Acta Neuropathol Commun 2023; 11:28. [PMID: 36788566 PMCID: PMC9930245 DOI: 10.1186/s40478-023-01512-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/11/2023] [Indexed: 02/16/2023] Open
Abstract
Human cerebral organoids (COs) are three-dimensional self-organizing cultures of cerebral brain tissue differentiated from induced pluripotent stem cells. We have recently shown that COs are susceptible to infection with different subtypes of Creutzfeldt-Jakob disease (CJD) prions, which in humans cause different manifestations of the disease. The ability to study live human brain tissue infected with different CJD subtypes opens a wide array of possibilities from differentiating mechanisms of cell death and identifying neuronal selective vulnerabilities to testing therapeutics. However, the question remained as to whether the prions generated in the CO model truly represent those in the infecting inoculum. Mouse models expressing human prion protein are commonly used to characterize human prion disease as they reproduce many of the molecular and clinical phenotypes associated with CJD subtypes. We therefore inoculated these mice with COs that had been infected with two CJD subtypes (MV1 and MV2) to see if the original subtype characteristics (referred to as strains once transmitted into a model organism) of the infecting prions were maintained in the COs when compared with the original human brain inocula. We found that disease characteristics caused by the molecular subtype of the disease associated prion protein were similar in mice inoculated with either CO derived material or human brain material, demonstrating that the disease associated prions generated in COs shared strain characteristics with those in humans. As the first and only in vitro model of human neurodegenerative disease that can faithfully reproduce different subtypes of prion disease, these findings support the use of the CO model for investigating human prion diseases and their subtypes.
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Affiliation(s)
- Bradley R. Groveman
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
| | - Brent Race
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
| | - Simote T. Foliaki
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
| | - Katie Williams
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
| | - Andrew G. Hughson
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
| | - Chase Baune
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
| | - Gianluigi Zanusso
- grid.5611.30000 0004 1763 1124Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Cathryn L. Haigh
- grid.419681.30000 0001 2164 9667Laboratory of Persistent Viral Diseases, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT 59840 USA
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34
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So RWL, Watts JC. α-Synuclein Conformational Strains as Drivers of Phenotypic Heterogeneity in Neurodegenerative Diseases. J Mol Biol 2023:168011. [PMID: 36792008 DOI: 10.1016/j.jmb.2023.168011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/19/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
The synucleinopathies, which include Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy, are a class of human neurodegenerative disorders unified by the presence of α-synuclein aggregates in the brain. Considerable clinical and pathological heterogeneity exists within and among the individual synucleinopathies. A potential explanation for this variability is the existence of distinct conformational strains of α-synuclein aggregates that cause different disease manifestations. Like prion strains, α-synuclein strains can be delineated based on their structural architecture, with structural differences among α-synuclein aggregates leading to unique biochemical attributes and neuropathological properties in humans and animal models. Bolstered by recent high-resolution structural data from patient brain-derived material, it has now been firmly established that there are conformational differences among α-synuclein aggregates from different human synucleinopathies. Moreover, recombinant α-synuclein can be polymerized into several structurally distinct aggregates that exhibit unique pathological properties. In this review, we outline the evidence supporting the existence of α-synuclein strains and highlight how they can act as drivers of phenotypic heterogeneity in the human synucleinopathies.
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Affiliation(s)
- Raphaella W L So
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada. https://twitter.com/xsakuraphie
| | - Joel C Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada. https://twitter.com/JoelWattsLab
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35
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Sun JL, Kim S, Crowell J, Webster BK, Raisley EK, Lowe DC, Bian J, Korpenfelt SL, Benestad SL, Telling GC. Novel Prion Strain as Cause of Chronic Wasting Disease in a Moose, Finland. Emerg Infect Dis 2023; 29:323-332. [PMID: 36692340 PMCID: PMC9881765 DOI: 10.3201/eid2902.220882] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Our previous studies using gene-targeted mouse models of chronic wasting disease (CWD) demonstrated that Norway and North America cervids are infected with distinct prion strains that respond differently to naturally occurring amino acid variation at residue 226 of the prion protein. Here we performed transmissions in gene-targeted mice to investigate the properties of prions causing newly emergent CWD in moose in Finland. Although CWD prions from Finland and Norway moose had comparable responses to primary structural differences at residue 226, other distinctive criteria, including transmission kinetics, patterns of neuronal degeneration, and conformational features of prions generated in the brains of diseased mice, demonstrated that the strain properties of Finland moose CWD prions are different from those previously characterized in Norway CWD. Our findings add to a growing body of evidence for a diverse portfolio of emergent strains in Nordic countries that are etiologically distinct from the comparatively consistent strain profile of North America CWD.
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36
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Block AJ, York TC, Benedict R, Ma J, Bartz JC. Prion protein amino acid sequence influences formation of authentic synthetic PrP Sc. Sci Rep 2023; 13:441. [PMID: 36624174 PMCID: PMC9829857 DOI: 10.1038/s41598-022-26300-0] [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: 10/07/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Synthetic prions, generated de novo from minimal, non-infectious components, cause bona fide prion disease in animals. Transmission of synthetic prions to hosts expressing syngeneic PrPC results in extended, variable incubation periods and incomplete attack rates. In contrast, murine synthetic prions (MSP) generated via PMCA with minimal cofactors readily infected mice and hamsters and rapidly adapted to both species. To investigate if hamster synthetic prions (HSP) generated under the same conditions as the MSP are also highly infectious, we inoculated hamsters with HSP generated with either hamster wild type or mutant (ΔG54, ΔG54/M139I, M139I/I205M) recombinant PrP. None of the inoculated hamsters developed clinical signs of prion disease, however, brain homogenate from HSPWT- and HSPΔG54-infected hamsters contained PrPSc, indicating subclinical infection. Serial passage in hamsters resulted in clinical disease at second passage accompanied by changes in incubation period and PrPSc conformational stability between second and third passage. These data suggest the HSP, in contrast to the MSP, are not comprised of PrPSc, and instead generate authentic PrPSc via deformed templating. Differences in infectivity between the MSP and HSP suggest that, under similar generation conditions, the amino acid sequence of PrP influences generation of authentic PrPSc.
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Affiliation(s)
- Alyssa J. Block
- grid.254748.80000 0004 1936 8876Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE 68178 USA
| | - Taylor C. York
- grid.254748.80000 0004 1936 8876Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE 68178 USA
| | - Romilly Benedict
- grid.17088.360000 0001 2150 1785Department of Plant, Soil, and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI USA
| | - Jiyan Ma
- grid.251017.00000 0004 0406 2057Van Andel Institute, Center for Neurodegenerative Science, Grand Rapids, MI USA
| | - Jason C. Bartz
- grid.254748.80000 0004 1936 8876Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE 68178 USA
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37
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Exploring different computational approaches for effective diagnosis of breast cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:141-150. [PMID: 36509230 DOI: 10.1016/j.pbiomolbio.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Breast cancer has been identified as one among the top causes of female death worldwide. According to recent research, earlier detection plays an important role toward fortunate medicaments and thus, decreasing the mortality rate due to breast cancer among females. This review provides a fleeting summary involving traditional diagnostic procedures from the past and today, and also modern computational tools that have greatly aided in the identification of breast cancer. Computational techniques involving different algorithms such as Support vector machines, deep learning techniques and robotics are popular among the academicians for detection of breast cancer. They discovered that Convolutional neural network was a common option for categorization among such approaches. Deep learning techniques are evaluated using performance indicators such as accuracy, sensitivity, specificity, or measure. Furthermore, molecular docking, homology modeling and Molecular dynamics Simulation gives a road map for future discussions about developing improved early detection approaches that holds greater potential in increasing the survival rate of cancer patients. The different computational techniques can be a new dominion among researchers and combating the challenges associated with breast cancer.
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Mollica L, Giachin G. Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study. J Chem Inf Model 2022; 63:531-545. [PMID: 36580661 PMCID: PMC9875307 DOI: 10.1021/acs.jcim.2c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Immunotherapy using antibodies to target the aggregation of flexible proteins holds promise for therapeutic interventions in neurodegenerative diseases caused by protein misfolding. Prions or PrPSc, the causal agents of transmissible spongiform encephalopathies (TSE), represent a model target for immunotherapies as TSE are prototypical protein misfolding diseases. The X-ray crystal structure of the wild-type (WT) human prion protein (HuPrP) bound to a camelid antibody fragment, denoted as Nanobody 484 (Nb484), has been previously solved. Nb484 was found to inhibit prion aggregation in vitro through a unique mechanism of structural stabilization of two disordered epitopes, that is, the palindromic motif (residues 113-120) and the β2-α2 loop region (residues 164-185). The study of the structural basis for antibody recognition of flexible proteins requires appropriate sampling techniques for the identification of conformational states occurring in disordered epitopes. To elucidate the Nb484-HuPrP recognition mechanisms, here we applied molecular dynamics (MD) simulations complemented with available NMR and X-ray crystallography data collected on the WT HuPrP to describe the conformational spaces occurring on HuPrP prior to Nb484 binding. We observe the experimentally determined binding competent conformations within the ensembles of pre-existing conformational states in solution before binding. We also described the Nb484 recognition mechanisms in two HuPrP carrying a polymorphism (E219K) and a TSE-causing mutation (V210I). Our hybrid approaches allow the identification of dynamic conformational landscapes existing on HuPrP and highly characterized by molecular disorder to identify physiologically relevant and druggable transitions.
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Affiliation(s)
- Luca Mollica
- Department
of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, 20090 Milan, Italy,
| | - Gabriele Giachin
- Department
of Chemical Sciences (DiSC), University
of Padua, 35131 Padova, Italy,
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39
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Pal S, Udgaonkar JB. Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form. J Mol Biol 2022; 434:167854. [PMID: 36228749 DOI: 10.1016/j.jmb.2022.167854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen-deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research, Pune, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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40
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Cortez LM, Morrison AJ, Garen CR, Patterson S, Uyesugi T, Petrosyan R, Sekar RV, Harms MJ, Woodside MT, Sim VL. Probing the origin of prion protein misfolding via reconstruction of ancestral proteins. Protein Sci 2022; 31:e4477. [PMID: 36254680 PMCID: PMC9667828 DOI: 10.1002/pro.4477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 12/13/2022]
Abstract
Prion diseases are fatal neurodegenerative diseases caused by pathogenic misfolding of the prion protein, PrP. They are transmissible between hosts, and sometimes between different species, as with transmission of bovine spongiform encephalopathy to humans. Although PrP is found in a wide range of vertebrates, prion diseases are seen only in certain mammals, suggesting that infectious misfolding was a recent evolutionary development. To explore when PrP acquired the ability to misfold infectiously, we reconstructed the sequences of ancestral versions of PrP from the last common primate, primate-rodent, artiodactyl, placental, bird, and amniote. Recombinant ancestral PrPs were then tested for their ability to form β-sheet aggregates, either spontaneously or when seeded with infectious prion strains from human, cervid, or rodent species. The ability to aggregate developed after the oldest ancestor (last common amniote), and aggregation capabilities diverged along evolutionary pathways consistent with modern-day susceptibilities. Ancestral bird PrP could not be seeded with modern-day prions, just as modern-day birds are resistant to prion disease. Computational modeling of structures suggested that differences in helix 2 could account for the resistance of ancestral bird PrP to seeding. Interestingly, ancestral primate PrP could be converted by all prion seeds, including both human and cervid prions, raising the possibility that species descended from an ancestral primate have retained the susceptibility to conversion by cervid prions. More generally, the results suggest that susceptibility to prion disease emerged prior to ~100 million years ago, with placental mammals possibly being generally susceptible to disease.
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Affiliation(s)
- Leonardo M. Cortez
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Division of Neurology, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada
- Neuroscience and Mental Health InstituteUniversity of AlbertaEdmontonAlbertaCanada
| | - Anneliese J. Morrison
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Craig R. Garen
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
| | - Sawyer Patterson
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
| | - Toshi Uyesugi
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
| | - Rafayel Petrosyan
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Zaven & Sonia Akian College of Science and EngineeringAmerican University of ArmeniaYerevanArmenia
| | | | - Michael J. Harms
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Michael T. Woodside
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Valerie L. Sim
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Division of Neurology, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada
- Neuroscience and Mental Health InstituteUniversity of AlbertaEdmontonAlbertaCanada
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41
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Igel A, Fornara B, Rezaei H, Béringue V. Prion assemblies: structural heterogeneity, mechanisms of formation, and role in species barrier. Cell Tissue Res 2022; 392:149-166. [PMID: 36399162 PMCID: PMC10113350 DOI: 10.1007/s00441-022-03700-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
AbstractPrions are proteinaceous pathogens responsible for a wide range of neurodegenerative diseases in animal and human. Prions are formed from misfolded, ß-sheet rich, and aggregated conformers (PrPSc) of the host-encoded prion protein (PrPC). Prion replication stems from the capacity of PrPSc to self-replicate by templating PrPC conversion and polymerization. The question then arises about the molecular mechanisms of prion replication, host invasion, and capacity to contaminate other species. Studying these mechanisms has gained in recent years further complexity with evidence that PrPSc is a pleiomorphic protein. There is indeed compelling evidence for PrPSc structural heterogeneity at different scales: (i) within prion susceptible host populations with the existence of different strains with specific biological features due to different PrPSc conformers, (ii) within a single infected host with the co-propagation of different strains, and (iii) within a single strain with evidence for co-propagation of PrPSc assemblies differing in their secondary to quaternary structure. This review summarizes current knowledge of prion assembly heterogeneity, potential mechanisms of formation during the replication process, and importance when crossing the species barrier.
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Essential Components of Synthetic Infectious Prion Formation De Novo. Biomolecules 2022; 12:biom12111694. [DOI: 10.3390/biom12111694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Prion diseases are a class of neurodegenerative diseases that are uniquely infectious. Whilst their general replication mechanism is well understood, the components required for the formation and propagation of highly infectious prions are poorly characterized. The protein-only hypothesis posits that the prion protein (PrP) is the only component of the prion; however, additional co-factors are required for its assembly into infectious prions. These can be provided by brain homogenate, but synthetic lipids and non-coding RNA have also been used in vitro. Here, we review a range of experimental approaches, which generate PrP amyloid assemblies de novo. These synthetic PrP assemblies share some, but not necessarily all, properties of genuine infectious prions. We will discuss the different experimental approaches, how a prion is defined, the non-protein requirements of a prion, and provide an overview of the current state of prion amplification and generation in vitro.
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Lövestam S, Scheres SHW. High-throughput cryo-EM structure determination of amyloids. Faraday Discuss 2022; 240:243-260. [PMID: 35913272 PMCID: PMC9642048 DOI: 10.1039/d2fd00034b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The formation of amyloid filaments is characteristic of various degenerative diseases. Recent breakthroughs in electron cryo-microscopy (cryo-EM) have led to atomic structure determination of multiple amyloid filaments, both of filaments assembled in vitro from recombinant proteins, and of filaments extracted from diseased tissue. These observations revealed that a single protein may adopt multiple different amyloid folds, and that in vitro assembly does not necessarily lead to the same filaments as those observed in disease. In order to develop relevant model systems for disease, and ultimately to better understand the molecular mechanisms of disease, it will be important to determine which factors determine the formation of distinct amyloid folds. High-throughput cryo-EM, in which structure determination becomes a tool rather than a project in itself, will facilitate the screening of large numbers of in vitro assembly conditions. To this end, we describe a new filament picking algorithm based on the Topaz approach, and we outline image processing strategies in Relion that enable atomic structure determination of amyloids within days.
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Affiliation(s)
- Sofia Lövestam
- MRC Laboratory of Molecular BiologyFrancis Crick AvenueCambridge Biomedical CampusCB2 0QHCambridgeUK
| | - Sjors H. W. Scheres
- MRC Laboratory of Molecular BiologyFrancis Crick AvenueCambridge Biomedical CampusCB2 0QHCambridgeUK
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Hoyt F, Alam P, Artikis E, Schwartz CL, Hughson AG, Race B, Baune C, Raymond GJ, Baron GS, Kraus A, Caughey B. Cryo-EM of prion strains from the same genotype of host identifies conformational determinants. PLoS Pathog 2022; 18:e1010947. [PMID: 36342968 PMCID: PMC9671466 DOI: 10.1371/journal.ppat.1010947] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/17/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 Å resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors [anchorless (a) 22L]. Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register β-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype. Prions are protein-based pathogens that can spread within and between hosts without carrying a pathogen-specific nucleic acid genome. Given this protein-based propagation mechanism, a long-standing mystery in the prion disease field has been the molecular basis of distinct, faithfully propagating strains in a single type of mammalian host. Here we provide a direct, high-resolution cryo-EM-based comparison of the structures of two highly infectious prion strains isolated from the brains of mice of a single genotype. We show in detail how these two prion strains are protein filaments of mouse PrP molecules that display distinct conformational templates for growth on their tips. Our results identify purely conformational, rather than sequence-based, underpinnings of infectious and deadly prion strains.
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Affiliation(s)
- Forrest Hoyt
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Parvez Alam
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Efrosini Artikis
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Cindi L. Schwartz
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Andrew G. Hughson
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brent Race
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Chase Baune
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Gregory J. Raymond
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Gerald S. Baron
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Allison Kraus
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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The Mutability of Yeast Prions. Viruses 2022; 14:v14112337. [PMID: 36366434 PMCID: PMC9696419 DOI: 10.3390/v14112337] [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: 08/01/2022] [Revised: 10/10/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
Prions replicate by a self-templating mechanism. Infidelity in the process can lead to the emergence of new infectious structures, referred to as variants or strains. The question of whether prions are prone to mis-templating is not completely answered. Our previous experiments with 23 variants of the yeast [PSI+] prion do not support broad mutability. However, it became clear recently that the heat shock protein Hsp104 can restrict [PSI+] strain variation. This raises the possibility that many transmutable variants of the prion may have been mistaken as faithful-propagating simply because the mutant structure was too sturdy or too frail to take root in the wild-type cell. Here, I alter the strength of Hsp104 in yeast, overexpressing wild-type Hsp104 or expressing the hypo-active Hsp104T160M mutant, and check if the new environments enable the variants to mutate. Two variants hitherto thought of as faithful-propagating are discovered to generate different structures, which are stabilized with the hypo-active chaperone. In contrast, most transmutable variants discovered in cells overexpressing Hsp104 have been correctly identified as such previously in wild-type cells without the overexpression. The majority of transmutable variants only mis-template the structure of VH, VK, or VL, which are the most frequently observed variants and do not spontaneously mutate. There are four additional variants that never give rise to different structures in all cell conditions tested. Therefore, quite a few [PSI+] variants are faithful-propagating, and even the transmutable ones do not freely evolve but can only change to limited structural types.
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Raspadori A, Vignali V, Murello A, Giachin G, Samorì B, Tanaka M, Bustamante C, Zuccheri G, Legname G. Evidence of Orientation-Dependent Early States of Prion Protein Misfolded Structures from Single Molecule Force Spectroscopy. BIOLOGY 2022; 11:1358. [PMID: 36138837 PMCID: PMC9495685 DOI: 10.3390/biology11091358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Prion diseases are neurodegenerative disorders characterized by the presence of oligomers and amyloid fibrils. These are the result of protein aggregation processes of the cellular prion protein (PrPC) into amyloidal forms denoted as prions or PrPSc. We employed atomic force microscopy (AFM) for single molecule pulling (single molecule force spectroscopy, SMFS) experiments on the recombinant truncated murine prion protein (PrP) domain to characterize its conformations and potential initial oligomerization processes. Our AFM-SMFS results point to a complex scenario of structural heterogeneity of PrP at the monomeric and dimer level, like other amyloid proteins involved in similar pathologies. By applying this technique, we revealed that the PrP C-terminal domain unfolds in a two-state process. We used two dimeric constructs with different PrP reciprocal orientations: one construct with two sequential PrP in the N- to C-terminal orientation (N-C dimer) and a second one in the C- to C-terminal orientation (C-C dimer). The analysis revealed that the different behavior in terms of unfolding force, whereby the dimer placed C-C dimer unfolds at a higher force compared to the N-C orientation. We propose that the C-C dimer orientation may represent a building block of amyloid fibril formation.
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Affiliation(s)
- Andrea Raspadori
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Valentina Vignali
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy
| | - Anna Murello
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences (DiSC), University of Padua, 35131 Padova, Italy
| | - Bruno Samorì
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy
| | - Motomasa Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Brain Science Institute, Wako 351-0198, Saitama, Japan
| | - Carlos Bustamante
- QB3 Institute, University of California, 642 Stanley Hall #3220, Berkeley, CA 94720-3220, USA
| | - Giampaolo Zuccheri
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy
- S3 Center of the Institute of Nanoscience of the Italian National Research Council (CNR), 41125 Modena, Italy
- Interdepartmental Center for Industrial Research on Health Science and Technologies, University of Bologna, 40126 Bologna, Italy
| | - Giuseppe Legname
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
- ELETTRA Sincrotrone Trieste S.C.p.A, Basovizza, 34139 Trieste, Italy
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Ma J, Zhang J, Yan R. Recombinant Mammalian Prions: The “Correctly” Misfolded Prion Protein Conformers. Viruses 2022; 14:v14091940. [PMID: 36146746 PMCID: PMC9504972 DOI: 10.3390/v14091940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
Generating a prion with exogenously produced recombinant prion protein is widely accepted as the ultimate proof of the prion hypothesis. Over the years, a plethora of misfolded recPrP conformers have been generated, but despite their seeding capability, many of them have failed to elicit a fatal neurodegenerative disorder in wild-type animals like a naturally occurring prion. The application of the protein misfolding cyclic amplification technique and the inclusion of non-protein cofactors in the reaction mixture have led to the generation of authentic recombinant prions that fully recapitulate the characteristics of native prions. Together, these studies reveal that recPrP can stably exist in a variety of misfolded conformations and when inoculated into wild-type animals, misfolded recPrP conformers cause a wide range of outcomes, from being completely innocuous to lethal. Since all these recPrP conformers possess seeding capabilities, these results clearly suggest that seeding activity alone is not equivalent to prion activity. Instead, authentic prions are those PrP conformers that are not only heritable (the ability to seed the conversion of normal PrP) but also pathogenic (the ability to cause fatal neurodegeneration). The knowledge gained from the studies of the recombinant prion is important for us to understand the pathogenesis of prion disease and the roles of misfolded proteins in other neurodegenerative disorders.
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Manka SW, Wenborn A, Collinge J, Wadsworth JDF. Prion strains viewed through the lens of cryo-EM. Cell Tissue Res 2022; 392:167-178. [PMID: 36028585 PMCID: PMC10113314 DOI: 10.1007/s00441-022-03676-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Mammalian prions are lethal transmissible pathogens that cause fatal neurodegenerative diseases in humans and animals. They consist of fibrils of misfolded, host-encoded prion protein (PrP) which propagate through templated protein polymerisation. Prion strains produce distinct clinicopathological phenotypes in the same host and appear to be encoded by distinct misfolded PrP conformations and assembly states. Despite fundamental advances in our understanding of prion biology, key knowledge gaps remain. These include precise delineation of prion replication mechanisms, detailed explanation of the molecular basis of prion strains and inter-species transmission barriers, and the structural definition of neurotoxic PrP species. Central to addressing these questions is the determination of prion structure. While high-resolution definition of ex vivo prion fibrils once seemed unlikely, recent advances in cryo-electron microscopy (cryo-EM) and computational methods for 3D reconstruction of amyloids have now made this possible. Recently, near-atomic resolution structures of highly infectious, ex vivo prion fibrils from hamster 263K and mouse RML prion strains were reported. The fibrils have a comparable parallel in-register intermolecular β-sheet (PIRIBS) architecture that now provides a structural foundation for understanding prion strain diversity in mammals. Here, we review these new findings and discuss directions for future research.
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Affiliation(s)
- Szymon W Manka
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, 33 Cleveland Street, London, W1W 7FF, UK
| | - Adam Wenborn
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, 33 Cleveland Street, London, W1W 7FF, UK
| | - John Collinge
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, 33 Cleveland Street, London, W1W 7FF, UK.
| | - Jonathan D F Wadsworth
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, 33 Cleveland Street, London, W1W 7FF, UK.
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Requena JR. Unlatching a window into the molecular landscape of prion toxicity. Nat Struct Mol Biol 2022; 29:733-735. [PMID: 35948769 DOI: 10.1038/s41594-022-00817-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Santiago de Compostela, Spain.
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50
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The shape of things to come: structural insights into how prion proteins encipher heritable information. Nat Commun 2022; 13:4003. [PMID: 35831278 PMCID: PMC9279361 DOI: 10.1038/s41467-022-31460-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/16/2022] [Indexed: 01/21/2023] Open
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