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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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2
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Jung R, Lechler MC, Fernandez-Villegas A, Chung CW, Jones HC, Choi YH, Thompson MA, Rödelsperger C, Röseler W, Kaminski Schierle GS, Sommer RJ, David DC. A safety mechanism enables tissue-specific resistance to protein aggregation during aging in C. elegans. PLoS Biol 2023; 21:e3002284. [PMID: 37708127 PMCID: PMC10501630 DOI: 10.1371/journal.pbio.3002284] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/01/2023] [Indexed: 09/16/2023] Open
Abstract
During aging, proteostasis capacity declines and distinct proteins become unstable and can accumulate as protein aggregates inside and outside of cells. Both in disease and during aging, proteins selectively aggregate in certain tissues and not others. Yet, tissue-specific regulation of cytoplasmic protein aggregation remains poorly understood. Surprisingly, we found that the inhibition of 3 core protein quality control systems, namely chaperones, the proteasome, and macroautophagy, leads to lower levels of age-dependent protein aggregation in Caenorhabditis elegans pharyngeal muscles, but higher levels in body-wall muscles. We describe a novel safety mechanism that selectively targets newly synthesized proteins to suppress their aggregation and associated proteotoxicity. The safety mechanism relies on macroautophagy-independent lysosomal degradation and involves several previously uncharacterized components of the intracellular pathogen response (IPR). We propose that this protective mechanism engages an anti-aggregation machinery targeting aggregating proteins for lysosomal degradation.
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Affiliation(s)
- Raimund Jung
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Marie C. Lechler
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, Tübingen, Germany
| | - Ana Fernandez-Villegas
- Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Chyi Wei Chung
- Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Harry C. Jones
- The Babraham Institute, Signalling Program, Cambridge, United Kingdom
| | - Yoon Hee Choi
- The Babraham Institute, Signalling Program, Cambridge, United Kingdom
| | | | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Tübingen, Germany
| | - Waltraud Röseler
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Tübingen, Germany
| | | | - Ralf J. Sommer
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Tübingen, Germany
| | - Della C. David
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- The Babraham Institute, Signalling Program, Cambridge, United Kingdom
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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3
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Tseng YL, Lu PC, Lee CC, He RY, Huang YA, Tseng YC, Cheng TJR, Huang JJT, Fang JM. Degradation of neurodegenerative disease-associated TDP-43 aggregates and oligomers via a proteolysis-targeting chimera. J Biomed Sci 2023; 30:27. [PMID: 37101169 PMCID: PMC10131537 DOI: 10.1186/s12929-023-00921-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) associated with TAR DNA-binding protein 43 (TDP-43) aggregation has been considered as a lethal and progressive motor neuron disease. Recent studies have shown that both C-terminal TDP-43 (C-TDP-43) aggregates and oligomers were neurotoxic and pathologic agents in ALS and frontotemporal lobar degeneration (FTLD). However, misfolding protein has long been considered as an undruggable target by applying conventional inhibitors, agonists, or antagonists. To provide this unmet medical need, we aim to degrade these misfolding proteins by designing a series of proteolysis targeting chimeras (PROTACs) against C-TDP-43. METHODS By applying filter trap assay, western blotting, and microscopy imaging, the degradation efficiency of C-TDP-43 aggregates was studied in Neuro-2a cells overexpressing eGFP-C-TDP-43 or mCherry-C-TDP-43. The cell viability was characterized by alarmarBlue assay. The beneficial and disaggregating effects of TDP-43 PROTAC were examined with the YFP-C-TDP-43 transgenic C. elegans by motility assay and confocal microscopy. The impact of TDP-43 PROTAC on C-TDP-43 oligomeric intermediates was monitored by fluorescence lifetime imaging microscopy and size exclusion chromatography in the Neuro-2a cells co-expressing eGFP-C-TDP-43 and mCherry-C-TDP-43. RESULTS Four PROTACs with different linker lengths were synthesized and characterized. Among these chimeras, PROTAC 2 decreased C-TDP-43 aggregates and relieved C-TDP-43-induced cytotoxicity in Neuro-2a cells without affecting endogenous TDP-43. We showed that PROTAC 2 bound to C-TDP-43 aggregates and E3 ligase to initiate ubiquitination and proteolytic degradation. By applying advanced microscopy, it was further shown that PROTAC 2 decreased the compactness and population of C-TDP-43 oligomers. In addition to cellular model, PROTAC 2 also improved the motility of transgenic C. elegans by reducing the C-TDP-43 aggregates in the nervous system. CONCLUSIONS Our study demonstrated the dual-targeting capacity of the newly-designed PROTAC 2 against both C-TDP-43 aggregates and oligomers to reduce their neurotoxicity, which shed light on the potential drug development for ALS as well as other neurodegenerative diseases.
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Affiliation(s)
- Yu-Ling Tseng
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Po-Chao Lu
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department and Graduate Institute of Pharmacology, National Taiwan University, Taipei, 100, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ruei-Yu He
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yung-An Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yin-Chen Tseng
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Department of Applied Chemistry, National Chiayi University, Chiayi City, 600, Taiwan.
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, 115, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
- The Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
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4
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Estaun-Panzano J, Arotcarena ML, Bezard E. Monitoring α-synuclein aggregation. Neurobiol Dis 2023; 176:105966. [PMID: 36527982 PMCID: PMC9875312 DOI: 10.1016/j.nbd.2022.105966] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Synucleinopathies, including Parkinson's disease (PD), dementia with Lewy Bodies (DLB), and multiple system atrophy (MSA), are characterized by the misfolding and subsequent aggregation of alpha-synuclein (α-syn) that accumulates in cytoplasmic inclusions bodies in the cells of affected brain regions. Since the seminal report of likely-aggregated α-syn presence within the Lewy bodies by Spillantini et al. in 1997, the keyword "synuclein aggregation" has appeared in over 6000 papers (Source: PubMed October 2022). Studying, observing, describing, and quantifying α-syn aggregation is therefore of paramount importance, whether it happens in tubo, in vitro, in post-mortem samples, or in vivo. The past few years have witnessed tremendous progress in understanding aggregation mechanisms and identifying various polymorphs. In this context of growing complexity, it is of utmost importance to understand what tools we possess, what exact information they provide, and in what context they may be applied. Nonetheless, it is also crucial to rationalize the relevance of the information and the limitations of these methods for gauging the final result. In this review, we present the main techniques that have shaped the current views about α-syn structure and dynamics, with particular emphasis on the recent breakthroughs that may change our understanding of synucleinopathies.
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Affiliation(s)
| | | | - Erwan Bezard
- Univ. Bordeaux, CNRS, IMN, UMR 5293, F-33000 Bordeaux, France; Motac Neuroscience Ltd, Manchester, United Kingdom.
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5
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Dissecting aggregation and seeding dynamics of α-Syn polymorphs using the phasor approach to FLIM. Commun Biol 2022; 5:1345. [PMID: 36477485 PMCID: PMC9729209 DOI: 10.1038/s42003-022-04289-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Synucleinopathies are a heterogenous group of neurodegenerative diseases characterized by the progressive accumulation of pathological α-synuclein (α-Syn). The importance of structural polymorphism of α-Syn assemblies for distinct synucleinopathies and their progression is increasingly recognized. However, the underlying mechanisms are poorly understood. Here we use fluorescence lifetime imaging microscopy (FLIM) to investigate seeded aggregation of α-Syn in a biosensor cell line. We show that conformationally distinct α-Syn polymorphs exhibit characteristic fluorescence lifetimes. FLIM further revealed that α-Syn polymorphs were differentially processed by cellular clearance pathways, yielding fibrillar species with increased seeding capacity. Thus, FLIM is not only a powerful tool to distinguish different amyloid structures, but also to monitor the dynamic process of amyloid remodeling by the cellular environment. Our data suggest that the accumulation of highly seeding competent degradation products for particular polymorphs may account for accelerated disease progression in some patients.
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6
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Molecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau. Nat Commun 2022; 13:4586. [PMID: 35933508 PMCID: PMC9357037 DOI: 10.1038/s41467-022-32350-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
Amyloid aggregation of α-synuclein (αS) is the hallmark of Parkinson’s disease and other synucleinopathies. Recently, Tau protein, generally associated with Alzheimer’s disease, has been linked to αS pathology and observed to co-localize in αS-rich disease inclusions, although the molecular mechanisms for the co-aggregation of both proteins remain elusive. We report here that αS phase-separates into liquid condensates by electrostatic complex coacervation with positively charged polypeptides such as Tau. Condensates undergo either fast gelation or coalescence followed by slow amyloid aggregation depending on the affinity of αS for the poly-cation and the rate of valence exhaustion of the condensate network. By combining a set of advanced biophysical techniques, we have been able to characterize αS/Tau liquid-liquid phase separation and identified key factors that lead to the formation of hetero-aggregates containing both proteins in the interior of the liquid protein condensates. Here, the authors report that α-synuclein phase-separates into liquid condensates with positively charged polypeptides such as Tau. The condensates undergo different maturation processes, including the formation of α-synuclein/Tau amyloid hetero-aggregates inside the condensates.
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7
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Gorensek-Benitez AH, Kirk B, Myers JK. Protein Fibrillation under Crowded Conditions. Biomolecules 2022; 12:biom12070950. [PMID: 35883507 PMCID: PMC9312947 DOI: 10.3390/biom12070950] [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: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 12/04/2022] Open
Abstract
Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.
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Affiliation(s)
- Annelise H. Gorensek-Benitez
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, CO 80903, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
| | - Bryan Kirk
- Department of Biology, Davidson College, Davidson, NC 28035, USA;
| | - Jeffrey K. Myers
- Department of Chemistry, Davidson College, Davidson, NC 28035, USA
- Correspondence: (A.H.G.-B.); (J.K.M.)
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8
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Claesson K, Chew YL, Ecroyd H. Exploiting flow cytometry for the unbiased quantification of protein inclusions in Caenorhabditis elegans. J Neurochem 2022; 161:281-292. [PMID: 35170035 PMCID: PMC9541147 DOI: 10.1111/jnc.15591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/28/2022] [Accepted: 02/12/2022] [Indexed: 11/29/2022]
Abstract
The aggregation of proteins into inclusions or plaques is a prominent hallmark of a diverse range of pathologies including neurodegenerative diseases. The quantification of such inclusions in Caenorhabditis elegans models of aggregation is usually achieved by fluorescence microscopy or other techniques involving biochemical fractionation of worm lysates. Here, we describe a simple and rapid flow cytometry-based approach that allows fluorescently tagged inclusions to be enumerated in whole worm lysate in a quantitative and unbiased fashion. We demonstrate that this technique is applicable to multiple C. elegans models of aggregation and importantly, can be used to monitor the dynamics of inclusion formation in response to heat shock and during ageing. This includes the characterisation of physicochemical properties of inclusions, such as their apparent size, which may reveal how aggregate formation is distinct in different tissues or at different stages of pathology or ageing. This new method can be used as a powerful technique for the medium- to high-throughput quantification of inclusions in future studies of genetic or chemical modulators of aggregation in C. elegans.
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Affiliation(s)
- Kristian Claesson
- Molecular Horizons and School of Chemistry and Molecular BioscienceUniversity of WollongongWollongongNSWAustralia
- Illawarra Health & Medical Research InstituteWollongongNew South WalesAustralia
| | - Yee Lian Chew
- Molecular Horizons and School of Chemistry and Molecular BioscienceUniversity of WollongongWollongongNSWAustralia
- Illawarra Health & Medical Research InstituteWollongongNew South WalesAustralia
- Flinders Health and Medical Research Institute, College of Medicine and Public HealthFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular BioscienceUniversity of WollongongWollongongNSWAustralia
- Illawarra Health & Medical Research InstituteWollongongNew South WalesAustralia
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9
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Wan Q, Mouton SN, Veenhoff LM, Boersma AJ. A FRET-based method for monitoring structural transitions in protein self-organization. CELL REPORTS METHODS 2022; 2:100184. [PMID: 35475219 PMCID: PMC8960284 DOI: 10.1016/j.crmeth.2022.100184] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
Abstract
Proteins assemble into a variety of dynamic and functional structures. Their structural transitions are often challenging to distinguish inside cells, particularly with a high spatiotemporal resolution. Here, we present a fluorescence resonance energy transfer (FRET)-based method for continuous and high-throughput monitoring of protein self-assemblies to reveal well-resolved transient intermediate states. Intermolecular FRET with both the donor and acceptor proteins at the same target protein provides high sensitivity while retaining the advantage of straightforward ratiometric imaging. We apply this method to monitor self-assembly of three proteins. We show that the mutant Huntingtin exon1 (mHttex1) first forms less-ordered assemblies, which develop into fibril-like aggregates, and demonstrate that the chaperone protein DNAJB6b increases the critical saturation concentration of mHttex1. We also monitor the structural changes in fused in sarcoma (FUS) condensates. This method adds to the toolbox for protein self-assembly structure and kinetics determination, and implementation with native or non-native proteins can inform studies involving protein condensation or aggregation.
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Affiliation(s)
- Qi Wan
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Sara N. Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnold J. Boersma
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
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10
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Trusova V, Tarabara U, Zhytniakivska O, Vus K, Gorbenko G. Fӧrster resonance energy transfer analysis of amyloid state of proteins. BBA ADVANCES 2022; 2:100059. [PMID: 37082586 PMCID: PMC10074846 DOI: 10.1016/j.bbadva.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
The Förster resonance energy transfer (FRET) is a well-established and versatile spectroscopic technique extensively used for exploring a variety of biomolecular interactions and processes. The present review is intended to cover the main results of our FRET studies focused on amyloid fibrils, a particular type of disease-associated protein aggregates. Based on the examples of several fibril-forming proteins including insulin, lysozyme and amyloidogenic variants of N-terminal fragment of apolipoprotein A-I, it was demonstrated that: (i) the two- and three-step FRET with the classical amyloid marker Thioflavin T as an input donor has a high amyloid-sensing potential and can be used to refine the amyloid detection assays; (ii) the intermolecular time-resolved and single-molecule pulse interleaved excitation FRET can give quantitative information on the nucleation of amyloid fibrils; (iii) FRET between the membrane fluorescent probes and protein-associated intrinsic or extrinsic fluorophores is suitable for monitoring the membrane binding of fibrillar proteins, exploring their location relative to lipid-water interface and restructuring on a lipid matrix; (iv) the FRET-based distance estimation between fibril-bound donor and acceptor fluorophores can serve as one of the verification criteria upon structural modeling of amyloid fibrils.
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11
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Fontana NA, Rosse AD, Watts A, Coelho PSR, Costa-Filho AJ. In vivo observation of amyloid-like fibrils produced under stress. Int J Biol Macromol 2021; 199:42-50. [PMID: 34942208 DOI: 10.1016/j.ijbiomac.2021.12.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
The participation of amyloids in neurodegenerative diseases and functional processes has triggered the quest for methods allowing their direct detection in vivo. Despite the plethora of data, those methods are still lacking. The autofluorescence from the extended β-sheets of amyloids is here used to follow fibrillation of S. cerevisiae Golgi Reassembly and Stacking Protein (Grh1). Grh1 has been implicated in starvation-triggered unconventional protein secretion (UPS), and here its participation also in heat shock response (HSR) is suggested. Fluorescence Lifetime Imaging (FLIM) is used to detect fibril autofluorescence in cells (E. coli and yeast) under stress (starvation and higher temperature). The formation of Grh1 large complexes under stress is further supported by size exclusion chromatography and ultracentrifugation. The data show for the first time in vivo detection of amyloids without the use of extrinsic probes as well as bring new perspectives on the participation of Grh1 in UPS and HSR.
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Affiliation(s)
- Natália A Fontana
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ariane D Rosse
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Paulo S R Coelho
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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12
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Pigazzini ML, Lawrenz M, Margineanu A, Kaminski Schierle GS, Kirstein J. An Expanded Polyproline Domain Maintains Mutant Huntingtin Soluble in vivo and During Aging. Front Mol Neurosci 2021; 14:721749. [PMID: 34720872 PMCID: PMC8554126 DOI: 10.3389/fnmol.2021.721749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/30/2021] [Indexed: 02/02/2023] Open
Abstract
Huntington's disease is a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG repeat, encoding for the amino acid glutamine (Q), present in the first exon of the protein huntingtin. Over the threshold of Q39 HTT exon 1 (HTTEx1) tends to misfold and aggregate into large intracellular structures, but whether these end-stage aggregates or their on-pathway intermediates are responsible for cytotoxicity is still debated. HTTEx1 can be separated into three domains: an N-terminal 17 amino acid region, the polyglutamine (polyQ) expansion and a C-terminal proline rich domain (PRD). Alongside the expanded polyQ, these flanking domains influence the aggregation propensity of HTTEx1: with the N17 initiating and promoting aggregation, and the PRD modulating it. In this study we focus on the first 11 amino acids of the PRD, a stretch of pure prolines, which are an evolutionary recent addition to the expanding polyQ region. We hypothesize that this proline region is expanding alongside the polyQ to counteract its ability to misfold and cause toxicity, and that expanding this proline region would be overall beneficial. We generated HTTEx1 mutants lacking both flanking domains singularly, missing the first 11 prolines of the PRD, or with this stretch of prolines expanded. We then followed their aggregation landscape in vitro with a battery of biochemical assays, and in vivo in novel models of C. elegans expressing the HTTEx1 mutants pan-neuronally. Employing fluorescence lifetime imaging we could observe the aggregation propensity of all HTTEx1 mutants during aging and correlate this with toxicity via various phenotypic assays. We found that the presence of an expanded proline stretch is beneficial in maintaining HTTEx1 soluble over time, regardless of polyQ length. However, the expanded prolines were only advantageous in promoting the survival and fitness of an organism carrying a pathogenic stretch of Q48 but were extremely deleterious to the nematode expressing a physiological stretch of Q23. Our results reveal the unique importance of the prolines which have and still are evolving alongside expanding glutamines to promote the function of HTTEx1 and avoid pathology.
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Affiliation(s)
- Maria Lucia Pigazzini
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mandy Lawrenz
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
| | - Anca Margineanu
- Advanced Light Microscopy, Max-Delbrück Centrum for Molecular Medicine (MDC), Berlin, Germany
| | - Gabriele S. Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Janine Kirstein
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- Department of Cell Biology, University of Bremen, Bremen, Germany
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13
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Perni M, van der Goot A, Limbocker R, van Ham TJ, Aprile FA, Xu CK, Flagmeier P, Thijssen K, Sormanni P, Fusco G, Chen SW, Challa PK, Kirkegaard JB, Laine RF, Ma KY, Müller MBD, Sinnige T, Kumita JR, Cohen SIA, Seinstra R, Kaminski Schierle GS, Kaminski CF, Barbut D, De Simone A, Knowles TPJ, Zasloff M, Nollen EAA, Vendruscolo M, Dobson CM. Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease. Front Cell Dev Biol 2021; 9:552549. [PMID: 33829010 PMCID: PMC8019828 DOI: 10.3389/fcell.2021.552549] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/16/2021] [Indexed: 02/02/2023] Open
Abstract
The aggregation of α-synuclein is a hallmark of Parkinson's disease (PD) and a variety of related neurological disorders. A number of mutations in this protein, including A30P and A53T, are associated with familial forms of the disease. Patients carrying the A30P mutation typically exhibit a similar age of onset and symptoms as sporadic PD, while those carrying the A53T mutation generally have an earlier age of onset and an accelerated progression. We report two C. elegans models of PD (PDA30P and PDA53T), which express these mutational variants in the muscle cells, and probed their behavior relative to animals expressing the wild-type protein (PDWT). PDA30P worms showed a reduced speed of movement and an increased paralysis rate, control worms, but no change in the frequency of body bends. By contrast, in PDA53T worms both speed and frequency of body bends were significantly decreased, and paralysis rate was increased. α-Synuclein was also observed to be less well localized into aggregates in PDA30P worms compared to PDA53T and PDWT worms, and amyloid-like features were evident later in the life of the animals, despite comparable levels of expression of α-synuclein. Furthermore, squalamine, a natural product currently in clinical trials for treating symptomatic aspects of PD, was found to reduce significantly the aggregation of α-synuclein and its associated toxicity in PDA53T and PDWT worms, but had less marked effects in PDA30P. In addition, using an antibody that targets the N-terminal region of α-synuclein, we observed a suppression of toxicity in PDA30P, PDA53T and PDWT worms. These results illustrate the use of these two C. elegans models in fundamental and applied PD research.
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Affiliation(s)
- Michele Perni
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Annemieke van der Goot
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Ryan Limbocker
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,Department of Chemistry and Life Science, United States Military Academy, West Point, NY, United States
| | - Tjakko J. van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A. Aprile
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Catherine K. Xu
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Flagmeier
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Karen Thijssen
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Pietro Sormanni
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Giuliana Fusco
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Serene W. Chen
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Pavan K. Challa
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Julius B. Kirkegaard
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology (LMCB) University College London, London, United Kingdom
| | - Kai Yu Ma
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Martin B. D. Müller
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Tessa Sinnige
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Janet R. Kumita
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Samuel I. A. Cohen
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Renée Seinstra
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | | | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Denise Barbut
- MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Michael Zasloff
- MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, United States
| | - Ellen A. A. Nollen
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands,*Correspondence: Ellen A. A. Nollen
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,Michele Vendruscolo
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
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14
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Hardenberg MC, Sinnige T, Casford S, Dada ST, Poudel C, Robinson EA, Fuxreiter M, Kaminksi CF, Kaminski Schierle GS, Nollen EAA, Dobson CM, Vendruscolo M. Observation of an α-synuclein liquid droplet state and its maturation into Lewy body-like assemblies. J Mol Cell Biol 2021; 13:282-294. [PMID: 33386842 DOI: 10.1093/jmcb/mjaa075] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/09/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Misfolded α-synuclein is a major component of Lewy bodies, which are a hallmark of Parkinson's disease (PD). A large body of evidence shows that α-synuclein can aggregate into amyloid fibrils, but the relationship between α-synuclein self-assembly and Lewy body formation remains unclear. Here, we show, both in vitro and in a Caenorhabditis elegans model of PD, that α-synuclein undergoes liquid‒liquid phase separation by forming a liquid droplet state, which converts into an amyloid-rich hydrogel with Lewy-body-like properties. This maturation process towards the amyloid state is delayed in the presence of model synaptic vesicles in vitro. Taken together, these results suggest that the formation of Lewy bodies may be linked to the arrested maturation of α-synuclein condensates in the presence of lipids and other cellular components.
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Affiliation(s)
- Maarten C Hardenberg
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Tessa Sinnige
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Sam Casford
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Samuel T Dada
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Chetan Poudel
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Elizabeth A Robinson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary
| | - Clemens F Kaminksi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | | | - Ellen A A Nollen
- European Research Institute for the Biology of Aging, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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15
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Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives. Q Rev Biophys 2020; 53:e12. [PMID: 33148356 DOI: 10.1017/s0033583520000086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.
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16
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Fan C, Wang YL, Zhao PJ, Qu HQ, Su YX, Li C, Zhu MQ. AIE-Based Dynamic in Situ Nanoscale Visualization of Amyloid Fibrillation from Hen Egg White Lysozyme. Bioconjug Chem 2020; 31:2303-2311. [PMID: 33002360 DOI: 10.1021/acs.bioconjchem.0c00379] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein misfolding and denaturation, represented by amyloid fibrillation, are associated with many diseases. However, as a general chemical biological process, the dynamic structure information on amyloid fibrillation has not been demonstrated categorically. Herein, hen egg white lysozyme (HEWL) was used as the model protein of interest to realize in situ nanoscale imaging of protein fibrillation process using the fluorophores with aggregation-induced emission (AIE) activity. The AIE-active fluorophores exhibit the reversible capability of association and dissociation with β-sheet structure and thus dynamic binding-induced emission, which causes the spontaneous switching of fluorescence. The entire HEWL denaturation process induced by sodium dodecyl sulfate (SDS) at ambient conditions was demonstrated in detail by using two AIE-active fluorophores (TPE-NaSO3 and PD-BZ-OH) through reversible electrostatic interaction and specific labeling between AIE probes and β-sheet structures of amyloid fibrils, respectively. The results indicate that PD-BZ-OH is more specific AIE probe for amyloid fibrils than TPE-NaSO3. In comparison, the SEM and TEM results show the same denaturation process of protein fibrillation induced by SDS at different concentrations. The static super-resolution imaging of amyloid fibrils is performed with a resolution of 35 nm using PD-BZ-OH aqueous solution without additional auxiliary conditions. The dynamic evolution process of HEWL amyloid fibrillation is in situ visualized through super-resolution fluorescent microscopy with nanoscale resolution. Both static and dynamic super-resolution imaging of amyloid fibrillation provides detailed nanoscale structure information exceeding 50 nm resolution, which is of great significance in the exploration of amyloid fibrillation and related diseases.
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Affiliation(s)
- Cheng Fan
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ya-Long Wang
- School of Biomedical Engineering, Hainan University, Haikou, Hainan 570228, China
| | - Peng-Ju Zhao
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou 510640, China
| | - Hong-Qing Qu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu-Xuan Su
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chong Li
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ming-Qiang Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,School of Biomedical Engineering, Hainan University, Haikou, Hainan 570228, China
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17
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Gallrein C, Iburg M, Michelberger T, Koçak A, Puchkov D, Liu F, Ayala Mariscal SM, Nayak T, Kaminski Schierle GS, Kirstein J. Novel amyloid-beta pathology C. elegans model reveals distinct neurons as seeds of pathogenicity. Prog Neurobiol 2020; 198:101907. [PMID: 32926945 DOI: 10.1016/j.pneurobio.2020.101907] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/28/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022]
Abstract
Protein misfolding and aggregation are hallmarks of neurodegenerative diseases such as Alzheimer's disease (AD). In AD, the accumulation and aggregation of tau and the amyloid-beta peptide Aβ1-42 precedes the onset of AD symptoms. Modelling the aggregation of Aβ is technically very challenging in vivo due to its size of only 42 aa. Here, we employed sub-stoichiometric labelling of Aβ1-42 in C. elegans to enable tracking of the peptide in vivo, combined with the "native" aggregation of unlabeled Aβ1-42. Expression of Aβ1-42 leads to severe physiological defects, neuronal dysfunction and neurodegeneration. Moreover, we can demonstrate spreading of neuronal Aβ to other tissues. Fluorescence lifetime imaging microscopy enabled a quantification of the formation of amyloid fibrils with ageing and revealed a heterogenic yet specific pattern of aggregation. Notably, we found that Aβ aggregation starts in a subset of neurons of the anterior head ganglion, the six IL2 neurons. We further demonstrate that cell-specific, RNAi-mediated depletion of Aβ in these IL2 neurons systemically delays Aβ aggregation and pathology.
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Affiliation(s)
- Christian Gallrein
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Manuel Iburg
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Tim Michelberger
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Alen Koçak
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Dmytro Puchkov
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Fan Liu
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Sara Maria Ayala Mariscal
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany
| | - Tanmoyita Nayak
- University of Bremen, Faculty 2, Cell Biology, Leobener Strasse, 28359, Bremen, Germany
| | - Gabriele S Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Janine Kirstein
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V., R.-Roessle-Strasse 10, Berlin, 13125, Germany; University of Bremen, Faculty 2, Cell Biology, Leobener Strasse, 28359, Bremen, Germany.
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18
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Alpha-Synuclein FRET Biosensors Reveal Early Alpha-Synuclein Aggregation in the Endoplasmic Reticulum. Life (Basel) 2020; 10:life10080147. [PMID: 32796544 PMCID: PMC7460339 DOI: 10.3390/life10080147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 11/17/2022] Open
Abstract
Endoplasmic reticulum (ER) dysfunction is important for alpha-synuclein (αS) acquired toxicity. When targeted to the ER in SH-SY5Y cells, transient or stable expression of αS resulted in the formation of compact αS-positive structures in a small subpopulation of cells, resembling αS inclusions. Thus, because of the limitations of immunofluorescence, we developed a set of αS FRET biosensors (AFBs) able to track αS conformation in cells. In native conditions, expression in i36, a stable cell line for ER αS, of intermolecular AFBs, reporters in which CFP or YFP has been fused with the C-terminal of αS (αS-CFP/αS-YFP), resulted in no Förster resonance energy transfer (FRET), whereas expression of the intramolecular AFB, a probe obtained by fusing YFP and CFP with αS N- or C- termini (YFP-αS-CFP), showed a positive FRET signal. These data confirmed that αS has a predominantly globular, monomeric conformation in native conditions. Differently, under pro-aggregating conditions, the intermolecular AFB was able to sense significantly formation of αS oligomers, when AFB was expressed in the ER rather than ubiquitously, suggesting that the ER can favor changes in αS conformation when aggregation is stimulated. These results show the potential of AFBs as a new, valuable tool to track αS conformational changes in vivo.
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19
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Lautenschläger J, Wagner-Valladolid S, Stephens AD, Fernández-Villegas A, Hockings C, Mishra A, Manton JD, Fantham MJ, Lu M, Rees EJ, Kaminski CF, Kaminski Schierle GS. Intramitochondrial proteostasis is directly coupled to α-synuclein and amyloid β1-42 pathologies. J Biol Chem 2020; 295:10138-10152. [PMID: 32385113 PMCID: PMC7383368 DOI: 10.1074/jbc.ra119.011650] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysfunction has long been implicated in the neurodegenerative disorder Parkinson's disease (PD); however, it is unclear how mitochondrial impairment and α-synuclein pathology are coupled. Using specific mitochondrial inhibitors, EM analysis, and biochemical assays, we report here that intramitochondrial protein homeostasis plays a major role in α-synuclein aggregation. We found that interference with intramitochondrial proteases, such as HtrA2 and Lon protease, and mitochondrial protein import significantly aggravates α-synuclein seeding. In contrast, direct inhibition of mitochondrial complex I, an increase in intracellular calcium concentration, or formation of reactive oxygen species, all of which have been associated with mitochondrial stress, did not affect α-synuclein pathology. We further demonstrate that similar mechanisms are involved in amyloid-β 1-42 (Aβ42) aggregation. Our results suggest that, in addition to other protein quality control pathways, such as the ubiquitin-proteasome system, mitochondria per se can influence protein homeostasis of cytosolic aggregation-prone proteins. We propose that approaches that seek to maintain mitochondrial fitness, rather than target downstream mitochondrial dysfunction, may aid in the search for therapeutic strategies to manage PD and related neuropathologies.
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Affiliation(s)
- Janin Lautenschläger
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom ;
| | - Sara Wagner-Valladolid
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Amberley D Stephens
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Ana Fernández-Villegas
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Colin Hockings
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Ajay Mishra
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - James D Manton
- Quantitative Imaging Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Marcus J Fantham
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Meng Lu
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Eric J Rees
- Quantitative Imaging Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom
| | - Gabriele S Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive, Cambridge, United Kingdom ;
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20
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Bentz BZ, Mahalingam SM, Ysselstein D, Montenegro Larrea PC, Cannon JR, Rochet JC, Low PS, Webb K. Localization of Fluorescent Targets in Deep Tissue With Expanded Beam Illumination for Studies of Cancer and the Brain. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:2472-2481. [PMID: 32031935 PMCID: PMC7428064 DOI: 10.1109/tmi.2020.2972200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Imaging fluorescence through millimeters or centimeters of tissue has important in vivo applications, such as guiding surgery and studying the brain. Often, the important information is the location of one of more optical reporters, rather than the specifics of the local geometry, motivating the need for a localization method that provides this information. We present an optimization approach based on a diffusion model for the fast localization of fluorescent inhomogeneities in deep tissue with expanded beam illumination that simplifies the experiment and the reconstruction. We show that the position of a fluorescent inhomogeneity can be estimated while assuming homogeneous tissue parameters and without having to model the excitation profile, reducing the computational burden and improving the utility of the method. We perform two experiments as a demonstration. First, a tumor in a mouse is localized using a near infrared folate-targeted fluorescent agent (OTL38). This result shows that localization can quickly provide tumor depth information, which could reduce damage to healthy tissue during fluorescence-guided surgery. Second, another near infrared fluorescent agent (ATTO647N) is injected into the brain of a rat, and localized through the intact skull and surface tissue. This result will enable studies of protein aggregation and neuron signaling.
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21
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Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases. Q Rev Biophys 2020; 49:e22. [PMID: 32493529 DOI: 10.1017/s0033583520000025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the formation of the aberrant conformational states of proteins whose neurotoxic effects underlie these diseases. We discuss in particular models based on the transgenic expression of amyloid-β (Aβ) and tau in AD, and α-synuclein in PD. Because biophysical methods have enabled an accurate quantification and a detailed understanding of the molecular mechanisms underlying protein misfolding and aggregation in vitro, we expect that the further development of these methods to probe directly the corresponding mechanisms in vivo will open effective routes for diagnostic and therapeutic interventions.
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22
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Sandhof CA, Hoppe SO, Druffel-Augustin S, Gallrein C, Kirstein J, Voisine C, Nussbaum-Krammer C. Reducing INS-IGF1 signaling protects against non-cell autonomous vesicle rupture caused by SNCA spreading. Autophagy 2020; 16:878-899. [PMID: 31354022 PMCID: PMC7144869 DOI: 10.1080/15548627.2019.1643657] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 01/28/2023] Open
Abstract
Aging is associated with a gradual decline of cellular proteostasis, giving rise to devastating protein misfolding diseases, such as Alzheimer disease (AD) or Parkinson disease (PD). These diseases often exhibit a complex pathology involving non-cell autonomous proteotoxic effects, which are still poorly understood. Using Caenorhabditis elegans we investigated how local protein misfolding is affecting neighboring cells and tissues showing that misfolded PD-associated SNCA/α-synuclein is accumulating in highly dynamic endo-lysosomal vesicles. Irrespective of whether being expressed in muscle cells or dopaminergic neurons, accumulated proteins were transmitted into the hypodermis with increasing age, indicating that epithelial cells might play a role in remote degradation when the local endo-lysosomal degradation capacity is overloaded. Cell biological and genetic approaches revealed that inter-tissue dissemination of SNCA was regulated by endo- and exocytosis (neuron/muscle to hypodermis) and basement membrane remodeling (muscle to hypodermis). Transferred SNCA conformers were, however, inefficiently cleared and induced endo-lysosomal membrane permeabilization. Remarkably, reducing INS (insulin)-IGF1 (insulin-like growth factor 1) signaling provided protection by maintaining endo-lysosomal integrity. This study suggests that the degradation of lysosomal substrates is coordinated across different tissues in metazoan organisms. Because the chronic dissemination of poorly degradable disease proteins into neighboring tissues exerts a non-cell autonomous toxicity, this implies that restoring endo-lysosomal function not only in cells with pathological inclusions, but also in apparently unaffected cell types might help to halt disease progression.Abbreviations: AD: Alzheimer disease; BM: basement membrane; BWM: body wall muscle; CEP: cephalic sensilla; CLEM: correlative light and electron microscopy; CTNS-1: cystinosin (lysosomal protein) homolog; DA: dopaminergic; DAF-2: abnormal dauer formation; ECM: extracellular matrix; FLIM: fluorescence lifetime imaging microscopy; fps: frames per second; GFP: green fluorescent protein; HPF: high pressure freezing; IGF1: insulin-like growth factor 1; INS: insulin; KD: knockdown; LMP: lysosomal membrane permeabilization; MVB: multivesicular body; NOC: nocodazole; PD: Parkinson disease; RFP: red fluorescent protein; RNAi: RNA interference; sfGFP: superfolder GFP; SNCA: synuclein alpha; TEM: transmission electron microscopy; TNTs: tunneling nanotubes; TCSPC: time correlated single photon counting; YFP: yellow fluorescent protein.
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Affiliation(s)
- Carl Alexander Sandhof
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Simon Oliver Hoppe
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Silke Druffel-Augustin
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Gallrein
- Department of Molecular Physiology and Cell Biology, Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin e.V, Berlin, Germany
| | - Janine Kirstein
- Department of Molecular Physiology and Cell Biology, Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin e.V, Berlin, Germany
| | - Cindy Voisine
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Carmen Nussbaum-Krammer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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23
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Methods for protein delivery into cells: from current approaches to future perspectives. Biochem Soc Trans 2020; 48:357-365. [DOI: 10.1042/bst20190039] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022]
Abstract
The manipulation of cultured mammalian cells by the delivery of exogenous macromolecules is one of the cornerstones of experimental cell biology. Although the transfection of cells with DNA expressions constructs that encode proteins is routine and simple to perform, the direct delivery of proteins into cells has many advantages. For example, proteins can be chemically modified, assembled into defined complexes and subject to biophysical analyses prior to their delivery into cells. Here, we review new approaches to the injection and electroporation of proteins into cultured cells. In particular, we focus on how recent developments in nanoscale injection probes and localized electroporation devices enable proteins to be delivered whilst minimizing cellular damage. Moreover, we discuss how nanopore sensing may ultimately enable the quantification of protein delivery at single-molecule resolution.
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24
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Pigazzini ML, Gallrein C, Iburg M, Kaminski Schierle G, Kirstein J. Characterization of Amyloid Structures in Aging C. Elegans Using Fluorescence Lifetime Imaging. J Vis Exp 2020:10.3791/61004. [PMID: 32281971 PMCID: PMC7614926 DOI: 10.3791/61004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Amyloid fibrils are associated with a number of neurodegenerative diseases such as Huntington's, Parkinson's, or Alzheimer's disease. These amyloid fibrils can sequester endogenous metastable proteins as well as components of the proteostasis network (PN) and thereby exacerbate protein misfolding in the cell. There are a limited number of tools available to assess the aggregation process of amyloid proteins within an animal. We present a protocol for fluorescence lifetime microscopy (FLIM) that allows monitoring as well as quantification of the amyloid fibrilization in specific cells, such as neurons, in a noninvasive manner and with the progression of aging and upon perturbation of the PN. FLIM is independent of the expression levels of the fluorophore and enables an analysis of the aggregation process without any further staining or bleaching. Fluorophores are quenched when they are in close vicinity of amyloid structures, which results in a decrease of the fluorescence lifetime. The quenching directly correlates with the aggregation of the amyloid protein. FLIM is a versatile technique that can be applied to compare the fibrilization process of different amyloid proteins, environmental stimuli, or genetic backgrounds in vivo in a non-invasive manner.
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Affiliation(s)
- Maria Lucia Pigazzini
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin; NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin
| | - Christian Gallrein
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin
| | - Manuel Iburg
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin
| | - Gabriele Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge
| | - Janine Kirstein
- Leibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin; Cell Biology, University of Bremen;
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25
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Klementieva O, Sandt C, Martinsson I, Kansiz M, Gouras GK, Borondics F. Super-Resolution Infrared Imaging of Polymorphic Amyloid Aggregates Directly in Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903004. [PMID: 32195099 PMCID: PMC7080554 DOI: 10.1002/advs.201903004] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/12/2020] [Indexed: 05/06/2023]
Abstract
Loss of memory during Alzheimer's disease (AD), a fatal neurodegenerative disorder, is associated with neuronal loss and the aggregation of amyloid proteins into neurotoxic β-sheet enriched structures. However, the mechanism of amyloid protein aggregation is still not well understood due to many challenges when studying the endogenous amyloid structures in neurons or in brain tissue. Available methods either require chemical processing of the sample or may affect the amyloid protein structure itself. Therefore, new approaches, which allow studying molecular structures directly in neurons, are urgently needed. A novel approach is tested, based on label-free optical photothermal infrared super-resolution microspectroscopy, to study AD-related amyloid protein aggregation directly in the neuron at sub-micrometer resolution. Using this approach, amyloid protein aggregates are detected at the subcellular level, along the neurites and strikingly, in dendritic spines, which has not been possible until now. Here, a polymorphic nature of amyloid structures that exist in AD transgenic neurons is reported. Based on the findings of this work, it is suggested that structural polymorphism of amyloid proteins that occur already in neurons may trigger different mechanisms of AD progression.
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Affiliation(s)
- Oxana Klementieva
- Medical Microspectroscopy Research GroupDepartment of Experimental Medical ScienceLund University22180LundSweden
- Lund Institute for advanced Neutron and X‐ray Science (LINXS)223 70LundSweden
| | - Christophe Sandt
- Synchrotron SOLEILL'Orme des Merisiers91192Gif Sur YvetteCedexFrance
| | - Isak Martinsson
- Experimental Dementia ResearchDepartment of Experimental Medical ScienceLund University22180LundSweden
| | - Mustafa Kansiz
- Photothermal Spectroscopy CorporationSanta BarbaraCA93101USA
| | - Gunnar K. Gouras
- Experimental Dementia ResearchDepartment of Experimental Medical ScienceLund University22180LundSweden
| | - Ferenc Borondics
- Synchrotron SOLEILL'Orme des Merisiers91192Gif Sur YvetteCedexFrance
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26
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Poudel C, Mela I, Kaminski CF. High-throughput, multi-parametric, and correlative fluorescence lifetime imaging. Methods Appl Fluoresc 2020; 8:024005. [PMID: 32028271 PMCID: PMC8208541 DOI: 10.1088/2050-6120/ab7364] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/18/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
In this review, we discuss methods and advancements in fluorescence lifetime imaging microscopy that permit measurements to be performed at faster speed and higher resolution than previously possible. We review fast single-photon timing technologies and the use of parallelized detection schemes to enable high-throughput and high content imaging applications. We appraise different technological implementations of fluorescence lifetime imaging, primarily in the time-domain. We also review combinations of fluorescence lifetime with other imaging modalities to capture multi-dimensional and correlative information from a single sample. Throughout the review, we focus on applications in biomedical research. We conclude with a critical outlook on current challenges and future opportunities in this rapidly developing field.
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Affiliation(s)
- Chetan Poudel
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology,
Philippa Fawcett Drive, University of
Cambridge, Cambridge CB3 0AS, United
Kingdom
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27
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Lu M, Kaminski CF, Schierle GSK. Advanced fluorescence imaging of in situ protein aggregation. Phys Biol 2020; 17:021001. [DOI: 10.1088/1478-3975/ab694e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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28
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Goya ME, Xue F, Sampedro-Torres-Quevedo C, Arnaouteli S, Riquelme-Dominguez L, Romanowski A, Brydon J, Ball KL, Stanley-Wall NR, Doitsidou M. Probiotic Bacillus subtilis Protects against α-Synuclein Aggregation in C. elegans. Cell Rep 2020; 30:367-380.e7. [PMID: 31940482 PMCID: PMC6963774 DOI: 10.1016/j.celrep.2019.12.078] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/23/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Recent discoveries have implicated the gut microbiome in the progression and severity of Parkinson's disease; however, how gut bacteria affect such neurodegenerative disorders remains unclear. Here, we report that the Bacillus subtilis probiotic strain PXN21 inhibits α-synuclein aggregation and clears preformed aggregates in an established Caenorhabditis elegans model of synucleinopathy. This protection is seen in young and aging animals and is partly mediated by DAF-16. Multiple B. subtilis strains trigger the protective effect via both spores and vegetative cells, partly due to a biofilm formation in the gut of the worms and the release of bacterial metabolites. We identify several host metabolic pathways differentially regulated in response to probiotic exposure, including sphingolipid metabolism. We further demonstrate functional roles of the sphingolipid metabolism genes lagr-1, asm-3, and sptl-3 in the anti-aggregation effect. Our findings provide a basis for exploring the disease-modifying potential of B. subtilis as a dietary supplement.
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Affiliation(s)
- María Eugenia Goya
- University of Edinburgh, Centre for Discovery Brain Sciences, Edinburgh, Scotland
| | - Feng Xue
- University of Edinburgh, Centre for Discovery Brain Sciences, Edinburgh, Scotland
| | | | | | | | - Andrés Romanowski
- University of Edinburgh, School of Biological Sciences, Edinburgh, Scotland
| | - Jack Brydon
- University of Edinburgh, Institute of Genetics & Molecular Medicine, Edinburgh, Scotland
| | - Kathryn L Ball
- University of Edinburgh, Institute of Genetics & Molecular Medicine, Edinburgh, Scotland
| | | | - Maria Doitsidou
- University of Edinburgh, Centre for Discovery Brain Sciences, Edinburgh, Scotland.
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29
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Bracha D, Walls MT, Brangwynne CP. Probing and engineering liquid-phase organelles. Nat Biotechnol 2019; 37:1435-1445. [DOI: 10.1038/s41587-019-0341-6] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023]
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30
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Protein Microgels from Amyloid Fibril Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:223-263. [PMID: 31713201 DOI: 10.1007/978-981-13-9791-2_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Nanofibrillar forms of amyloidogenic proteins were initially discovered in the context of protein misfolding and disease but have more recently been found at the origin of key biological functionality in many naturally occurring functional materials, such as adhesives and biofilm coatings. Their physiological roles in nature reflect their great strength and stability, which has led to the exploration of their use as the basis of artificial protein-based functional materials. Particularly for biomedical applications, they represent attractive building blocks for the development of, for instance, drug carrier agents due to their inherent biocompatibility and biodegradability. Furthermore, the propensity of proteins to self-assemble into amyloid fibrils can be exploited under microconfinement, afforded by droplet microfluidic techniques. This approach allows the generation of multi-scale functional microgels that can host biological additives and can be designed to incorporate additional functionality, such as to aid targeted drug delivery.
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31
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Gorbenko G, Trusova V, Deligeorgiev T, Gadjev N, Mizuguchi C, Saito H. Two-step FRET as a tool for probing the amyloid state of proteins. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Laine RF, Sinnige T, Ma KY, Haack AJ, Poudel C, Gaida P, Curry N, Perni M, Nollen EA, Dobson CM, Vendruscolo M, Kaminski Schierle GS, Kaminski CF. Fast Fluorescence Lifetime Imaging Reveals the Aggregation Processes of α-Synuclein and Polyglutamine in Aging Caenorhabditis elegans. ACS Chem Biol 2019; 14:1628-1636. [PMID: 31246415 PMCID: PMC7612977 DOI: 10.1021/acschembio.9b00354] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The nematode worm Caenorhabditis elegans has emerged as an important model organism in the study of the molecular mechanisms of protein misfolding diseases associated with amyloid formation because of its small size, ease of genetic manipulation, and optical transparency. Obtaining a reliable and quantitative read-out of protein aggregation in this system, however, remains a challenge. To address this problem, we here present a fast time-gated fluorescence lifetime imaging (TG-FLIM) method and show that it provides functional insights into the process of protein aggregation in living animals by enabling the rapid characterization of different types of aggregates. Specifically, in longitudinal studies of C. elegans models of Parkinson's and Huntington's diseases, we observed marked differences in the aggregation kinetics and the nature of the protein inclusions formed by α-synuclein and polyglutamine. In particular, we found that α-synuclein inclusions do not display amyloid-like features until late in the life of the worms, whereas polyglutamine forms amyloid characteristics rapidly in early adulthood. Furthermore, we show that the TG-FLIM method is capable of imaging live and non-anaesthetized worms moving in specially designed agarose microchambers. Taken together, our results show that the TG-FLIM method enables high-throughput functional imaging of living C. elegans that can be used to study in vivo mechanisms of protein aggregation and that has the potential to aid the search for therapeutic modifiers of protein aggregation and toxicity.
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Affiliation(s)
- Romain F. Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Tessa Sinnige
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Kai Yu Ma
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Amanda J. Haack
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Chetan Poudel
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Peter Gaida
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Nathan Curry
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Ellen A.A. Nollen
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, 9700 AD Groningen, The Netherlands
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele S. Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Clemens F. Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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33
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Huang C, Wagner-Valladolid S, Stephens AD, Jung R, Poudel C, Sinnige T, Lechler MC, Schlörit N, Lu M, Laine RF, Michel CH, Vendruscolo M, Kaminski CF, Kaminski Schierle GS, David DC. Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in Caenorhabditis elegans. eLife 2019; 8:e43059. [PMID: 31050339 PMCID: PMC6524967 DOI: 10.7554/elife.43059] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/02/2019] [Indexed: 12/13/2022] Open
Abstract
Reduced protein homeostasis leading to increased protein instability is a common molecular feature of aging, but it remains unclear whether this is a cause or consequence of the aging process. In neurodegenerative diseases and other amyloidoses, specific proteins self-assemble into amyloid fibrils and accumulate as pathological aggregates in different tissues. More recently, widespread protein aggregation has been described during normal aging. Until now, an extensive characterization of the nature of age-dependent protein aggregation has been lacking. Here, we show that age-dependent aggregates are rapidly formed by newly synthesized proteins and have an amyloid-like structure resembling that of protein aggregates observed in disease. We then demonstrate that age-dependent protein aggregation accelerates the functional decline of different tissues in C. elegans. Together, these findings imply that amyloid-like aggregates contribute to the aging process and therefore could be important targets for strategies designed to maintain physiological functions in the late stages of life.
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Affiliation(s)
- Chaolie Huang
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
| | - Sara Wagner-Valladolid
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Amberley D Stephens
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Raimund Jung
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
| | - Chetan Poudel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Tessa Sinnige
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Marie C Lechler
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
- Graduate Training Centre of NeuroscienceUniversity of TübingenTübingenGermany
| | - Nicole Schlörit
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
- Graduate Training Centre of NeuroscienceUniversity of TübingenTübingenGermany
| | - Meng Lu
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Romain F Laine
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Claire H Michel
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Clemens F Kaminski
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Della C David
- German Center for Neurodegenerative Diseases (DZNE)TübingenGermany
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34
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Kundel F, Tosatto L, Whiten DR, Wirthensohn DC, Horrocks MH, Klenerman D. Shedding light on aberrant interactions - a review of modern tools for studying protein aggregates. FEBS J 2018; 285:3604-3630. [PMID: 29453901 DOI: 10.1111/febs.14409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/27/2018] [Accepted: 02/12/2018] [Indexed: 12/15/2022]
Abstract
The link between protein aggregation and neurodegenerative disease is well established. However, given the heterogeneity of species formed during the aggregation process, it is difficult to delineate details of the molecular events involved in generating pathological aggregates from those producing soluble monomers. As aberrant aggregates are possible pharmacological targets for the treatment of neurodegenerative diseases, the need to observe and characterise soluble oligomers has pushed traditional biophysical techniques to their limits, leading to the development of a plethora of new tools capable of detecting soluble oligomers with high precision and specificity. In this review, we discuss a range of modern biophysical techniques that have been developed to study protein aggregation, and give an overview of how they have been used to understand, in detail, the aberrant aggregation of amyloidogenic proteins associated with the two most common neurodegenerative disorders, Alzheimer's disease and Parkinson's disease.
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Affiliation(s)
| | - Laura Tosatto
- Centre for Integrative Biology, Università degli Studi di Trento, Italy
| | | | | | | | - David Klenerman
- Department of Chemistry, University of Cambridge, UK.,UK Dementia Research Institute, University of Cambridge, UK
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35
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Sirangelo I, Borriello M, Irace G, Iannuzzi C. Intrinsic blue-green fluorescence in amyloyd fibrils. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.2.155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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36
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Abstract
Semiconductors are central to the modern electronics and optics industries. Conventional semiconductive materials bear inherent limitations, especially in emerging fields such as interfacing with biological systems and bottom-up fabrication. A promising candidate for bioinspired and durable nanoscale semiconductors is the family of self-assembled nanostructures comprising short peptides. The highly ordered and directional intermolecular π-π interactions and hydrogen-bonding network allow the formation of quantum confined structures within the peptide self-assemblies, thus decreasing the band gaps of the superstructures into semiconductor regions. As a result of the diverse architectures and ease of modification of peptide self-assemblies, their semiconductivity can be readily tuned, doped, and functionalized. Therefore, this family of electroactive supramolecular materials may bridge the gap between the inorganic semiconductor world and biological systems.
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Affiliation(s)
- Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Pandeeswar Makam
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ruth Aizen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
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37
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Gan Z, Xu H. Photoluminescence of Diphenylalanine Peptide Nano/Microstructures: From Mechanisms to Applications. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700370] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/29/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Zhixing Gan
- Key Laboratory of Optoelectronic Technology of Jiangsu Province; School of Physics and Technology; Nanjing Normal University; Nanjing 210023 China
| | - Hao Xu
- Faculty of Science; Ningbo University; Ningbo 315211 China
- Advanced Light Microscopy; Royal Institute of Technology; Science for Life Laboratory; Solna SE-17121 Sweden
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38
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Peronio P, Labanca I, Acconcia G, Ruggeri A, Lavdas AA, Hicks AA, Pramstaller PP, Ghioni M, Rech I. 32-channel time-correlated-single-photon-counting system for high-throughput lifetime imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:083704. [PMID: 28863689 DOI: 10.1063/1.4986049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Time-Correlated Single Photon Counting (TCSPC) is a very efficient technique for measuring weak and fast optical signals, but it is mainly limited by the relatively "long" measurement time. Multichannel systems have been developed in recent years aiming to overcome this limitation by managing several detectors or TCSPC devices in parallel. Nevertheless, if we look at state-of-the-art systems, there is still a strong trade-off between the parallelism level and performance: the higher the number of channels, the poorer the performance. In 2013, we presented a complete and compact 32 × 1 TCSPC system, composed of an array of 32 single-photon avalanche diodes connected to 32 time-to-amplitude converters, which showed that it was possible to overcome the existing trade-off. In this paper, we present an evolution of the previous work that is conceived for high-throughput fluorescence lifetime imaging microscopy. This application can be addressed by the new system thanks to a centralized logic, fast data management and an interface to a microscope. The new conceived hardware structure is presented, as well as the firmware developed to manage the operation of the module. Finally, preliminary results, obtained from the practical application of the technology, are shown to validate the developed system.
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Affiliation(s)
- P Peronio
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - I Labanca
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - G Acconcia
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - A Ruggeri
- Micro Photon Devices S.R.L., via Stradivari 4, 39100 Bolzano, Italy
| | - A A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, via Galvani 31, 39100 Bolzano, Italy
| | - A A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, via Galvani 31, 39100 Bolzano, Italy
| | - P P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, via Galvani 31, 39100 Bolzano, Italy
| | - M Ghioni
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - I Rech
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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39
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Diaferia C, Sibillano T, Giannini C, Roviello V, Vitagliano L, Morelli G, Accardo A. Photoluminescent Peptide-Based Nanostructures as FRET Donor for Fluorophore Dye. Chemistry 2017; 23:8741-8748. [PMID: 28508550 DOI: 10.1002/chem.201701381] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Indexed: 12/22/2022]
Abstract
A great interest has been recently generated by the discovery that peptide-based nanostructures (NSs) endowed with cross-β structure may show interesting photoluminescent (PL) properties. It was shown that NSs formed by PEGylated hexaphenylalanine (PEG8 -F6, PEG=polyethylene glycol) are able to emit at 460 nm when excited at 370 or 410 nm. Here, the possibility to transfer the fluorescence of these PEG8 -F6-based NSs by foster resonance electron transfer (FRET) phenomenon to a fluorescent dye was explored. To achieve this aim, the 4-chloro-7-nitrobenzofurazan (NBD) dye was encapsulated in these NSs. Structural data in solution and in solid state, obtained by a variety of techniques (circular dichroism, Fourier-transform infrared spectroscopy, wide-angle X-ray scattering, and small-angle X-ray scattering), indicated that the organization of the peptide spine of PEG8 -F6 NS, which consists of anti-parallel β-sheets separated by a dry interface made of interacting phenylalanine side chains, was maintained upon NBD encapsulation. The spectroscopic characterization of these NSs clearly showed a red-shift of the emission fluorescence peak both in solution and in solid state. This shift from 460 to 530 nm indicated that a FRET phenomenon from the peptide-based to the fluorophore-encapsulated NS occurred. FRET could also be detected in the PEG8 -F6 conjugate, in which the NBD was covalently bound to the amine of the compound. On the basis of these results, it is suggested that the red-shift of the intrinsic PL of NSs may be exploited in the bio-imaging field.
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Affiliation(s)
- Carlo Diaferia
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), CNR, Via Amendola 122, 70126, Bari, Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and CeSMA (Centro Servizi Metereologici Avanzati), University of Naples "Federico II", Corso Nicolangelo Protopisani, 80146, Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
| | - Antonella Accardo
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II" and DFM Scarl, Via Mezzocannone 16, 80134, Naples, Italy
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40
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Grisanti L, Pinotsi D, Gebauer R, Kaminski Schierle GS, Hassanali AA. A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils. Phys Chem Chem Phys 2017; 19:4030-4040. [PMID: 28111679 PMCID: PMC7612978 DOI: 10.1039/c6cp07564a] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Amyloid fibrils have been shown to have peculiar optical properties since they can exhibit fluorescence in the absence of aromatic residues. In a recent study, we have shown that proton transfer (PT) events along hydrogen bonds (HBs) are coupled to absorption in the near UV range. Here, we gain more insights into the different types of hydrogen bonding interactions that occur in our model systems and the molecular factors that control the susceptibility of the protons to undergo PT and how this couples to the optical properties. In the case of the strong N-C termini interactions, a nearby methionine residue stabilizes the non-zwitterionic NH2-COOH pair, while zwitterionic NH3+-COO- is stabilized by the proximity of nearby crystallographic water molecules. Proton motion along the hydrogen bonds in the fibril is intimately coupled to the compression of the heavier atoms, similar to what is observed in bulk water. Small changes in the compression of the hydrogen bonds in the protein can lead to significant changes in both the ground and excited state potential energy surfaces associated with PT. Finally, we also reinforce the importance of nuclear quantum fluctuations of protons in the HBs of the amyloid proteins.
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Affiliation(s)
- Luca Grisanti
- International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy.
| | - Dorothea Pinotsi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, UK
| | - Ralph Gebauer
- International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy.
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, UK
| | - Ali A Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy.
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41
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Holmes BB, Diamond MI. Cellular Models for the Study of Prions. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a024026. [PMID: 27815306 DOI: 10.1101/cshperspect.a024026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It is now established that numerous amyloid proteins associated with neurodegenerative diseases, including tau and α-synuclein, have essential characteristics of prions, including the ability to create transmissible cellular pathology in vivo. We have developed cellular bioassays that report on the various features of prion activity using genetic engineering and quantitative fluorescence-based detection systems. We have exploited these biosensors to measure the binding and uptake of tau seeds into cells in culture and to quantify seeding activity in brain samples. These cell models have also been used to propagate tau prion strains indefinitely in culture. In this review, we illustrate the utility of cellular biosensors to gain mechanistic insight into prion transmission and to study neurodegenerative diseases in a reductionist fashion.
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Affiliation(s)
- Brandon B Holmes
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri 63110.,Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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42
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Chen W, Young LJ, Lu M, Zaccone A, Ströhl F, Yu N, Kaminski Schierle GS, Kaminski CF. Fluorescence Self-Quenching from Reporter Dyes Informs on the Structural Properties of Amyloid Clusters Formed in Vitro and in Cells. NANO LETTERS 2017; 17:143-149. [PMID: 28073262 PMCID: PMC5338000 DOI: 10.1021/acs.nanolett.6b03686] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/26/2016] [Indexed: 05/26/2023]
Abstract
The characterization of the aggregation kinetics of protein amyloids and the structural properties of the ensuing aggregates are vital in the study of the pathogenesis of many neurodegenerative diseases and the discovery of therapeutic targets. In this article, we show that the fluorescence lifetime of synthetic dyes covalently attached to amyloid proteins informs on the structural properties of amyloid clusters formed both in vitro and in cells. We demonstrate that the mechanism behind such a "lifetime sensor" of protein aggregation is based on fluorescence self-quenching and that it offers a good dynamic range to report on various stages of aggregation without significantly perturbing the process under investigation. We show that the sensor informs on the structural density of amyloid clusters in a high-throughput and quantitative manner and in these aspects the sensor outperforms super-resolution imaging techniques. We demonstrate the power and speed of the method, offering capabilities, for example, in therapeutic screenings that monitor biological self-assembly. We investigate the mechanism and advantages of the lifetime sensor in studies of the K18 protein fragment of the Alzheimer's disease related protein tau and its amyloid aggregates formed in vitro. Finally, we demonstrate the sensor in the study of aggregates of polyglutamine protein, a model used in studies related to Huntington's disease, by performing correlative fluorescence lifetime imaging microscopy and structured-illumination microscopy experiments in cells.
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43
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de Pomerai DI, Iqbal N, Lafayette I, Nagarajan A, Kaviani Moghadam M, Fineberg A, Reader T, Greedy S, Smartt C, Thomas DWP. Microwave fields have little effect on α-synuclein aggregation in a Caenorhabditis elegans model of Parkinson's disease. Bioelectromagnetics 2016; 37:116-29. [PMID: 26879225 DOI: 10.1002/bem.21959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/22/2016] [Indexed: 12/24/2022]
Abstract
Potential health effects of radiofrequency (RF) radiation from mobile phones arouse widespread public concern. RF fields from handheld devices near the brain might trigger or aggravate brain tumors or neurodegenerative diseases such as Parkinson's disease (PD). Aggregation of neural α-synuclein (S) is central to PD pathophysiology, and invertebrate models expressing human S have helped elucidate factors affecting the aggregation process. We have recently developed a transgenic strain of Caenorhabditis elegans carrying two S constructs: SC tagged with cyan (C) blue fluorescent protein (CFP), and SV with the Venus (V) variant of yellow fluorescent protein (YFP). During S aggregation in these SC+SV worms, CFP, and YFP tags are brought close enough to allow Foerster Resonance Energy Transfer (FRET). As a positive control, S aggregation was promoted at low Hg(2+) concentrations, whereas higher concentrations activated stress-response genes. Using two different exposure systems described previously, we tested whether RF fields (1.0 GHz CW, 0.002-0.02 W kg(-1); 1.8 GHz CW or GSM, 1.8 W kg(-1)) could influence S aggregation in SC+SV worms. YFP fluorescence in similar SV-only worms provided internal controls, which should show opposite changes due to FRET quenching during S aggregation. No statistically significant changes were observed over several independent runs at 2.5, 24, or 96 h. Although our worm model is sensitive to chemical promoters of aggregation, no similar effects were attributable to RF exposures.
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Affiliation(s)
| | - Nooria Iqbal
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Ivan Lafayette
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Archana Nagarajan
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | | | - April Fineberg
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Tom Reader
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Steve Greedy
- Department of Electrical and Electronic Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Chris Smartt
- Department of Electrical and Electronic Engineering, University of Nottingham, Nottingham, United Kingdom
| | - David W P Thomas
- Department of Electrical and Electronic Engineering, University of Nottingham, Nottingham, United Kingdom
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44
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Kaminski CF, Kaminski Schierle GS. Probing amyloid protein aggregation with optical superresolution methods: from the test tube to models of disease. NEUROPHOTONICS 2016; 3:041807. [PMID: 27413767 PMCID: PMC4925874 DOI: 10.1117/1.nph.3.4.041807] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/13/2016] [Indexed: 05/02/2023]
Abstract
The misfolding and self-assembly of intrinsically disordered proteins into insoluble amyloid structures are central to many neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Optical imaging of this self-assembly process in vitro and in cells is revolutionizing our understanding of the molecular mechanisms behind these devastating conditions. In contrast to conventional biophysical methods, optical imaging and, in particular, optical superresolution imaging, permits the dynamic investigation of the molecular self-assembly process in vitro and in cells, at molecular-level resolution. In this article, current state-of-the-art imaging methods are reviewed and discussed in the context of research into neurodegeneration.
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Affiliation(s)
- Clemens F. Kaminski
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Pembroke Street, Cambridge CB2 3RA, United Kingdom
- Address all correspondence to: Clemens F. Kaminski, E-mail:
| | - Gabriele S. Kaminski Schierle
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Pembroke Street, Cambridge CB2 3RA, United Kingdom
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45
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Mongeon R, Venkatachalam V, Yellen G. Cytosolic NADH-NAD(+) Redox Visualized in Brain Slices by Two-Photon Fluorescence Lifetime Biosensor Imaging. Antioxid Redox Signal 2016; 25:553-63. [PMID: 26857245 PMCID: PMC5041510 DOI: 10.1089/ars.2015.6593] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIM Cytosolic NADH-NAD(+) redox state is central to cellular metabolism and a valuable indicator of glucose and lactate metabolism in living cells. Here we sought to quantitatively determine NADH-NAD(+) redox in live cells and brain tissue using a fluorescence lifetime imaging of the genetically-encoded single-fluorophore biosensor Peredox. RESULTS We show that Peredox exhibits a substantial change in its fluorescence lifetime over its sensing range of NADH-NAD(+) ratio. This allows changes in cytosolic NADH redox to be visualized in living cells using a two-photon scanning microscope with fluorescence lifetime imaging capabilities (2p-FLIM), using time-correlated single photon counting. INNOVATION Because the lifetime readout is absolutely calibrated (in nanoseconds) and is independent of sensor concentration, we demonstrate that quantitative assessment of NADH redox is possible using a single fluorophore biosensor. CONCLUSION Imaging of the sensor in mouse hippocampal brain slices reveals that astrocytes are typically much more reduced (with higher NADH:NAD(+) ratio) than neurons under basal conditions, consistent with the hypothesis that astrocytes are more glycolytic than neurons. Antioxid. Redox Signal. 25, 553-563.
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Affiliation(s)
- Rebecca Mongeon
- Department of Neurobiology, Harvard Medical School , Boston, Massachusetts
| | | | - Gary Yellen
- Department of Neurobiology, Harvard Medical School , Boston, Massachusetts
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46
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Laine RF, Kaminski Schierle GS, van de Linde S, Kaminski CF. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review. Methods Appl Fluoresc 2016; 4:022004. [PMID: 28809165 PMCID: PMC5390958 DOI: 10.1088/2050-6120/4/2/022004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/09/2016] [Accepted: 05/19/2016] [Indexed: 12/03/2022]
Abstract
For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.
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Affiliation(s)
- Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Gabriele S Kaminski Schierle
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University, Am Hubland, D-97074 Würzburg, Germany
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
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47
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Schierle GSK, Michel CH, Gasparini L. Advanced imaging of tau pathology in Alzheimer Disease: New perspectives from super resolution microscopy and label-free nanoscopy. Microsc Res Tech 2016; 79:677-83. [DOI: 10.1002/jemt.22698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/19/2016] [Indexed: 01/20/2023]
Affiliation(s)
- Gabriele S. Kaminski Schierle
- Department of Chemical Engineering and Biotechnology; Pembroke Street, University of Cambridge; Cambridge CB2 3RA United Kingdom
| | - Claire H. Michel
- Department of Chemical Engineering and Biotechnology; Pembroke Street, University of Cambridge; Cambridge CB2 3RA United Kingdom
| | - Laura Gasparini
- Department of Neuroscience and Brain Technologies; Istituto Italiano di Tecnologia; Via Morego 30 Genova Italy
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48
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Kaushik A, Jayant RD, Tiwari S, Vashist A, Nair M. Nano-biosensors to detect beta-amyloid for Alzheimer's disease management. Biosens Bioelectron 2016; 80:273-287. [PMID: 26851586 PMCID: PMC4786026 DOI: 10.1016/j.bios.2016.01.065] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
Beta-amyloid (β-A) peptides are potential biomarkers to monitor Alzheimer's diseases (AD) for diagnostic purposes. Increased β-A level is neurotoxic and induces oxidative stress in brain resulting in neurodegeneration and causes dementia. As of now, no sensitive and inexpensive method is available for β-A detection under physiological and pathological conditions. Although, available methods such as neuroimaging, enzyme-linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR) detect β-A, but they are not yet extended at point-of-care (POC) due to sophisticated equipments, need of high expertize, complicated operations, and challenge of low detection limit. Recently, β-A antibody based electrochemical immuno-sensing approach has been explored to detect β-A at pM levels within 30-40 min compared to 6-8h of ELISA test. The introduction of nano-enabling electrochemical sensing technology could enable rapid detection of β-A at POC and may facilitate fast personalized health care delivery. This review explores recent advancements in nano-enabling electrochemical β-A sensing technologies towards POC application to AD management. These analytical tools can serve as an analytical tool for AD management program to obtain bio-informatics needed to optimize therapeutics for neurodegenerative diseases diagnosis management.
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Affiliation(s)
- Ajeet Kaushik
- Center for Personalized Nanomedicine, Institute of Neuro immune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
| | - Rahul Dev Jayant
- Center for Personalized Nanomedicine, Institute of Neuro immune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Sneham Tiwari
- Center for Personalized Nanomedicine, Institute of Neuro immune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Arti Vashist
- Center for Personalized Nanomedicine, Institute of Neuro immune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Madhavan Nair
- Center for Personalized Nanomedicine, Institute of Neuro immune Pharmacology, Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
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49
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Pinotsi D, Grisanti L, Mahou P, Gebauer R, Kaminski CF, Hassanali A, Kaminski Schierle GS. Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures. J Am Chem Soc 2016; 138:3046-57. [PMID: 26824778 DOI: 10.1021/jacs.5b11012] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein structures which form fibrils have recently been shown to absorb light at energies in the near UV range and to exhibit a structure-specific fluorescence in the visible range even in the absence of aromatic amino acids. However, the molecular origin of this phenomenon has so far remained elusive. Here, we combine ab initio molecular dynamics simulations and fluorescence spectroscopy to demonstrate that these intrinsically fluorescent protein fibrils are permissive to proton transfer across hydrogen bonds which can lower electron excitation energies and thereby decrease the likelihood of energy dissipation associated with conventional hydrogen bonds. The importance of proton transfer on the intrinsic fluorescence observed in protein fibrils is signified by large reductions in the fluorescence intensity upon either fully protonating, or deprotonating, the fibrils at pH = 0 or 14, respectively. Thus, our results point to the existence of a structure-specific fluorophore that does not require the presence of aromatic residues or multiple bond conjugation that characterize conventional fluorescent systems. The phenomenon may have a wide range of implications in biological systems and in the design of self-assembled functional materials.
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Affiliation(s)
- Dorothea Pinotsi
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - Luca Grisanti
- International Centre for Theoretical Physics , Strada Costiera 11, Trieste 34151 Italy
| | - Pierre Mahou
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - Ralph Gebauer
- International Centre for Theoretical Physics , Strada Costiera 11, Trieste 34151 Italy
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Pembroke Street, Cambridge CB2 3RA, United Kingdom
| | - Ali Hassanali
- International Centre for Theoretical Physics , Strada Costiera 11, Trieste 34151 Italy
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Pembroke Street, Cambridge CB2 3RA, United Kingdom
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50
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Pinotsi D, Kaminski Schierle GS, Kaminski CF. Optical Super-Resolution Imaging of β-Amyloid Aggregation In Vitro and In Vivo: Method and Techniques. Methods Mol Biol 2016; 1303:125-141. [PMID: 26235063 DOI: 10.1007/978-1-4939-2627-5_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Super-resolution microscopy has emerged as a powerful and non-invasive tool for the study of molecular processes both in vitro and in live cells. In particular, super-resolution microscopy has proven valuable for research studies in protein aggregation. In this chapter we present details of recent advances in this method and the specific techniques, enabling the study of amyloid beta aggregation optically, both in vitro and in cells. First, we show that variants of optical super-resolution microscopy provide a capability to visualize oligomeric and fibrillar structures directly, providing detailed information on species morphology in vitro and even in situ, in the cellular environment. We focus on direct Stochastic Optical Reconstruction Microscopy, dSTORM, which provides morphological detail on spatial scales below 20 nm, and provide detailed protocols for its implementation in the context of amyloid beta research. Secondly, we present a range of optical techniques that offer super-resolution indirectly, which we call multi-parametric microscopy. The latter offers molecular scale information on self-assembly reactions via changes in protein or fluorophore spectral signatures. These techniques are empowered by our recent discovery that disease related amyloid proteins adopt intrinsic energy states upon fibrilisation. We show that fluorescence lifetime imaging provides a particularly sensitive readout to report on the aggregation state, which is robustly quantifiable for experiments performed either in vitro or in vivo.
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Affiliation(s)
- Dorothea Pinotsi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK,
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