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Dada ST, Toprakcioglu Z, Cali MP, Röntgen A, Hardenberg MC, Morris OM, Mrugalla LK, Knowles TPJ, Vendruscolo M. Pharmacological inhibition of α-synuclein aggregation within liquid condensates. Nat Commun 2024; 15:3835. [PMID: 38714700 PMCID: PMC11076612 DOI: 10.1038/s41467-024-47585-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/03/2024] [Indexed: 05/10/2024] Open
Abstract
Aggregated forms of α-synuclein constitute the major component of Lewy bodies, the proteinaceous aggregates characteristic of Parkinson's disease. Emerging evidence suggests that α-synuclein aggregation may occur within liquid condensates formed through phase separation. This mechanism of aggregation creates new challenges and opportunities for drug discovery for Parkinson's disease, which is otherwise still incurable. Here we show that the condensation-driven aggregation pathway of α-synuclein can be inhibited using small molecules. We report that the aminosterol claramine stabilizes α-synuclein condensates and inhibits α-synuclein aggregation within the condensates both in vitro and in a Caenorhabditis elegans model of Parkinson's disease. By using a chemical kinetics approach, we show that the mechanism of action of claramine is to inhibit primary nucleation within the condensates. These results illustrate a possible therapeutic route based on the inhibition of protein aggregation within condensates, a phenomenon likely to be relevant in other neurodegenerative disorders.
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Affiliation(s)
- Samuel T Dada
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Zenon Toprakcioglu
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Mariana P Cali
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alexander Röntgen
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Maarten C Hardenberg
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Owen M Morris
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Lena K Mrugalla
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK.
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2
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Romussi S, Giunti S, Andersen N, De Rosa MJ. C. elegans: a prominent platform for modeling and drug screening in neurological disorders. Expert Opin Drug Discov 2024; 19:565-585. [PMID: 38509691 DOI: 10.1080/17460441.2024.2329103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Human neurodevelopmental and neurodegenerative diseases (NDevDs and NDegDs, respectively) encompass a broad spectrum of disorders affecting the nervous system with an increasing incidence. In this context, the nematode C. elegans, has emerged as a benchmark model for biological research, especially in the field of neuroscience. AREAS COVERED The authors highlight the numerous advantages of this tiny worm as a model for exploring nervous system pathologies and as a platform for drug discovery. There is a particular focus given to describing the existing models of C. elegans for the study of NDevDs and NDegDs. Specifically, the authors underscore their strong applicability in preclinical drug development. Furthermore, they place particular emphasis on detailing the common techniques employed to explore the nervous system in both healthy and diseased states. EXPERT OPINION Drug discovery constitutes a long and expensive process. The incorporation of invertebrate models, such as C. elegans, stands as an exemplary strategy for mitigating costs and expediting timelines. The utilization of C. elegans as a platform to replicate nervous system pathologies and conduct high-throughput automated assays in the initial phases of drug discovery is pivotal for rendering therapeutic options more attainable and cost-effective.
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Affiliation(s)
- Stefano Romussi
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
| | - Sebastián Giunti
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Natalia Andersen
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - María José De Rosa
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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3
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Caldero-Escudero E, Romero-Sanz S, De la Fuente S. Using C. elegans as a model for neurodegenerative diseases: Methodology and evaluation. Methods Cell Biol 2024; 188:1-34. [PMID: 38880519 DOI: 10.1016/bs.mcb.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Caenorhabditis elegans is a nematode that has been used as an animal model for almost 50years. It has primitive and simple tissues and organs, making it an ideal model for studying neurological pathways involved in neurodegenerative diseases like Alzheimer's disease (AD) and Parkinson's disease (PD). C. elegans has conserved neurological pathways and is able to mimic human diseases, providing valuable insights into the human disease phenotype. This methodological review presents current approaches to generate neurodegenerative-like models of AD and PD in C. elegans, and evaluates the experiments commonly used to validate the diseases. These experimental approaches include assessing survival, fertility, mobility, electropharyngeogram assays, confocal mitochondrial imaging, RNA extraction for qRT-PCR or RT-PCR, and rate of defecation. This review also summarizes the current knowledge acquired on AD and PD using the aforementioned experimental approaches. Additionally, gaps in knowledge and future directions for research are also discussed in the review.
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4
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Baumanns S, Schmitt F, Spahn C, Ringelmann AE, Beis DM, Eckert GP, Wenzel U. Caprylic acid attenuates amyloid-β proteotoxicity by supplying energy via β-oxidation in an Alzheimer's disease model of the nematode Caenorhabditis elegans. Nutr Neurosci 2024; 27:252-261. [PMID: 36800228 DOI: 10.1080/1028415x.2023.2180870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Computer-based analysis of motility was used as a measure of amyloid-β (Aβ) proteotoxicity in the transgenic strain GMC101, expressing human Aβ1-42 in body wall muscle cells. Aβ-aggregation was quantified to relate the effects of caprylic acid (CA) to the amount of the proteotoxic protein. Gene knockdowns were induced through RNA-interference (RNAi). Moreover, the estimation of adenosine triphosphate (ATP) levels, the mitochondrial membrane potential (MMP) and oxygen consumption served the evaluation of mitochondrial function. CA improved the motility of GMC101 nematodes and reduced Aβ aggregation. Whereas RNAi for orthologues encoding key enzymes for α-lipoic acid and ketone bodies synthesis did not affect motility stimulation by CA, knockdown of orthologues involved in β-oxidation of fatty acids diminished its effects. The efficient energy gain by application of CA was finally proven by the increase of ATP levels in association with increased oxygen consumption and MMP. In conclusion, CA attenuates Aβ proteotoxicity by supplying energy via FAO. Since especially glucose oxidation is disturbed in Alzheimer´s disease, CA could potentially serve as an alternative energy fuel.
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Affiliation(s)
- Stefan Baumanns
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Fabian Schmitt
- Nutrition in Prevention and Therapy, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Christopher Spahn
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Anne E Ringelmann
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Daniel M Beis
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Gunter P Eckert
- Nutrition in Prevention and Therapy, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Uwe Wenzel
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Giessen, Germany
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5
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Lin Y, Lin C, Cao Y, Chen Y. Caenorhabditis elegans as an in vivo model for the identification of natural antioxidants with anti-aging actions. Biomed Pharmacother 2023; 167:115594. [PMID: 37776641 DOI: 10.1016/j.biopha.2023.115594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023] Open
Abstract
Natural antioxidants have recently emerged as a highly exciting and significant topic in anti-aging research. Diverse organism models present a viable protocol for future research. Notably, many breakthroughs on natural antioxidants have been achieved in the nematode Caenorhabditis elegans, an animal model frequently utilized for the study of aging research and anti-aging drugs in vivo. Due to the conservation of signaling pathways on oxidative stress resistance, lifespan regulation, and aging disease between C. elegans and multiple high-level organisms (humans), as well as the low and controllable cost of time and labor, it gradually develops into a trustworthy in vivo model for high-throughput screening and validation of natural antioxidants with anti-aging actions. First, information and models on free radicals and aging are presented in this review. We also describe indexes, detection methods, and molecular mechanisms for studying the in vivo antioxidant and anti-aging effects of natural antioxidants using C. elegans. It includes lifespan, physiological aging processes, oxidative stress levels, antioxidant enzyme activation, and anti-aging pathways. Furthermore, oxidative stress and healthspan improvement induced by natural antioxidants in humans and C. elegans are compared, to understand the potential and limitations of the screening model in preclinical studies. Finally, we emphasize that C. elegans is a useful model for exploring more natural antioxidant resources and uncovering the mechanisms underlying aging-related risk factors and diseases.
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Affiliation(s)
- Yugui Lin
- Microbiology Laboratory, Zhongshan Bo'ai Hospital, Southern Medical University, Zhongshan 528400, China; Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Chunxiu Lin
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China; State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Yunjiao Chen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China.
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6
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Alonso A, Kirkegaard JB. Fast detection of slender bodies in high density microscopy data. Commun Biol 2023; 6:754. [PMID: 37468539 PMCID: PMC10356847 DOI: 10.1038/s42003-023-05098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
Computer-aided analysis of biological microscopy data has seen a massive improvement with the utilization of general-purpose deep learning techniques. Yet, in microscopy studies of multi-organism systems, the problem of collision and overlap remains challenging. This is particularly true for systems composed of slender bodies such as swimming nematodes, swimming spermatozoa, or the beating of eukaryotic or prokaryotic flagella. Here, we develop a end-to-end deep learning approach to extract precise shape trajectories of generally motile and overlapping slender bodies. Our method works in low resolution settings where feature keypoints are hard to define and detect. Detection is fast and we demonstrate the ability to track thousands of overlapping organisms simultaneously. While our approach is agnostic to area of application, we present it in the setting of and exemplify its usability on dense experiments of swimming Caenorhabditis elegans. The model training is achieved purely on synthetic data, utilizing a physics-based model for nematode motility, and we demonstrate the model's ability to generalize from simulations to experimental videos.
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Affiliation(s)
- Albert Alonso
- Niels Bohr Institute & Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Julius B Kirkegaard
- Niels Bohr Institute & Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.
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7
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Baumanns S, Muehlemeyer F, Miesbauer LC, Baake J, Roloff EM, Beis DM, Wenzel U. 4-Phenylbutyric acid attenuates amyloid-β proteotoxicity through activation of HSF-1 in an Alzheimer's disease model of the nematode Caenorhabditiselegans. Biochem Biophys Res Commun 2023; 673:16-22. [PMID: 37354655 DOI: 10.1016/j.bbrc.2023.06.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder and the most common form of dementia. The pathogenesis is a complex process, in which the proteotoxicity of amyloid-β (Aβ) was identified as a major factor. 4-Phenylbutyric acid (4-PBA) is an aromatic short-chain fatty acid that may attenuate Aβ proteotoxicity through its already shown properties as a chemical chaperone or by inhibition of histone deacetylases (HDACs). In the present study, we investigated the molecular effects of 4-PBA on Aβ proteotoxicity using the nematode Caenorhabditis elegans as a model. Computer-based analysis of motility was used as a measure of Aβ proteotoxicity in the transgenic strain GMC101, expressing human Aβ1-42 in body wall muscle cells. Aβ aggregation was quantified using the fluorescent probe NIAD-4 to correlate the effects of 4-PBA on motility with the amount of the proteotoxic protein. Furthermore, these approaches were supplemented by gene regulation via RNA interference (RNAi) to identify molecular targets of 4-PBA. 4-PBA improved the motility of GMC101 nematodes and reduced Aβ aggregation significantly. Knockdown of hsf-1, encoding an ortholog essential for the cytosolic heat shock response, prevented the increase in motility and decrease in Aβ aggregation by 4-PBA incubation. RNAi for hda-1, encoding an ortholog of histone deacetylase 2, also increased motility. Double RNAi for hsf-1 and hda-1 revealed a dominant effect of hsf-1 RNAi. Moreover, 4-PBA failed to further increase motility under hda-1 RNAi. Accordingly, the results suggest that 4-PBA attenuates Aβ proteotoxicity in an AD-model of C. elegans through activation of HSF-1 via inhibition of HDA-1.
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Affiliation(s)
- Stefan Baumanns
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Felix Muehlemeyer
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Laura C Miesbauer
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Jonas Baake
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Eva M Roloff
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Daniel M Beis
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Uwe Wenzel
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany.
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8
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Wilson MR, Satapathy S, Vendruscolo M. Extracellular protein homeostasis in neurodegenerative diseases. Nat Rev Neurol 2023; 19:235-245. [PMID: 36828943 DOI: 10.1038/s41582-023-00786-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 02/26/2023]
Abstract
The protein homeostasis (proteostasis) system encompasses the cellular processes that regulate protein synthesis, folding, concentration, trafficking and degradation. In the case of intracellular proteostasis, the identity and nature of these processes have been extensively studied and are relatively well known. By contrast, the mechanisms of extracellular proteostasis are yet to be fully elucidated, although evidence is accumulating that their age-related progressive impairment might contribute to neuronal death in neurodegenerative diseases. Constitutively secreted extracellular chaperones are emerging as key players in processes that operate to protect neurons and other brain cells by neutralizing the toxicity of extracellular protein aggregates and promoting their safe clearance and disposal. Growing evidence indicates that these extracellular chaperones exert multiple effects to promote cell viability and protect neurons against pathologies arising from the misfolding and aggregation of proteins in the synaptic space and interstitial fluid. In this Review, we outline the current knowledge of the mechanisms of extracellular proteostasis linked to neurodegenerative diseases, and we examine the latest understanding of key molecules and processes that protect the brain from the pathological consequences of extracellular protein aggregation and proteotoxicity. Finally, we contemplate possible therapeutic opportunities for neurodegenerative diseases on the basis of this emerging knowledge.
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Affiliation(s)
- Mark R Wilson
- School of Chemistry and Molecular Bioscience, Molecular Horizons Research Institute, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Sandeep Satapathy
- Blavatnik Institute of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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9
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Joshi P, Chia S, Yang X, Perni M, Gabriel JM, Gilmer M, Limbocker R, Habchi J, Vendruscolo M. Combinations of Vitamin A and Vitamin E Metabolites Confer Resilience against Amyloid-β Aggregation. ACS Chem Neurosci 2023; 14:657-666. [PMID: 36728544 PMCID: PMC9936541 DOI: 10.1021/acschemneuro.2c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease is characterized by the presence in the brain of amyloid plaques formed by the aberrant deposition of the amyloid-β peptide (Aβ). Since many vitamins are dysregulated in this disease, we explored whether these molecules contribute to the protein homeostasis system by modulating Aβ aggregation. By screening 18 fat-soluble and water-soluble vitamin metabolites, we found that retinoic acid and α-tocopherol, two metabolites of vitamin A and vitamin E, respectively, affect Aβ aggregation both in vitro and in a Caenorhabditis elegans model of Aβ toxicity. We then show that the effects of these two vitamin metabolites in specific combinations cancel each other out, consistent with the "resilience in complexity" hypothesis, according to which the complex composition of the cellular environment could have an overall protective role against protein aggregation through the simultaneous presence of aggregation promoters and inhibitors. Taken together, these results indicate that vitamins can be added to the list of components of the protein homeostasis system that regulate protein aggregation.
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Affiliation(s)
- Priyanka Joshi
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.,The
California Institute for Quantitative Biosciences, Department of Nutritional
Sciences and Toxicology, University of California, Berkeley, California 94720, United States,
| | - Sean Chia
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Xiaoting Yang
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Michele Perni
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Justus M. Gabriel
- Department
of Chemistry and Life Science, United States
Military Academy, West Point, New York 10996, United States
| | - Marshall Gilmer
- Department
of Chemistry and Life Science, United States
Military Academy, West Point, New York 10996, United States
| | - Ryan Limbocker
- Department
of Chemistry and Life Science, United States
Military Academy, West Point, New York 10996, United States
| | - Johnny Habchi
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.,
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10
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Baumanns S, Beis DM, Wenzel U. RNA-interference in the nematode Caenorhabditis elegans is effective using paraformaldehyde-inactivated E. coli HT115 bacteria as a food source. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119375. [PMID: 36208773 DOI: 10.1016/j.bbamcr.2022.119375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022]
Abstract
The nematode Caenorhabditis elegans is a widely used research model for the investigation of metabolism, aging and age-associated diseases. However, when investigating the impact of natural compounds or drugs on those topics, a major confounder is the metabolism of these test substances by live E. coli bacteria, the standard food source of C. elegans. Using paraformaldehyde instead of heat to inactivate E. coli, which allows for high-throughput technologies and better food availability, it is shown here that RNA-interference works equally well, thus demonstrating the absence of considerable interfering modifications of paraformaldehyde with nucleic acids.
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Affiliation(s)
- Stefan Baumanns
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Daniel M Beis
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Uwe Wenzel
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.
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11
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Žofka M, Thuy Nguyen L, Mašátová E, Matoušková P. Image recognition based on deep learning in Haemonchus contortus motility assays. Comput Struct Biotechnol J 2022; 20:2372-2380. [PMID: 35664223 PMCID: PMC9127531 DOI: 10.1016/j.csbj.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/22/2022] [Accepted: 05/08/2022] [Indexed: 11/04/2022] Open
Abstract
Poor efficacy of some anthelmintics and rising concerns about the widespread drug resistance have highlighted the need for new drug discovery. The parasitic nematode Haemonchus contortus is an important model organism widely used for studies of drug resistance and drug screening with the current gold standard being the motility assay. We applied a deep learning approach Mask R-CNN for analysing motility videos containing varying rates of motile worms and compared it to other commonly used algorithms with different levels of complexity, namely the Wiggle Index and the Wide Field-of-View Nematode Tracking Platform. Mask R-CNN consistently outperformed the other algorithms in terms of the detection of worms as well as the precision of motility forecasts, having a mean absolute percentage error of 7.6% and a mean absolute error of 5.6% for the detection and motility forecasts, respectively. Using Mask R-CNN for motility assays confirmed the common problem with algorithms that use non-maximum suppression in detecting overlapping objects, which negatively impacts the overall precision. The use of intersect over union as a measure of the classification of motile / non-motile instances had an overall accuracy of 89%, indicating that it is a viable alternative to previously used methods based on movement characteristics, such as body bends. In comparison to the existing methods evaluated here, Mask R-CNN performed better and we anticipate that this method will broaden the number of possible approaches to video analysis of worm motility.
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12
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Bates K, Le KN, Lu H. Deep learning for robust and flexible tracking in behavioral studies for C. elegans. PLoS Comput Biol 2022; 18:e1009942. [PMID: 35395006 PMCID: PMC9020731 DOI: 10.1371/journal.pcbi.1009942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 04/20/2022] [Accepted: 02/21/2022] [Indexed: 12/02/2022] Open
Abstract
Robust and accurate behavioral tracking is essential for ethological studies. Common methods for tracking and extracting behavior rely on user adjusted heuristics that can significantly vary across different individuals, environments, and experimental conditions. As a result, they are difficult to implement in large-scale behavioral studies with complex, heterogenous environmental conditions. Recently developed deep-learning methods for object recognition such as Faster R-CNN have advantages in their speed, accuracy, and robustness. Here, we show that Faster R-CNN can be employed for identification and detection of Caenorhabditis elegans in a variety of life stages in complex environments. We applied the algorithm to track animal speeds during development, fecundity rates and spatial distribution in reproductive adults, and behavioral decline in aging populations. By doing so, we demonstrate the flexibility, speed, and scalability of Faster R-CNN across a variety of experimental conditions, illustrating its generalized use for future large-scale behavioral studies.
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Affiliation(s)
- Kathleen Bates
- Interdisciplinary Program in Bioengineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Kim N. Le
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Hang Lu
- Interdisciplinary Program in Bioengineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
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13
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Modeling Alzheimer's Disease in Caenorhabditis elegans. Biomedicines 2022; 10:biomedicines10020288. [PMID: 35203497 PMCID: PMC8869312 DOI: 10.3390/biomedicines10020288] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Alzheimer’s disease (AD) is the most frequent cause of dementia. After decades of research, we know the importance of the accumulation of protein aggregates such as β-amyloid peptide and phosphorylated tau. We also know that mutations in certain proteins generate early-onset Alzheimer’s disease (EOAD), and many other genes modulate the disease in its sporadic form. However, the precise molecular mechanisms underlying AD pathology are still unclear. Because of ethical limitations, we need to use animal models to investigate these processes. The nematode Caenorhabditis elegans has received considerable attention in the last 25 years, since the first AD models overexpressing Aβ peptide were described. We review here the main results obtained using this model to study AD. We include works studying the basic molecular mechanisms of the disease, as well as those searching for new therapeutic targets. Although this model also has important limitations, the ability of this nematode to generate knock-out or overexpression models of any gene, single or combined, and to carry out toxicity, recovery or survival studies in short timeframes with many individuals and at low cost is difficult to overcome. We can predict that its use as a model for various diseases will certainly continue to increase.
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14
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Runfola M, Perni M, Yang X, Marchese M, Bacci A, Mero S, Santorelli FM, Polini B, Chiellini G, Giuliani D, Vilella A, Bodria M, Daini E, Vandini E, Rudge S, Gul S, Wakelam MOJ, Vendruscolo M, Rapposelli S. Identification of a Thyroid Hormone Derivative as a Pleiotropic Agent for the Treatment of Alzheimer's Disease. Pharmaceuticals (Basel) 2021; 14:1330. [PMID: 34959730 PMCID: PMC8704018 DOI: 10.3390/ph14121330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023] Open
Abstract
The identification of effective pharmacological tools for Alzheimer's disease (AD) represents one of the main challenges for therapeutic discovery. Due to the variety of pathological processes associated with AD, a promising route for pharmacological intervention involves the development of new chemical entities that can restore cellular homeostasis. To investigate this strategy, we designed and synthetized SG2, a compound related to the thyroid hormone thyroxine, that shares a pleiotropic activity with its endogenous parent compound, including autophagic flux promotion, neuroprotection, and metabolic reprogramming. We demonstrate herein that SG2 acts in a pleiotropic manner to induce recovery in a C. elegans model of AD based on the overexpression of Aβ42 and improves learning abilities in the 5XFAD mouse model of AD. Further, in vitro ADME-Tox profiling and toxicological studies in zebrafish confirmed the low toxicity of this compound, which represents a chemical starting point for AD drug development.
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Affiliation(s)
- Massimiliano Runfola
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (M.R.); (A.B.)
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; (M.P.); (X.Y.)
| | - Xiaoting Yang
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; (M.P.); (X.Y.)
| | - Maria Marchese
- Molecular Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Stella Maris, Via dei Giacinti 2, 56128 Calambrone, Italy; (M.M.); (S.M.); (F.M.S.)
| | - Andrea Bacci
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (M.R.); (A.B.)
| | - Serena Mero
- Molecular Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Stella Maris, Via dei Giacinti 2, 56128 Calambrone, Italy; (M.M.); (S.M.); (F.M.S.)
| | - Filippo M. Santorelli
- Molecular Medicine, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Stella Maris, Via dei Giacinti 2, 56128 Calambrone, Italy; (M.M.); (S.M.); (F.M.S.)
| | - Beatrice Polini
- Department of Pathology, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (B.P.); (G.C.)
| | - Grazia Chiellini
- Department of Pathology, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (B.P.); (G.C.)
| | - Daniela Giuliani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (D.G.); (A.V.); (M.B.); (E.D.); (E.V.)
| | - Antonietta Vilella
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (D.G.); (A.V.); (M.B.); (E.D.); (E.V.)
| | - Martina Bodria
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (D.G.); (A.V.); (M.B.); (E.D.); (E.V.)
| | - Eleonora Daini
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (D.G.); (A.V.); (M.B.); (E.D.); (E.V.)
| | - Eleonora Vandini
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy; (D.G.); (A.V.); (M.B.); (E.D.); (E.V.)
| | - Simon Rudge
- Ibabraham Research Campus, The Babraham Institute, Cambridge CB22 3AT, UK; (S.R.); (M.O.J.W.)
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany;
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hamburg Site, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Michale O. J. Wakelam
- Ibabraham Research Campus, The Babraham Institute, Cambridge CB22 3AT, UK; (S.R.); (M.O.J.W.)
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; (M.P.); (X.Y.)
| | - Simona Rapposelli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; (M.R.); (A.B.)
- CISUP, Center for Instrument Sharing, University of Pisa, 56126 Pisa, Italy
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15
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Limbocker R, Errico S, Barbut D, Knowles TPJ, Vendruscolo M, Chiti F, Zasloff M. Squalamine and trodusquemine: two natural products for neurodegenerative diseases, from physical chemistry to the clinic. Nat Prod Rep 2021; 39:742-753. [PMID: 34698757 DOI: 10.1039/d1np00042j] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 1993 to 2021 (mainly 2017-2021)Alzheimer's and Parkinson's diseases are neurodegenerative conditions affecting over 50 million people worldwide. Since these disorders are still largely intractable pharmacologically, discovering effective treatments is of great urgency and importance. These conditions are characteristically associated with the aberrant deposition of proteinaceous aggregates in the brain, and with the formation of metastable intermediates known as protein misfolded oligomers that play a central role in their aetiology. In this Highlight article, we review the evidence at the physicochemical, cellular, animal model and clinical levels on how the natural products squalamine and trodusquemine offer promising opportunities for chronic treatments for these progressive conditions by preventing both the formation of neurotoxic oligomers and their interaction with cell membranes.
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Affiliation(s)
- Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York 10996, USA
| | - Silvia Errico
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy. .,Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Denise Barbut
- Enterin Inc., 3624 Market Street, Philadelphia, Pennsylvania 19104, USA
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy.
| | - Michael Zasloff
- Enterin Inc., 3624 Market Street, Philadelphia, Pennsylvania 19104, USA.,MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC 20010, USA.
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16
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Koopman M, Janssen L, Nollen EAA. An economical and highly adaptable optogenetics system for individual and population-level manipulation of Caenorhabditis elegans. BMC Biol 2021; 19:170. [PMID: 34429103 PMCID: PMC8386059 DOI: 10.1186/s12915-021-01085-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Optogenetics allows the experimental manipulation of excitable cells by a light stimulus without the need for technically challenging and invasive procedures. The high degree of spatial, temporal, and intensity control that can be achieved with a light stimulus, combined with cell type-specific expression of light-sensitive ion channels, enables highly specific and precise stimulation of excitable cells. Optogenetic tools have therefore revolutionized the study of neuronal circuits in a number of models, including Caenorhabditis elegans. Despite the existence of several optogenetic systems that allow spatial and temporal photoactivation of light-sensitive actuators in C. elegans, their high costs and low flexibility have limited wide access to optogenetics. Here, we developed an inexpensive, easy-to-build, modular, and adjustable optogenetics device for use on different microscopes and worm trackers, which we called the OptoArm. Results The OptoArm allows for single- and multiple-worm illumination and is adaptable in terms of light intensity, lighting profiles, and light color. We demonstrate OptoArm’s power in a population-based multi-parameter study on the contributions of motor circuit cells to age-related motility decline. We found that individual components of the neuromuscular system display different rates of age-dependent deterioration. The functional decline of cholinergic neurons mirrors motor decline, while GABAergic neurons and muscle cells are relatively age-resilient, suggesting that rate-limiting cells exist and determine neuronal circuit ageing. Conclusion We have assembled an economical, reliable, and highly adaptable optogenetics system which can be deployed to address diverse biological questions. We provide a detailed description of the construction as well as technical and biological validation of our set-up. Importantly, use of the OptoArm is not limited to C. elegans and may benefit studies in multiple model organisms, making optogenetics more accessible to the broader research community. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01085-2.
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Affiliation(s)
- M Koopman
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - L Janssen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - E A A Nollen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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17
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Nowicka U, Chroscicki P, Stroobants K, Sladowska M, Turek M, Uszczynska-Ratajczak B, Kundra R, Goral T, Perni M, Dobson CM, Vendruscolo M, Chacinska A. Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins. eLife 2021; 10:65484. [PMID: 34292154 PMCID: PMC8457837 DOI: 10.7554/elife.65484] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are organelles with their own genomes, but they rely on the import of nuclear-encoded proteins that are translated by cytosolic ribosomes. Therefore, it is important to understand whether failures in the mitochondrial uptake of these nuclear-encoded proteins can cause proteotoxic stress and identify response mechanisms that may counteract it. Here, we report that upon impairments in mitochondrial protein import, high-risk precursor and immature forms of mitochondrial proteins form aberrant deposits in the cytosol. These deposits then cause further cytosolic accumulation and consequently aggregation of other mitochondrial proteins and disease-related proteins, including α-synuclein and amyloid β. This aggregation triggers a cytosolic protein homeostasis imbalance that is accompanied by specific molecular chaperone responses at both the transcriptomic and protein levels. Altogether, our results provide evidence that mitochondrial dysfunction, specifically protein import defects, contributes to impairments in protein homeostasis, thus revealing a possible molecular mechanism by which mitochondria are involved in neurodegenerative diseases.
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Affiliation(s)
- Urszula Nowicka
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Piotr Chroscicki
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Karen Stroobants
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maria Sladowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michal Turek
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Rishika Kundra
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tomasz Goral
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michele Perni
- Chemistry, University of Cambridge, Cambridge, United Kingdom
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18
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Perni M, Mannini B, Xu CK, Kumita JR, Dobson CM, Chiti F, Vendruscolo M. Exogenous misfolded protein oligomers can cross the intestinal barrier and cause a disease phenotype in C. elegans. Sci Rep 2021; 11:14391. [PMID: 34257326 PMCID: PMC8277765 DOI: 10.1038/s41598-021-93527-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Misfolded protein oligomers are increasingly recognized as highly cytotoxic agents in a wide range of human disorders associated with protein aggregation. In this study, we assessed the possible uptake and resulting toxic effects of model protein oligomers administered to C. elegans through the culture medium. We used an automated machine-vision, high-throughput screening procedure to monitor the phenotypic changes in the worms, in combination with confocal microscopy to monitor the diffusion of the oligomers, and oxidative stress assays to detect their toxic effects. Our results suggest that the oligomers can diffuse from the intestinal lumen to other tissues, resulting in a disease phenotype. We also observed that pre-incubation of the oligomers with a molecular chaperone (αB-crystallin) or a small molecule inhibitor of protein aggregation (squalamine), reduced the oligomer absorption. These results indicate that exogenous misfolded protein oligomers can be taken up by the worms from their environment and spread across tissues, giving rise to pathological effects in regions distant from their place of absorbance.
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Affiliation(s)
- Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Janet R Kumita
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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19
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Joshi P, Perni M, Limbocker R, Mannini B, Casford S, Chia S, Habchi J, Labbadia J, Dobson CM, Vendruscolo M. Two human metabolites rescue a C. elegans model of Alzheimer's disease via a cytosolic unfolded protein response. Commun Biol 2021; 4:843. [PMID: 34234268 PMCID: PMC8263720 DOI: 10.1038/s42003-021-02218-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
Age-related changes in cellular metabolism can affect brain homeostasis, creating conditions that are permissive to the onset and progression of neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Although the roles of metabolites have been extensively studied with regard to cellular signaling pathways, their effects on protein aggregation remain relatively unexplored. By computationally analysing the Human Metabolome Database, we identified two endogenous metabolites, carnosine and kynurenic acid, that inhibit the aggregation of the amyloid beta peptide (Aβ) and rescue a C. elegans model of Alzheimer's disease. We found that these metabolites act by triggering a cytosolic unfolded protein response through the transcription factor HSF-1 and downstream chaperones HSP40/J-proteins DNJ-12 and DNJ-19. These results help rationalise previous observations regarding the possible anti-ageing benefits of these metabolites by providing a mechanism for their action. Taken together, our findings provide a link between metabolite homeostasis and protein homeostasis, which could inspire preventative interventions against neurodegenerative disorders.
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Affiliation(s)
- Priyanka Joshi
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK ,grid.47840.3f0000 0001 2181 7878Present Address: The California Institute for Quantitative Biosciences (QB3-Berkeley), University of California, Berkeley, CA USA
| | - Michele Perni
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Ryan Limbocker
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK ,grid.419884.80000 0001 2287 2270Present Address: Department of Chemistry and Life Science, United States Military Academy, West Point, NY USA
| | - Benedetta Mannini
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Sam Casford
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Sean Chia
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Johnny Habchi
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Johnathan Labbadia
- grid.83440.3b0000000121901201Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Christopher M. Dobson
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- grid.5335.00000000121885934Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
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20
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Giunti S, Andersen N, Rayes D, De Rosa MJ. Drug discovery: Insights from the invertebrate Caenorhabditis elegans. Pharmacol Res Perspect 2021; 9:e00721. [PMID: 33641258 PMCID: PMC7916527 DOI: 10.1002/prp2.721] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
Therapeutic drug development is a long, expensive, and complex process that usually takes 12-15 years. In the early phases of drug discovery, in particular, there is a growing need for animal models that ensure the reduction in both cost and time. Caenorhabditis elegans has been traditionally used to address fundamental aspects of key biological processes, such as apoptosis, aging, and gene expression regulation. During the last decade, with the advent of large-scale platforms for screenings, this invertebrate has also emerged as an essential tool in the pharmaceutical research industry to identify novel drugs and drug targets. In this review, we discuss the reasons why C. elegans has been positioned as an outstanding cost-effective option for drug discovery, highlighting both the advantages and drawbacks of this model. Particular attention is paid to the suitability of this nematode in large-scale genetic and pharmacological screenings. High-throughput screenings in C. elegans have indeed contributed to the breakthrough of a wide variety of candidate compounds involved in extensive fields including neurodegeneration, pathogen infections and metabolic disorders. The versatility of this nematode, which enables its instrumentation as a model of human diseases, is another attribute also herein underscored. As illustrative examples, we discuss the utility of C. elegans models of both human neurodegenerative diseases and parasitic nematodes in the drug discovery industry. Summing up, this review aims to demonstrate the impact of C. elegans models on the drug discovery pipeline.
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Affiliation(s)
- Sebastián Giunti
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Natalia Andersen
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - Diego Rayes
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
| | - María José De Rosa
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS‐CONICETBahía BlancaArgentina
- Dpto de Biología, Bioquímica y FarmaciaUniversidad Nacional del SurBahía BlancaArgentina
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21
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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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22
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Nakano Y, Moriuchi M, Fukushima Y, Hayashi K, Suico MA, Kai H, Koutaki G, Shuto T. Intrapopulation analysis of longitudinal lifespan in Caenorhabditis elegans identifies W09D10.4 as a novel AMPK-associated healthspan shortening factor. J Pharmacol Sci 2020; 145:241-252. [PMID: 33602504 DOI: 10.1016/j.jphs.2020.12.004] [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: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 11/27/2022] Open
Abstract
Caenorhabditis elegans is a model organism widely used for longevity studies. Current advances have been made in the methods that allow automated monitoring of C. elegans behavior. However, ordinary manual assays as well as automated methods have yet to achieve qualitative whole-life analysis of C. elegans longevity based on intrapopulation variation. Here, we utilized live-cell analysis system to determine the parameters of nematode lifespans. Image-based superposition method enabled to determine not only frailty in worms, but also to measure individual and longitudinal lifespan, healthspan, and frailspan. Notably, k-means clustering via principal component analysis revealed four clusters with distinct longevity patterns in wild-type C. elegans. Physiological relevance of clustering was confirmed by assays with pharmacological and/or genetic manipulation of AMP-activated protein kinase (AMPK), a crucial regulator of healthspan. Finally, we focused on W09D10.4 among the possible regulators extracted by integrative expression analysis with existing data sets. Importantly, W09D10.4 knockdown increased the high-healthspan populations only in the presence of AMPK, suggesting that W09D10.4 is a novel AMPK-associated healthspan shortening factor in C. elegans. Overall, the study establishes a novel platform of longitudinal lifespan in C. elegans, which is user-friendly, and may be a useful pharmacological tool to identify healthspan modulatory factors.
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Affiliation(s)
- Yoshio Nakano
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Masataka Moriuchi
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yutaro Fukushima
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Kyotaro Hayashi
- Department of Electrical and Computer Engineering, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Mary Ann Suico
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Go Koutaki
- Department of Electrical and Computer Engineering, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
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23
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Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, Vendruscolo M. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. SCIENCE ADVANCES 2020; 6:6/45/eabb5924. [PMID: 33148639 PMCID: PMC7673680 DOI: 10.1126/sciadv.abb5924] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/22/2020] [Indexed: 05/15/2023]
Abstract
Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes.
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Affiliation(s)
- Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco Simone Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Thomas Löhr
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry. CNRS UMR 3528, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
- Department of Pharmacy, University of Naples "Federico II," 80131 Naples, Italy
| | - Isabella C Felli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - 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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24
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Ikenoue T, Aprile FA, Sormanni P, Ruggeri FS, Perni M, Heller GT, Haas CP, Middel C, Limbocker R, Mannini B, Michaels TCT, Knowles TPJ, Dobson CM, Vendruscolo M. A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer's disease. Sci Rep 2020; 10:15280. [PMID: 32943652 PMCID: PMC7498612 DOI: 10.1038/s41598-020-69626-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31–42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer’s disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.
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Affiliation(s)
- Tatsuya Ikenoue
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Francesco S Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christian P Haas
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christoph Middel
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - 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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25
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Dilberger B, Baumanns S, Spieth ST, Wenzel U, Eckert GP. Infertility induced by auxin in PX627 Caenorhabditis elegans does not affect mitochondrial functions and aging parameters. Aging (Albany NY) 2020; 12:12268-12284. [PMID: 32516128 PMCID: PMC7343439 DOI: 10.18632/aging.103413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/01/2020] [Indexed: 12/17/2022]
Abstract
Caenorhabditis elegans is widely used for aging studies. 5-Fluoro-2´-deoxyuridine (FUdR) is commonly used to control offspring. While larvae are stopped from further development, also mitochondrial DNA and function may be affected. Since mitochondria and longevity are closely related, the use of FUdR may falsify possible studies. PX627, an auxin inducible infertility strain to control offspring, allows mitochondrial investigations during senescence without FUdR toxicity.Longevity and health parameters were assessed in 2- and 10-day old nematodes wild-type N2 and PX627 treated with FUdR or auxin, respectively. Mitochondrial membrane potential, energetic metabolites and reactive oxygen species levels, were determined. mRNA expression levels of key genes involved were quantified using quantitative real-time PCR.FUdR significantly increased lifespan and health parameters, as well as, mitochondrial function compared to untreated controls and auxin treated PX627. Although a decrease in all parameters could be observed in aged nematodes, this was less severe after FUdR exposure. Glycolysis was significantly up-regulated in aged PX627 compared to N2. Expression levels of daf-16, sir-2.1, aak-2, skn-1, atp-2 and atfs-1 were regulated accordingly.Hence, auxin in PX627 might be a good alternative to control progeny, for mitochondrial- and longevity-related investigations in nematodes.
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Affiliation(s)
- Benjamin Dilberger
- Institute of Nutritional Sciences, Laboratory for Nutrition in Prevention and Therapy, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, Giessen 35392, Germany
| | - Stefan Baumanns
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Salome T Spieth
- Institute of Nutritional Sciences, Laboratory for Nutrition in Prevention and Therapy, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, Giessen 35392, Germany
| | - Uwe Wenzel
- Molecular Nutrition Research, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Gunter P Eckert
- Institute of Nutritional Sciences, Laboratory for Nutrition in Prevention and Therapy, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, Giessen 35392, Germany
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26
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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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27
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Assessing motor-related phenotypes of Caenorhabditis elegans with the wide field-of-view nematode tracking platform. Nat Protoc 2020; 15:2071-2106. [PMID: 32433626 DOI: 10.1038/s41596-020-0321-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/16/2020] [Indexed: 01/23/2023]
Abstract
Caenorhabditis elegans is a valuable model organism in biomedical research that has led to major discoveries in the fields of neurodegeneration, cancer and aging. Because movement phenotypes are commonly used and represent strong indicators of C. elegans fitness, there is an increasing need to replace manual assessments of worm motility with automated measurements to increase throughput and minimize observer biases. Here, we provide a protocol for the implementation of the improved wide field-of-view nematode tracking platform (WF-NTP), which enables the simultaneous analysis of hundreds of worms with respect to multiple behavioral parameters. The protocol takes only a few hours to complete, excluding the time spent culturing C. elegans, and includes (i) experimental design and preparation of samples, (ii) data recording, (iii) software management with appropriate parameter choices and (iv) post-experimental data analysis. We compare the WF-NTP with other existing worm trackers, including those having high spatial resolution. The main benefits of WF-NTP relate to the high number of worms that can be assessed at the same time on a whole-plate basis and the number of phenotypes that can be screened for simultaneously.
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28
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Alvarez J, Alvarez-Illera P, García-Casas P, Fonteriz RI, Montero M. The Role of Ca 2+ Signaling in Aging and Neurodegeneration: Insights from Caenorhabditis elegans Models. Cells 2020; 9:cells9010204. [PMID: 31947609 PMCID: PMC7016793 DOI: 10.3390/cells9010204] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Ca2+ is a ubiquitous second messenger that plays an essential role in physiological processes such as muscle contraction, neuronal secretion, and cell proliferation or differentiation. There is ample evidence that the dysregulation of Ca2+ signaling is one of the key events in the development of neurodegenerative processes, an idea called the "calcium hypothesis" of neurodegeneration. Caenorhabditis elegans (C. elegans) is a very good model for the study of aging and neurodegeneration. In fact, many of the signaling pathways involved in longevity were first discovered in this nematode, and many models of neurodegenerative diseases have also been developed therein, either through mutations in the worm genome or by expressing human proteins involved in neurodegeneration (β-amyloid, α-synuclein, polyglutamine, or others) in defined worm tissues. The worm is completely transparent throughout its whole life, which makes it possible to carry out Ca2+ dynamics studies in vivo at any time, by expressing Ca2+ fluorescent probes in defined worm tissues, and even in specific organelles such as mitochondria. This review will summarize the evidence obtained using this model organism to understand the role of Ca2+ signaling in aging and neurodegeneration.
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29
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Felker DP, Robbins CE, McCormick MA. Automation of C. elegans lifespan measurement. TRANSLATIONAL MEDICINE OF AGING 2020. [DOI: 10.1016/j.tma.2019.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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30
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Delivoria DC, Chia S, Habchi J, Perni M, Matis I, Papaevgeniou N, Reczko M, Chondrogianni N, Dobson CM, Vendruscolo M, Skretas G. Bacterial production and direct functional screening of expanded molecular libraries for discovering inhibitors of protein aggregation. SCIENCE ADVANCES 2019; 5:eaax5108. [PMID: 31663025 PMCID: PMC6795521 DOI: 10.1126/sciadv.aax5108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/25/2019] [Indexed: 05/17/2023]
Abstract
Protein misfolding and aggregation are associated with a many human disorders, including Alzheimer's and Parkinson's diseases. Toward increasing the effectiveness of early-stage drug discovery for these conditions, we report a bacterial platform that enables the biosynthesis of molecular libraries with expanded diversities and their direct functional screening for discovering protein aggregation inhibitors. We illustrate this approach by performing, what is to our knowledge, the largest functional screen of small-size molecular entities described to date. We generated a combinatorial library of ~200 million drug-like, cyclic peptides and rapidly screened it for aggregation inhibitors against the amyloid-β peptide (Aβ42), linked to Alzheimer's disease. Through this procedure, we identified more than 400 macrocyclic compounds that efficiently reduce Aβ42 aggregation and toxicity in vitro and in vivo. Finally, we applied a combination of deep sequencing and mutagenesis analyses to demonstrate how this system can rapidly determine structure-activity relationships and define consensus motifs required for bioactivity.
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Affiliation(s)
- Dafni C. Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Ilias Matis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Nikoletta Papaevgeniou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Faculty of Biology and Pharmacy, Institute of Nutrition, Friedrich Schiller University of Jena, Jena 07743, Germany
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center “Alexander Fleming,” Athens 16672, Greece
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - 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
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Corresponding author.
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31
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Yang WH, Chen CY, Wang KL, Kwok HL, Stern A, Lo SJ, Yang HC. Reflex and habituation behavior of Caenorhabditis elegans assessed by a mechanical vibration system and image analysis. J Neurosci Methods 2019; 328:108415. [PMID: 31470028 DOI: 10.1016/j.jneumeth.2019.108415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 08/26/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND The nematode Caenorhabditis elegans is an emerging invertebrate animal model for investigating neuronal functions in behavioral assays. C. elegans mechanosensation was characterized by the use of a constant mechanical stimulation transmitter followed by quantitative imaging. NEW METHOD C. elegans reflex and habituation behaviors were characterized by mechanical vibration followed by image analysis. A custom-designed system consists of an aluminum alloy Petri dish holder frame coupled with a mechanical vibration buzzer delivering adjustable pulsed vibration to an agar plate. The basal and evoked movements of C. elegans were recorded by a microscopic digital camera followed by quantitative analysis using microscopic imaging software. RESULTS Application of the platform in C. elegans was demonstrated with three proof-of-concept experiments: (1) Evaluation of the reflex response stimulated by tapping and mechanical vibration with a mechano-sensation defective mutant. (2) Comparison of the reflex response stimulated by mechanical vibration between wild type and aging mutants. (3) Assessment of the efficacy of the mechanical vibration system on long-term memory for habituation. COMPARISON WITH EXISTING METHODS Conventional C. elegans mechanosensation techniques depend on stimulation either by manually touching a single animal or tapping the Petri dish followed by scoring via visual observation from the examiner. The mechanical vibration method has greater capacity compared to conventional methods which are labor-intensive, have low throughput and lack quantifiable parameters. CONCLUSIONS The mechanical vibration system followed by image analysis is a convenient and integrated platform for investigatingC. elegans reflex and habituation in aging and neural behavioral assays.
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Affiliation(s)
- Wan-Hua Yang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu, Taiwan; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Hsinchu Branch, Hsinchu, Taiwan
| | - Chia-Yi Chen
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | | | - Hong Luen Kwok
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Arnold Stern
- New York University School of Medicine, New York, USA
| | - Szecheng J Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hung-Chi Yang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu, Taiwan.
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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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Cascella R, Perni M, Chen SW, Fusco G, Cecchi C, Vendruscolo M, Chiti F, Dobson CM, De Simone A. Probing the Origin of the Toxicity of Oligomeric Aggregates of α-Synuclein with Antibodies. ACS Chem Biol 2019; 14:1352-1362. [PMID: 31050886 PMCID: PMC7007184 DOI: 10.1021/acschembio.9b00312] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
The
aggregation of α-synuclein, a protein involved in neurotransmitter
release at presynaptic terminals, is associated with a range of highly
debilitating neurodegenerative conditions, most notably Parkinson’s
disease. Intraneuronal inclusion bodies, primarily composed of α-synuclein
fibrils, are the major histopathological hallmarks of these disorders,
although small oligomeric assemblies are believed to play a crucial
role in neuronal impairment. We have probed the mechanism of neurotoxicity
of α-synuclein oligomers isolated in vitro using
antibodies targeting the N-terminal region of the protein and found
that the presence of the antibody resulted in a substantial reduction
of the damage induced by the aggregates when incubated with primary
cortical neurons and neuroblastoma cells. We observed a similar behavior in vivo using a strain of C. elegans overexpressing
α-synuclein, where the aggregation process itself is also partially
inhibited as a result of incubation with the antibodies. The similar
effects of the antibodies in reducing the toxicity of the aggregated
species formed in vitro and in vivo provide evidence for a common origin of cellular impairment induced
by α-synuclein aggregates.
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Affiliation(s)
- Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Serene W. Chen
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Giuliana Fusco
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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34
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Patel DS, Xu N, Lu H. Digging deeper: methodologies for high-content phenotyping in Caenorhabditis elegans. Lab Anim (NY) 2019; 48:207-216. [PMID: 31217565 DOI: 10.1038/s41684-019-0326-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/17/2019] [Indexed: 11/09/2022]
Abstract
Deep phenotyping is an emerging conceptual paradigm and experimental approach aimed at measuring and linking many aspects of a phenotype to understand its underlying biology. To date, deep phenotyping has been applied mostly in cultured cells and used less in multicellular organisms. However, in the past decade, it has increasingly been recognized that deep phenotyping could lead to a better understanding of how genetics, environment and stochasticity affect the development, physiology and behavior of an organism. The nematode Caenorhabditis elegans is an invaluable model system for studying how genes affect a phenotypic trait, and new technologies have taken advantage of the worm's physical attributes to increase the throughput and informational content of experiments. Coupling of these technical advancements with computational and analytical tools has enabled a boom in deep-phenotyping studies of C. elegans. In this Review, we highlight how these new technologies and tools are digging into the biological origins of complex, multidimensional phenotypes.
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Affiliation(s)
- Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nan Xu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.,The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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35
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Towards High-Throughput Chemobehavioural Phenomics in Neuropsychiatric Drug Discovery. Mar Drugs 2019; 17:md17060340. [PMID: 31174272 PMCID: PMC6627923 DOI: 10.3390/md17060340] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/19/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022] Open
Abstract
Identifying novel marine-derived neuroactive chemicals with therapeutic potential is difficult due to inherent complexities of the central nervous system (CNS), our limited understanding of the molecular foundations of neuro-psychiatric conditions, as well as the limited applications of effective high-throughput screening models that recapitulate functionalities of the intact CNS. Furthermore, nearly all neuro-modulating chemicals exhibit poorly characterized pleiotropic activities often referred to as polypharmacology. The latter renders conventional target-based in vitro screening approaches very difficult to accomplish. In this context, chemobehavioural phenotyping using innovative small organism models such as planarians and zebrafish represent powerful and highly integrative approaches to study the impact of new chemicals on central and peripheral nervous systems. In contrast to in vitro bioassays aimed predominantly at identification of chemicals acting on single targets, phenotypic chemobehavioural analysis allows for complex multi-target interactions to occur in combination with studies of polypharmacological effects of chemicals in a context of functional and intact milieu of the whole organism. In this review, we will outline recent advances in high-throughput chemobehavioural phenotyping and provide a future outlook on how those innovative methods can be utilized for rapidly screening and characterizing marine-derived compounds with prospective applications in neuropharmacology and psychosomatic medicine.
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36
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Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLoS One 2019; 14:e0217746. [PMID: 31150491 PMCID: PMC6544271 DOI: 10.1371/journal.pone.0217746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/19/2019] [Indexed: 12/21/2022] Open
Abstract
Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer’s disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer’s disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity.
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Affiliation(s)
- Tessa Sinnige
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Prashanth Ciryam
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Samuel Casford
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mario de Bono
- Cell Biology Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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37
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Trodusquemine enhances Aβ 42 aggregation but suppresses its toxicity by displacing oligomers from cell membranes. Nat Commun 2019; 10:225. [PMID: 30644384 PMCID: PMC6333784 DOI: 10.1038/s41467-018-07699-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/05/2018] [Indexed: 11/08/2022] Open
Abstract
Transient oligomeric species formed during the aggregation process of the 42-residue form of the amyloid-β peptide (Aβ42) are key pathogenic agents in Alzheimer's disease (AD). To investigate the relationship between Aβ42 aggregation and its cytotoxicity and the influence of a potential drug on both phenomena, we have studied the effects of trodusquemine. This aminosterol enhances the rate of aggregation by promoting monomer-dependent secondary nucleation, but significantly reduces the toxicity of the resulting oligomers to neuroblastoma cells by inhibiting their binding to the cellular membranes. When administered to a C. elegans model of AD, we again observe an increase in aggregate formation alongside the suppression of Aβ42-induced toxicity. In addition to oligomer displacement, the reduced toxicity could also point towards an increased rate of conversion of oligomers to less toxic fibrils. The ability of a small molecule to reduce the toxicity of oligomeric species represents a potential therapeutic strategy against AD.
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38
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Koopman M, Seinstra RI, Nollen EAA. C. elegans as a Model for Synucleinopathies and Other Neurodegenerative Diseases: Tools and Techniques. Methods Mol Biol 2019; 1948:93-112. [PMID: 30771173 DOI: 10.1007/978-1-4939-9124-2_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Caenorhabditis elegans is widely used to investigate biological processes related to health and disease. Multiple C. elegans models for human neurodegenerative diseases do exist, including those expressing human α-synuclein. Even though these models do not feature all pathological and molecular hallmarks of the disease they mimic, they allow for the identification and dissection of molecular pathways that are involved. In line with this, genetic screens have yielded multiple modifiers of proteotoxicity in C. elegans models for neurodegenerative diseases. Here, we describe a set of common screening approaches and tools that can be used to study synucleinopathies and other neurodegenerative diseases in C. elegans. RNA interference and mutagenesis screens can be used to find genes that affect proteotoxicity, while relatively simple molecular, cellular (fractionation studies), metabolic (respiration studies), and behavioral (thrashing and crawling) readouts can be used to study the effects of disease proteins and modifiers more closely.
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Affiliation(s)
- Mandy Koopman
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Aging, Groningen, The Netherlands
| | - Renée I Seinstra
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Aging, Groningen, The Netherlands
| | - Ellen A A Nollen
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Aging, Groningen, The Netherlands.
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39
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Mannini B, Habchi J, Chia S, Ruggeri FS, Perni M, Knowles TPJ, Dobson CM, Vendruscolo M. Stabilization and Characterization of Cytotoxic Aβ 40 Oligomers Isolated from an Aggregation Reaction in the Presence of Zinc Ions. ACS Chem Neurosci 2018; 9:2959-2971. [PMID: 29986583 DOI: 10.1021/acschemneuro.8b00141] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Small oligomers formed during the aggregation of certain peptides and proteins are highly cytotoxic in numerous neurodegenerative disorders. Because of their transient nature and conformational heterogeneity, however, the structural and biological features of these oligomers are still poorly understood. Here, we describe a method of generating stable oligomers formed by the Alzheimer's Aβ40 peptide by carrying out an aggregation reaction in the presence of zinc ions. The resulting oligomers are amenable to detailed biophysical and biological characterization, which reveals a homogeneous population with small size, high cross-β sheet structure content, and extended hydrophobic surface patches. We also show that these oligomers decrease the viability of neuroblastoma cells and impair the motility of C. elegans. The availability of these oligomers offers novel opportunities for studying the mechanisms of Aβ40 toxicity in vitro and in cellular and animal models of Alzheimer's disease.
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Affiliation(s)
- Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco S. Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - 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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40
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Javer A, Ripoll-Sánchez L, Brown AEX. Powerful and interpretable behavioural features for quantitative phenotyping of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0375. [PMID: 30201839 PMCID: PMC6158219 DOI: 10.1098/rstb.2017.0375] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 01/20/2023] Open
Abstract
Behaviour is a sensitive and integrative readout of nervous system function and therefore an attractive measure for assessing the effects of mutation or drug treatment on animals. Video data provide a rich but high-dimensional representation of behaviour, and so the first step of analysis is often some form of tracking and feature extraction to reduce dimensionality while maintaining relevant information. Modern machine-learning methods are powerful but notoriously difficult to interpret, while handcrafted features are interpretable but do not always perform as well. Here, we report a new set of handcrafted features to compactly quantify Caenorhabditis elegans behaviour. The features are designed to be interpretable but to capture as much of the phenotypic differences between worms as possible. We show that the full feature set is more powerful than a previously defined feature set in classifying mutant strains. We then use a combination of automated and manual feature selection to define a core set of interpretable features that still provides sufficient power to detect behavioural differences between mutant strains and the wild-type. Finally, we apply the new features to detect time-resolved behavioural differences in a series of optogenetic experiments targeting different neural subsets. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
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Affiliation(s)
- Avelino Javer
- MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Imperial College London, London, UK
| | - Lidia Ripoll-Sánchez
- MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Imperial College London, London, UK
| | - André E X Brown
- MRC London Institute of Medical Sciences, London, UK .,Institute of Clinical Sciences, Imperial College London, London, UK
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41
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Perni M, Flagmeier P, Limbocker R, Cascella R, Aprile FA, Galvagnion C, Heller GT, Meisl G, Chen SW, Kumita JR, Challa PK, Kirkegaard JB, Cohen SIA, Mannini B, Barbut D, Nollen EAA, Cecchi C, Cremades N, Knowles TPJ, Chiti F, Zasloff M, Vendruscolo M, Dobson CM. Multistep Inhibition of α-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine. ACS Chem Biol 2018; 13:2308-2319. [PMID: 29953201 DOI: 10.1021/acschembio.8b00466] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aggregation of α-synuclein, an intrinsically disordered protein that is highly abundant in neurons, is closely associated with the onset and progression of Parkinson's disease. We have shown previously that the aminosterol squalamine can inhibit the lipid induced initiation process in the aggregation of α-synuclein, and we report here that the related compound trodusquemine is capable of inhibiting not only this process but also the fibril-dependent secondary pathways in the aggregation reaction. We further demonstrate that trodusquemine can effectively suppress the toxicity of α-synuclein oligomers in neuronal cells, and that its administration, even after the initial growth phase, leads to a dramatic reduction in the number of α-synuclein inclusions in a Caenorhabditis elegans model of Parkinson's disease, eliminates the related muscle paralysis, and increases lifespan. On the basis of these findings, we show that trodusquemine is able to inhibit multiple events in the aggregation process of α-synuclein and hence to provide important information about the link between such events and neurodegeneration, as it is initiated and progresses. Particularly in the light of the previously reported ability of trodusquemine to cross the blood-brain barrier and to promote tissue regeneration, the present results suggest that this compound has the potential to be an important therapeutic candidate for Parkinson's disease and related disorders.
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Affiliation(s)
- Michele Perni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Ryan Limbocker
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Francesco A. Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Céline Galvagnion
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- German Centre for Neurodegenerative Diseases, DZNE, Sigmund-Freud-Strasse. 27, 53127, Bonn, Germany
| | - Gabriella T. Heller
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Serene W. Chen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Pavan K. Challa
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Julius B. Kirkegaard
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom
| | - Samuel I. A. Cohen
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Benedetta Mannini
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Denise Barbut
- Enterin Inc., 3624 Market Street, Philadelphia, Pennsylvania 19104, United States
| | - Ellen A. A. Nollen
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI)-Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, 50018 Zaragoza, Spain
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Michael Zasloff
- Enterin Inc., 3624 Market Street, Philadelphia, Pennsylvania 19104, United States
- MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC 20010, United States
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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