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Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF. Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. Dev Cell 2024:S1534-5807(24)00266-1. [PMID: 38810654 DOI: 10.1016/j.devcel.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/13/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here, we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue specific and not simply driven by protein expression differences. Experimental interrogation in killifish and yeast, combined with machine learning, indicates that this specificity is linked to protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during vertebrate aging and identify strong, tissue-specific associations with dysfunction and disease.
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Affiliation(s)
- Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Itamar Harel
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Eitan Moses
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Uri Goshtchevsky
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Ben E Machado
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
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The Ability of Some Polysaccharides to Disaggregate Lysozyme Amyloid Fibrils and Renature the Protein. Pharmaceutics 2023; 15:pharmaceutics15020624. [PMID: 36839946 PMCID: PMC9962556 DOI: 10.3390/pharmaceutics15020624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
The deposition of proteins in the form of insoluble amyloid fibril aggregates is linked to a range of diseases. The supramolecular architecture of such deposits is governed by the propagation of β-strands in the direction of protofilament growth. In the present study, we analyze the structural changes of hen egg-white lysozyme fibrils upon their interactions with a range of polysaccharides, using AFM and FTIR spectroscopy. Linear anionic polysaccharides, such as κ-carrageenan and sodium alginate, are shown to be capable to disaggregate protofilaments with eventual protein renaturation. The results help to understand the mechanism of amyloid disaggregation and create a platform for both the development of new therapeutic agents for amyloidose treatment, and the design of novel functional protein-polysaccharide complex-based nanomaterials.
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Paik YK, Overall CM, Corrales F, Deutsch EW, Lane L, Omenn GS. Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods. J Proteome Res 2019; 17:4023-4030. [PMID: 30985145 PMCID: PMC6288998 DOI: 10.1021/acs.jproteome.8b00885] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, College of Life Science and Technology, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | - Fernando Corrales
- Functional Proteomics Laboratory National Center of Biotechnology, CSIC
| | | | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, University of Geneva
| | - Gilbert S Omenn
- Institute for Systems Biology, Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics & School of Public Health, University of Michigan
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Vlahou A. Implementation of Clinical Proteomics: A Step Closer to Personalized Medicine? Proteomics Clin Appl 2018; 13:e1800088. [DOI: 10.1002/prca.201800088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Antonia Vlahou
- Biomedical Research FoundationAcademy of Athens Soranou Efessiou 4 11527 Athens Greece
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