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Gupta N, Ramakrishnan S, Wajid S. Emerging role of metabolomics in protein conformational disorders. Expert Rev Proteomics 2021; 18:395-410. [PMID: 34227444 DOI: 10.1080/14789450.2021.1948330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: Metabolomics focuses on interactions among different metabolites associated with various cellular functions in cells, tissues, and organs. In recent years, metabolomics has emerged as a powerful tool to identify perturbed metabolites, pathways influenced by the environment, for protein conformational diseases (PCDs) and also offers wide clinical application.Area Covered: This review provides a brief overview of recent advances in metabolomics as applied to identify metabolic variations in PCDs, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, prion disease, and cardiac amyloidosis. The 'PubMed' and 'Google Scholar' database search methods have been used to screen the published reports with key search terms: metabolomics, biomarkers, and protein conformational disorders.Expert opinion: Metabolomics is the large-scale study of metabolites and is deemed to overwhelm other omics. It plays a crucial role in finding variations in diseases due to protein conformational changes. However, many PCDs are yet to be identified. Metabolomics is still an emerging field; there is a need for new high-resolution analytical techniques and more studies need to be carried out to generate new information.
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Affiliation(s)
- Nimisha Gupta
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
| | | | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
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Eskandari-Sedighi G, Cortez LM, Yang J, Daude N, Shmeit K, Sim V, Westaway D. Quaternary Structure Changes for PrP Sc Predate PrP C Downregulation and Neuronal Death During Progression of Experimental Scrapie Disease. Mol Neurobiol 2021; 58:375-390. [PMID: 32959170 PMCID: PMC7695655 DOI: 10.1007/s12035-020-02112-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/01/2020] [Indexed: 01/20/2023]
Abstract
Prion diseases are fatal neurodegenerative diseases in mammals with the unique characteristics of misfolding and aggregation of the cellular prion protein (PrPC) to the scrapie prion (PrPSc). Although neuroinflammation and neuronal loss feature within the disease process, the details of PrPC/PrPSc molecular transition to generate different aggregated species, and the correlation between each species and sequence of cellular events in disease pathogenesis are not fully understood. In this study, using mice inoculated with the RML isolate of mouse-adapted scrapie as a model, we applied asymmetric flow field-flow fractionation to monitor PrPC and PrPSc particle sizes and we also measured seeding activity and resistance to proteases. For cellular analysis in brain tissue, we measured inflammatory markers and synaptic damage, and used the isotropic fractionator to measure neuronal loss; these techniques were applied at different timepoints in a cross-sectional study of disease progression. Our analyses align with previous reports defining significant decreases in PrPC levels at pre-clinical stages of the disease and demonstrate that these decreases become significant before neuronal loss. We also identified the earliest PrPSc assemblies at a timepoint equivalent to 40% elapsed time for the disease incubation period; we propose that these assemblies, mostly composed of proteinase K (PK)-sensitive species, play an important role in triggering disease pathogenesis. Lastly, we show that the PK-resistant assemblies of PrPSc that appear at timepoints close to the terminal stage have similar biophysical characteristics, and hence that preparative use of PK-digestion selects for this specific subpopulation. In sum, our data argue that qualitative, as well as quantitative, changes in PrP conformers occur at the midpoint of subclinical phase; these changes affect quaternary structure and may occur at the threshold where adaptive responses become inadequate to deal with pathogenic processes.
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Affiliation(s)
- Ghazaleh Eskandari-Sedighi
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada
| | - Leonardo M Cortez
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, AB, Canada
| | - Jing Yang
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada
| | - Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada
| | - Klinton Shmeit
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada
| | - Valerie Sim
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, AB, Canada
| | - David Westaway
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
- Centre for Prions and Protein Folding Diseases, University of Alberta, 204 Brain and Aging Research Building, Edmonton, AB, T6G 2M8, Canada.
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