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Proteomic Applications in Ageing and Neurodegenerative Conditions
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Proteomic Applications in Ageing and Neurodegenerative Conditions

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 10554

Special Issue Editors

Prof. Dr. Thomas Wishart

E-Mail Website
Guest Editor
The Roslin Institute, Royal (Dick) School of Veterinary Studies, College of Medicine and Veterinary Medicine, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK
Interests: neurodegeneration; synapse; comparative pathology; proteomics; pathway mapping
Dr. Rachel A. Kline

E-Mail Website
Guest Editor
The Roslin Institute, Royal (Dick) School of Veterinary Studies, College of Medicine and Veterinary Medicine, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK
Interests: neurodegeneration; synapses; systems biology; proteomics
Dr. Dominic Kurian

E-Mail Website
Guest Editor
The Roslin Institute, Royal (Dick) School of Veterinary Studies, College of Medicine and Veterinary Medicine, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK
Interests: proteomics; mass spectrometry; post-translational modifications; redox proteomics and proteostasis

Special Issue Information

Dear Colleagues,

Advances in mass spectrometric technologies, separation sciences and associated informatics over the last decade have ushered proteomics technologies to a position where we can address questions at the level of the effector molecule with sensitivity and precision greater than ever before. Probing thousands of proteins from clinical and biofluid samples or in tissues in the context of cellular and subcellular localisations and their post-translational variants now offer unprecedented opportunities in characterising complex disease phenotypes. The sheer breadth of data potentially generated by these advanced MS technologies encompasses analyte subsets ranging from lipids, metabolites, peptides, proteins and post-translational modifications. Each technique harbours its own merits and challenges, from experimental design to sample processing and data handling. This Special Issue will comprise new manuscripts describing the limitations and considerations required for effective -omics experimentation and novel research demonstrating the importance of MS-based -omics to our understanding of the molecular underpinnings of processes informing on and/or regulating ageing and/or neurodegeneration. 

Prof. Dr. Thomas Wishart
Dr. Rachel A. Kline
Dr. Dominic Kurian
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (4 papers)

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Research

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21 pages, 3437 KiB  
Article
Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics
by Evgeniya V. Smirnova, Tatiana V. Rakitina, Rustam H. Ziganshin, George A. Saratov, Georgij P. Arapidi, Alexey A. Belogurov, Jr. and Anna A. Kudriaeva
Cells 2023, 12(6), 944; https://doi.org/10.3390/cells12060944 - 20 Mar 2023
Cited by 1 | Viewed by 3057
Abstract
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. [...] Read more.
Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery—synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe2+ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath. Full article
(This article belongs to the Special Issue Proteomic Applications in Ageing and Neurodegenerative Conditions)
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18 pages, 3130 KiB  
Article
Lipid Dys-Homeostasis Contributes to APOE4-Associated AD Pathology
by Adina-Nicoleta Lazar, Linda Hanbouch, Lydie Boussicaut, Baptiste Fourmaux, Patricia Daira, Mark J. Millan, Nathalie Bernoud-Hubac and Marie-Claude Potier
Cells 2022, 11(22), 3616; https://doi.org/10.3390/cells11223616 - 15 Nov 2022
Cited by 2 | Viewed by 1773
Abstract
The association of the APOE4 (vs. APOE3) isoform with an increased risk of Alzheimer’s disease (AD) is unequivocal, but the underlying mechanisms remain incompletely elucidated. A prevailing hypothesis incriminates the impaired ability of APOE4 to clear neurotoxic amyloid-β peptides (Aβ) from the brain [...] Read more.
The association of the APOE4 (vs. APOE3) isoform with an increased risk of Alzheimer’s disease (AD) is unequivocal, but the underlying mechanisms remain incompletely elucidated. A prevailing hypothesis incriminates the impaired ability of APOE4 to clear neurotoxic amyloid-β peptides (Aβ) from the brain as the main mechanism linking the apolipoprotein isoform to disease etiology. The APOE protein mediates lipid transport both within the brain and from the brain to the periphery, suggesting that lipids may be potential co-factors in APOE4-associated physiopathology. The present study reveals several changes in the pathways of lipid homeostasis in the brains of mice expressing the human APOE4 vs. APOE3 isoform. Carriers of APOE4 had altered cholesterol turnover, an imbalance in the ratio of specific classes of phospholipids, lower levels of phosphatidylethanolamines bearing polyunsaturated fatty acids and an overall elevation in levels of monounsaturated fatty acids. These modifications in lipid homeostasis were related to increased production of Aβ peptides as well as augmented levels of tau and phosphorylated tau in primary neuronal cultures. This suite of APOE4-associated anomalies in lipid homeostasis and neurotoxic protein levels may be related to the accrued risk for AD in APOE4 carriers and provides novel insights into potential strategies for therapeutic intervention. Full article
(This article belongs to the Special Issue Proteomic Applications in Ageing and Neurodegenerative Conditions)
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25 pages, 6296 KiB  
Article
The Proteome Signatures of Fibroblasts from Patients with Severe, Intermediate and Mild Spinal Muscular Atrophy Show Limited Overlap
by Sharon J. Brown, Rachel A. Kline, Silvia A. Synowsky, Sally L. Shirran, Ian Holt, Kelly A. Sillence, Peter Claus, Brunhilde Wirth, Thomas M. Wishart and Heidi R. Fuller
Cells 2022, 11(17), 2624; https://doi.org/10.3390/cells11172624 - 23 Aug 2022
Cited by 5 | Viewed by 2802
Abstract
Most research to characterise the molecular consequences of spinal muscular atrophy (SMA) has focused on SMA I. Here, proteomic profiling of skin fibroblasts from severe (SMA I), intermediate (SMA II), and mild (SMA III) patients, alongside age-matched controls, was conducted using SWATH mass [...] Read more.
Most research to characterise the molecular consequences of spinal muscular atrophy (SMA) has focused on SMA I. Here, proteomic profiling of skin fibroblasts from severe (SMA I), intermediate (SMA II), and mild (SMA III) patients, alongside age-matched controls, was conducted using SWATH mass spectrometry analysis. Differentially expressed proteomic profiles showed limited overlap across each SMA type, and variability was greatest within SMA II fibroblasts, which was not explained by SMN2 copy number. Despite limited proteomic overlap, enriched canonical pathways common to two of three SMA severities with at least one differentially expressed protein from the third included mTOR signalling, regulation of eIF2 and eIF4 signalling, and protein ubiquitination. Network expression clustering analysis identified protein profiles that may discriminate or correlate with SMA severity. From these clusters, the differential expression of PYGB (SMA I), RAB3B (SMA II), and IMP1 and STAT1 (SMA III) was verified by Western blot. All SMA fibroblasts were transfected with an SMN-enhanced construct, but only RAB3B expression in SMA II fibroblasts demonstrated an SMN-dependent response. The diverse proteomic profiles and pathways identified here pave the way for studies to determine their utility as biomarkers for patient stratification or monitoring treatment efficacy and for the identification of severity-specific treatments. Full article
(This article belongs to the Special Issue Proteomic Applications in Ageing and Neurodegenerative Conditions)
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Review

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26 pages, 26373 KiB  
Review
An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research
by Rachel A. Kline, Lena Lößlein, Dominic Kurian, Judit Aguilar Martí, Samantha L. Eaton, Felipe A. Court, Thomas H. Gillingwater and Thomas M. Wishart
Cells 2022, 11(17), 2653; https://doi.org/10.3390/cells11172653 - 26 Aug 2022
Cited by 2 | Viewed by 2132
Abstract
Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment [...] Read more.
Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment itself is only the first step in yielding high-quality, translatable results. Indeed, the effectiveness and/or impact of the majority of contemporary proteomics screens are hindered not by commonly considered technical limitations such as low proteome coverage but rather by insufficient analyses. Proteomic experimentation requires a careful methodological selection to account for variables from sample collection, through to database searches for peptide identification to standardised post-mass spectrometry options directed analysis workflow, which should be adjusted for each study, from determining when and how to filter proteomic data to choosing holistic versus trend-wise analyses for biologically relevant patterns. Finally, we highlight and discuss the difficulties inherent in the modelling and study of the majority of progressive neurodegenerative conditions. We provide evidence (in the context of neurodegenerative research) for the benefit of undertaking a comparative approach through the application of the above considerations in the alignment of publicly available pre-existing data sets to identify potential novel regulators of neuronal stability. Full article
(This article belongs to the Special Issue Proteomic Applications in Ageing and Neurodegenerative Conditions)
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