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Biomolecules
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Advances in Neuroproteomics
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Advances in Neuroproteomics

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 8325

Special Issue Editors

Dr. Kenneth R. Williams

E-Mail Website
Guest Editor
1. Professor (Adjunct) of Research, Co-Director, Yale/NIDA Neuroproteomics Center, New Haven, CT, USA
2. Founder, Keck Foundation Biotechnology Resource Laboratory, Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, CT, USA
Interests: mass spectrometry; quantitative proteomics; neuroproteomics; disease biomarkers
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Angus C. Nairn

E-Mail Website
Guest Editor
1. Charles B. G. Murphy Professor of Psychiatry, Co-Director, Yale/NIDA Neuroproteomics Center, New Haven, CT, USA
2. Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
Interests: dopamine; Alzheimer disease; Parkinson disease; protein phosphorylation; signal transduction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Recent advances in mass spectrometry allow for deep exploration of the neuroproteome and of the protein-protein interactions that regulate virtually all nerve cell functions. However, the central nervous system (CNS) has ~100 billion neurons, each with 10,000 to 100,000 synaptic connections; and even larger numbers of glial cells. Moreover, there is a large variety in cell morphology with individual neurons being intermingled with several different types of neurons and with axonal projections from an individual neuron often projecting over relatively long distances. Since each of the ~100s of nerve cell types exhibit distinct patterns of gene expression, methodologies are needed to enable quantitative MS/proteomic analyses of specific neuronal cell types and their organelles.  This Special Issue will contain research and review articles that cover whole proteome analysis, proximity labeling, protein post-translational modifications, and protein:protein interactions within normal and diseased neurological tissues. We are especially interested in manuscripts that describe the use of single-cell proteomics, laser capture microscopy, fluorescence cytometry-related, and immuno-affinity technologies in conjunction with transgenic and viral methods to isolate and study neural cell type- and organelle-specific proteomes. Manuscripts are also sought that describe the quantitative proteomics analyses of biofluids, including studies of exosomal protein biomarkers for various neuropathological diseases.

Dr. Kenneth R. Williams
Prof. Dr. Angus C. Nairn
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. Biomolecules is an international peer-reviewed open access monthly 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.

Keywords

  • discovery mass spectrometry
  • neuroproteomics
  • mass spectrometry
  • quantitative proteomics
  • targeted mass spectrometry

Published Papers (5 papers)

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Research

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22 pages, 11609 KiB  
Article
Involvement of Glucosamine 6 Phosphate Isomerase 2 (GNPDA2) Overproduction in β-Amyloid- and Tau P301L-Driven Pathomechanisms
by Mercedes Lachén-Montes, Paz Cartas-Cejudo, Adriana Cortés, Elena Anaya-Cubero, Erika Peral, Karina Ausín, Ramón Díaz-Peña, Joaquín Fernández-Irigoyen and Enrique Santamaría
Biomolecules 2024, 14(4), 394; https://doi.org/10.3390/biom14040394 - 25 Mar 2024
Viewed by 690
Abstract
Alzheimer’s disease (AD) is a neurodegenerative olfactory disorder affecting millions of people worldwide. Alterations in the hexosamine- or glucose-related pathways have been described through AD progression. Specifically, an alteration in glucosamine 6 phosphate isomerase 2 (GNPDA2) protein levels has been observed in olfactory [...] Read more.
Alzheimer’s disease (AD) is a neurodegenerative olfactory disorder affecting millions of people worldwide. Alterations in the hexosamine- or glucose-related pathways have been described through AD progression. Specifically, an alteration in glucosamine 6 phosphate isomerase 2 (GNPDA2) protein levels has been observed in olfactory areas of AD subjects. However, the biological role of GNPDA2 in neurodegeneration remains unknown. Using mass spectrometry, multiple GNPDA2 interactors were identified in human nasal epithelial cells (NECs) mainly involved in intraciliary transport. Moreover, GNPDA2 overexpression induced an increment in NEC proliferation rates, accompanied by transcriptomic alterations in Type II interferon signaling or cellular stress responses. In contrast, the presence of beta-amyloid or mutated Tau-P301L in GNPDA2-overexpressing NECs induced a slowdown in the proliferative capacity in parallel with a disruption in protein processing. The proteomic characterization of Tau-P301L transgenic zebrafish embryos demonstrated that GNPDA2 overexpression interfered with collagen biosynthesis and RNA/protein processing, without inducing additional changes in axonal outgrowth defects or neuronal cell death. In humans, a significant increase in serum GNPDA2 levels was observed across multiple neurological proteinopathies (AD, Lewy body dementia, progressive supranuclear palsy, mixed dementia and amyotrophic lateral sclerosis) (n = 215). These data shed new light on GNPDA2-dependent mechanisms associated with the neurodegenerative process beyond the hexosamine route. Full article
(This article belongs to the Special Issue Advances in Neuroproteomics)
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17 pages, 3368 KiB  
Article
Identification of Central Nervous System Oncologic Disease Biomarkers in EVs from Cerebrospinal Fluid (CSF) of Pediatric Patients: A Pilot Neuro-Proteomic Study
by Xhuliana Kajana, Sonia Spinelli, Andrea Garbarino, Ganna Balagura, Martina Bartolucci, Andrea Petretto, Marco Pavanello, Giovanni Candiano, Isabella Panfoli and Maurizio Bruschi
Biomolecules 2023, 13(12), 1730; https://doi.org/10.3390/biom13121730 - 30 Nov 2023
Cited by 1 | Viewed by 1014
Abstract
Cerebrospinal fluid (CSF) is a biochemical–clinical window into the brain. Unfortunately, its wide dynamic range, low protein concentration, and small sample quantity significantly limit the possibility of using it routinely. Extraventricular drainage (EVD) of CSF allows us to solve quantitative problems and to [...] Read more.
Cerebrospinal fluid (CSF) is a biochemical–clinical window into the brain. Unfortunately, its wide dynamic range, low protein concentration, and small sample quantity significantly limit the possibility of using it routinely. Extraventricular drainage (EVD) of CSF allows us to solve quantitative problems and to study the biological role of extracellular vesicles (EVs). In this study, we implemented bioinformatic analysis of our previous data of EVD of CSF and its EVs obtained from congenital hydrocephalus with the aim of identifying a comprehensive list of potential tumor and non-tumor biomarkers of central nervous system diseases. Among all proteins identified, those enriched in EVs are associated with synapses, synaptosomes, and nervous system diseases including gliomas, embryonal tumors, and epilepsy. Among these EV-enriched proteins, given the broad consensus present in the recent scientific literature, we validated syntaxin-binding protein 1 (STXBP1) as a marker of malignancy in EVD of CSF and its EVs from patients with pilocytic astrocytoma and medulloblastoma. Our results show that STXBP1 is negatively enriched in EVs compared to non-tumor diseases and its downregulation correlates with adverse outcomes. Further experiments are needed to validate this and other EV markers in the blood of pediatric patients for translational medicine applications. Full article
(This article belongs to the Special Issue Advances in Neuroproteomics)
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19 pages, 3324 KiB  
Article
Neuroproteomic Analysis after SARS-CoV-2 Infection Reveals Overrepresented Neurodegeneration Pathways and Disrupted Metabolic Pathways
by Indranil Basak, Rhodri Harfoot, Jennifer E. Palmer, Abhishek Kumar, Miguel E. Quiñones-Mateu, Lucia Schweitzer and Stephanie M. Hughes
Biomolecules 2023, 13(11), 1597; https://doi.org/10.3390/biom13111597 - 30 Oct 2023
Cited by 1 | Viewed by 1987
Abstract
Besides respiratory illness, SARS-CoV-2, the causative agent of COVID-19, leads to neurological symptoms. The molecular mechanisms leading to neuropathology after SARS-CoV-2 infection are sparsely explored. SARS-CoV-2 enters human cells via different receptors, including ACE-2, TMPRSS2, and TMEM106B. In this study, we used a [...] Read more.
Besides respiratory illness, SARS-CoV-2, the causative agent of COVID-19, leads to neurological symptoms. The molecular mechanisms leading to neuropathology after SARS-CoV-2 infection are sparsely explored. SARS-CoV-2 enters human cells via different receptors, including ACE-2, TMPRSS2, and TMEM106B. In this study, we used a human-induced pluripotent stem cell-derived neuronal model, which expresses ACE-2, TMPRSS2, TMEM106B, and other possible SARS-CoV-2 receptors, to evaluate its susceptibility to SARS-CoV-2 infection. The neurons were exposed to SARS-CoV-2, followed by RT-qPCR, immunocytochemistry, and proteomic analyses of the infected neurons. Our findings showed that SARS-CoV-2 infects neurons at a lower rate than other human cells; however, the virus could not replicate or produce infectious virions in this neuronal model. Despite the aborted SARS-CoV-2 replication, the infected neuronal nuclei showed irregular morphology compared to other human cells. Since cytokine storm is a significant effect of SARS-CoV-2 infection in COVID-19 patients, in addition to the direct neuronal infection, the neurons were treated with pre-conditioned media from SARS-CoV-2-infected lung cells, and the neuroproteomic changes were investigated. The limited SARS-CoV-2 infection in the neurons and the neurons treated with the pre-conditioned media showed changes in the neuroproteomic profile, particularly affecting mitochondrial proteins and apoptotic and metabolic pathways, which may lead to the development of neurological complications. The findings from our study uncover a possible mechanism behind SARS-CoV-2-mediated neuropathology that might contribute to the lingering effects of the virus on the human brain. Full article
(This article belongs to the Special Issue Advances in Neuroproteomics)
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Review

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21 pages, 2613 KiB  
Review
Mitochondrial Proteomes in Neural Cells: A Systematic Review
by Aya Nusir, Patricia Sinclair and Nadine Kabbani
Biomolecules 2023, 13(11), 1638; https://doi.org/10.3390/biom13111638 - 11 Nov 2023
Viewed by 1402
Abstract
Mitochondria are ancient endosymbiotic double membrane organelles that support a wide range of eukaryotic cell functions through energy, metabolism, and cellular control. There are over 1000 known proteins that either reside within the mitochondria or are transiently associated with it. These mitochondrial proteins [...] Read more.
Mitochondria are ancient endosymbiotic double membrane organelles that support a wide range of eukaryotic cell functions through energy, metabolism, and cellular control. There are over 1000 known proteins that either reside within the mitochondria or are transiently associated with it. These mitochondrial proteins represent a functional subcellular protein network (mtProteome) that is encoded by mitochondrial and nuclear genomes and significantly varies between cell types and conditions. In neurons, the high metabolic demand and differential energy requirements at the synapses are met by specific modifications to the mtProteome, resulting in alterations in the expression and functional properties of the proteins involved in energy production and quality control, including fission and fusion. The composition of mtProteomes also impacts the localization of mitochondria in axons and dendrites with a growing number of neurodegenerative diseases associated with changes in mitochondrial proteins. This review summarizes the findings on the composition and properties of mtProteomes important for mitochondrial energy production, calcium and lipid signaling, and quality control in neural cells. We highlight strategies in mass spectrometry (MS) proteomic analysis of mtProteomes from cultured cells and tissue. The research into mtProteome composition and function provides opportunities in biomarker discovery and drug development for the treatment of metabolic and neurodegenerative disease. Full article
(This article belongs to the Special Issue Advances in Neuroproteomics)
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23 pages, 2364 KiB  
Review
Cell-Type-Specific Neuroproteomics of Synapses
by Yun Young Yim and Eric J. Nestler
Biomolecules 2023, 13(6), 998; https://doi.org/10.3390/biom13060998 - 16 Jun 2023
Viewed by 2340
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, [...] Read more.
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders. Full article
(This article belongs to the Special Issue Advances in Neuroproteomics)
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