1
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Allboani A, Kar S, Kavdia M. Computational modeling of neuronal nitric oxide synthase biochemical pathway: A mechanistic analysis of tetrahydrobiopterin and oxidative stress. Free Radic Biol Med 2024; 222:625-637. [PMID: 39004235 DOI: 10.1016/j.freeradbiomed.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/14/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Neuronal cell dysfunction plays an important role in neurodegenerative diseases. Oxidative stress can disrupt the redox balance within neuronal cells and may cause neuronal nitric oxide synthase (nNOS) to uncouple, contributing to the neurodegenerative processes. Experimental studies and clinical trials using nNOS cofactor tetrahydrobiopterin (BH4) and antioxidants in neuronal cell dysfunction have shown inconsistent results. A better mechanistic understanding of complex interactions of nNOS activity and oxidative stress in neuronal cell dysfunction is needed. In this study, we developed a computational model of neuronal cell using nNOS biochemical pathways to explore several key mechanisms that are known to influence neuronal cell redox homeostasis. We studied the effects of oxidative stress and BH4 synthesis on nNOS nitric oxide production and biopterin ratio (BH4/total biopterin). Results showed that nNOS remained coupled and maintained nitric oxide production for oxidative stress levels less than 230 nM/s. The results showed that neuronal oxidative stress above 230 nM/s increased the degree of nNOS uncoupling and introduced instability in the nitric oxide production. The nitric oxide production did not change irrespective of initial biopterin ratio of 0.05-0.99 for a given oxidative stress. Oxidative stress resulted in significant reduction in BH4 levels even when nitric oxide production was not affected. Enhancing BH4 synthesis or supplementation improved nNOS coupling, however the degree of improvement was determined by the levels of oxidative stress and BH4 synthesis. The results of our mechanistic analysis indicate that there is a potential for significant improvement in neuronal dysfunction by simultaneously increasing BH4 levels and reducing cellular oxidative stress.
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Affiliation(s)
- Amnah Allboani
- Department of Biomedical Engineering, Wayne State University, Detroit, MI, 48202, USA
| | - Saptarshi Kar
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Mahendra Kavdia
- Department of Biomedical Engineering, Wayne State University, Detroit, MI, 48202, USA.
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2
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Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024; 4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
Abstract
Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.
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Affiliation(s)
- Zicong Wang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Peng-Kai Liu
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Lachman
Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Wisconsin
Center for NanoBioSystems, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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3
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Soraci L, Corsonello A, Paparazzo E, Montesanto A, Piacenza F, Olivieri F, Gambuzza ME, Savedra EV, Marino S, Lattanzio F, Biscetti L. Neuroinflammaging: A Tight Line Between Normal Aging and Age-Related Neurodegenerative Disorders. Aging Dis 2024; 15:1726-1747. [PMID: 38300639 PMCID: PMC11272206 DOI: 10.14336/ad.2023.1001] [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: 08/12/2023] [Accepted: 10/01/2023] [Indexed: 02/02/2024] Open
Abstract
Aging in the healthy brain is characterized by a low-grade, chronic, and sterile inflammatory process known as neuroinflammaging. This condition, mainly consisting in an up-regulation of the inflammatory response at the brain level, contributes to the pathogenesis of age-related neurodegenerative disorders. Development of this proinflammatory state involves the interaction between genetic and environmental factors, able to induce age-related epigenetic modifications. Indeed, the exposure to environmental compounds, drugs, and infections, can contribute to epigenetic modifications of DNA methylome, histone fold proteins, and nucleosome positioning, leading to epigenetic modulation of neuroinflammatory responses. Furthermore, some epigenetic modifiers, which combine and interact during the life course, can contribute to modeling of epigenome dynamics to sustain, or dampen the neuroinflammatory phenotype. The aim of this review is to summarize current knowledge about neuroinflammaging with a particular focus on epigenetic mechanisms underlying the onset and progression of neuroinflammatory cascades in the central nervous system; furthermore, we describe some diagnostic biomarkers that may contribute to increase diagnostic accuracy and help tailor therapeutic strategies in patients with neurodegenerative diseases.
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Affiliation(s)
- Luca Soraci
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy.
| | - Andrea Corsonello
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy.
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy.
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Italian National Research Center of Aging (IRCCS INRCA), IRCCS INRCA, Ancona, Italy.
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.
- Clinic of Laboratory and Precision Medicine, Italian National Research Center of Aging (IRCCS INRCA), Ancona, Italy.
| | | | | | - Silvia Marino
- IRCCS Centro Neurolesi "Bonino-Pulejo”, Messina, Italy.
| | | | - Leonardo Biscetti
- Section of Neurology, Italian National Research Center on Aging (IRCCS INRCA), Ancona, Italy.
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4
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Astillero‐Lopez V, Villar‐Conde S, Gonzalez‐Rodriguez M, Flores‐Cuadrado A, Ubeda‐Banon I, Saiz‐Sanchez D, Martinez‐Marcos A. Proteomic analysis identifies HSP90AA1, PTK2B, and ANXA2 in the human entorhinal cortex in Alzheimer's disease: Potential role in synaptic homeostasis and Aβ pathology through microglial and astroglial cells. Brain Pathol 2024; 34:e13235. [PMID: 38247340 PMCID: PMC11189773 DOI: 10.1111/bpa.13235] [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: 09/05/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
Alzheimer's disease (AD), the most prevalent neurodegenerative disorder worldwide, is clinically characterized by cognitive deficits. Neuropathologically, AD brains accumulate deposits of amyloid-β (Aβ) and tau proteins. Furthermore, these misfolded proteins can propagate from cell to cell in a prion-like manner and induce native proteins to become pathological. The entorhinal cortex (EC) is among the earliest areas affected by tau accumulation along with volume reduction and neurodegeneration. Neuron-glia interactions have recently come into focus; however, the role of microglia and astroglia in the pathogenesis of AD remains unclear. Proteomic approaches allow the determination of changes in the proteome to better understand the pathology underlying AD. Bioinformatic analysis of proteomic data was performed to compare ECs from AD and non-AD human brain tissue. To validate the proteomic results, western blot, immunofluorescence, and confocal studies were carried out. The findings revealed that the most disturbed signaling pathway was synaptogenesis. Because of their involvement in synapse function, relationship with Aβ and tau proteins and interactions in the pathway analysis, three proteins were selected for in-depth study: HSP90AA1, PTK2B, and ANXA2. All these proteins showed colocalization with neurons and/or astroglia and microglia and with pathological Aβ and tau proteins. In particular, ANXA2, which is overexpressed in AD, colocalized with amoeboid microglial cells and Aβ plaques surrounded by astrocytes. Taken together, the evidence suggests that unbalanced expression of HSP90AA1, PTK2B, and ANXA2 may play a significant role in synaptic homeostasis and Aβ pathology through microglial and astroglial cells in the human EC in AD.
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Affiliation(s)
- Veronica Astillero‐Lopez
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
| | - Sandra Villar‐Conde
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
| | - Melania Gonzalez‐Rodriguez
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
| | - Alicia Flores‐Cuadrado
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
| | - Isabel Ubeda‐Banon
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
| | - Daniel Saiz‐Sanchez
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
| | - Alino Martinez‐Marcos
- Neuroplasticity and Neurodegeneration Laboratory, CRIB, Ciudad Real Medical SchoolUniversity of Castilla‐La Mancha (UCLM)Ciudad RealSpain
- Grupo de Neuroplasticidad y Neurodegeneración, Instituto de Investigación Sanitaria de Castilla‐La Mancha (IDISCAM)Castilla‐La ManchaSpain
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5
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Yadikar H, Ansari MA, Abu-Farha M, Joseph S, Thomas BT, Al-Mulla F. Deciphering Early and Progressive Molecular Signatures in Alzheimer's Disease through Integrated Longitudinal Proteomic and Pathway Analysis in a Rodent Model. Int J Mol Sci 2024; 25:6469. [PMID: 38928172 PMCID: PMC11203991 DOI: 10.3390/ijms25126469] [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: 04/18/2024] [Revised: 05/25/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
Alzheimer's disease (AD), the leading cause of dementia worldwide, remains a challenge due to its complex origin and degenerative character. The need for accurate biomarkers and treatment targets hinders early identification and intervention. To fill this gap, we used a novel longitudinal proteome methodology to examine the temporal development of molecular alterations in the cortex of an intracerebroventricular streptozotocin (ICV-STZ)-induced AD mouse model for disease initiation and progression at one, three-, and six-weeks post-treatment. Week 1 revealed metabolic protein downregulation, such as Aldoa and Pgk1. Week 3 showed increased Synapsin-1, and week 6 showed cytoskeletal protein alterations like Vimentin. The biological pathways, upstream regulators, and functional effects of proteome alterations were dissected using advanced bioinformatics methods, including Ingenuity Pathway Analysis (IPA) and machine learning algorithms. We identified Mitochondrial Dysfunction, Synaptic Vesicle Pathway, and Neuroinflammation Signaling as disease-causing pathways. Huntington's Disease Signaling and Synaptogenesis Signaling were stimulated while Glutamate Receptor and Calcium Signaling were repressed. IPA also found molecular connections between PPARGC1B and AGT, which are involved in myelination and possible neoplastic processes, and MTOR and AR, which imply mechanistic involvements beyond neurodegeneration. These results help us comprehend AD's molecular foundation and demonstrate the promise of focused proteomic techniques to uncover new biomarkers and therapeutic targets for AD, enabling personalized medicine.
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Affiliation(s)
- Hamad Yadikar
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sabah AlSalem University City, Kuwait City 13060, Kuwait
- OMICS Research Unit, Research Core Facility, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait;
| | - Mubeen A. Ansari
- Department of Pharmacology and Toxicology, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait;
| | - Mohamed Abu-Farha
- Department of Translational Research, Dasman Diabetes Institute, Kuwait City 15462, Kuwait; (M.A.-F.); (F.A.-M.)
| | - Shibu Joseph
- Department of Special Service Facility, Dasman Diabetes Institute, Kuwait City 15462, Kuwait;
| | - Betty T. Thomas
- OMICS Research Unit, Research Core Facility, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait;
| | - Fahd Al-Mulla
- Department of Translational Research, Dasman Diabetes Institute, Kuwait City 15462, Kuwait; (M.A.-F.); (F.A.-M.)
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6
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Liang Z, Zhuang H, Cao X, Ma G, Shen L. Subcellular proteomics insights into Alzheimer's disease development. Proteomics Clin Appl 2024; 18:e2200112. [PMID: 37650321 DOI: 10.1002/prca.202200112] [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: 04/30/2023] [Revised: 07/27/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
Alzheimer's disease (AD), one of the most common dementias, is a neurodegenerative disease characterized by cognitive impairment and decreased judgment function. The expected number of AD patient is increasing in the context of the world's advancing medical care and increasing human life expectancy. Since current molecular mechanism studies on AD pathogenesis are incomplete, there is no specific and effective therapeutic agent. Mass spectrometry (MS)-based unbiased proteomics studies provide an effective and comprehensive approach. Many advances have been made in the study of the mechanism, diagnostic markers, and drug targets of AD using proteomics. This paper focus on subcellular level studies, reviews studies using proteomics to study AD-associated mitochondrial dysfunction, synaptic, and myelin damage, the protein composition of amyloid plaques (APs) and neurofibrillary tangles (NFTs), changes in tissue extracellular vehicles (EVs) and exosome proteome, and the protein changes in ribosomes and lysosomes. The methods of sample separation and preparation and proteomic analysis as well as the main findings of these studies are involved. The results of these proteomics studies provide insights into the pathogenesis of AD and provide theoretical resource and direction for future research in AD, helping to identify new biomarkers and drugs targets for AD.
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Affiliation(s)
- Zhiyuan Liang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Hongbin Zhuang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
| | - Xueshan Cao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, P. R. China
| | - Guanwei Ma
- School of Public Health, the key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, P. R. China
| | - Liming Shen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, P. R. China
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7
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Brandão-Teles C, Zuccoli GS, de Moraes Vrechi TA, Ramos-da-Silva L, Santos AVS, Crunfli F, Martins-de-Souza D. Induced-pluripotent stem cells and neuroproteomics as tools for studying neurodegeneration. Biochem Soc Trans 2024; 52:163-176. [PMID: 38288874 DOI: 10.1042/bst20230341] [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: 10/16/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
The investigation of neurodegenerative diseases advanced significantly with the advent of cell-reprogramming technology, leading to the creation of new models of human illness. These models, derived from induced pluripotent stem cells (iPSCs), facilitate the study of sporadic as well as hereditary diseases and provide a comprehensive understanding of the molecular mechanisms involved with neurodegeneration. Through proteomics, a quantitative tool capable of identifying thousands of proteins from small sample volumes, researchers have attempted to identify disease mechanisms by detecting differentially expressed proteins and proteoforms in disease models, biofluids, and postmortem brain tissue. The integration of these two technologies allows for the identification of novel pathological targets within the realm of neurodegenerative diseases. Here, we highlight studies from the past 5 years on the contributions of iPSCs within neuroproteomic investigations, which uncover the molecular mechanisms behind these illnesses.
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Affiliation(s)
- Caroline Brandão-Teles
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Giuliana S Zuccoli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Talita Aparecida de Moraes Vrechi
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Lívia Ramos-da-Silva
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Aline Valéria Sousa Santos
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas 13083-862, SP, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria, Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D)
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
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8
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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9
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González Ibáñez F, Halvorson T, Sharma K, McKee CG, Carrier M, Picard K, Vernoux N, Bisht K, Deslauriers J, Lalowski M, Tremblay MÈ. Ketogenic diet changes microglial morphology and the hippocampal lipidomic profile differently in stress susceptible versus resistant male mice upon repeated social defeat. Brain Behav Immun 2023; 114:383-406. [PMID: 37689276 DOI: 10.1016/j.bbi.2023.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023] Open
Abstract
Psychological stress confers an increased risk for several diseases including psychiatric conditions. The susceptibility to psychological stress is modulated by various factors, many of them being modifiable lifestyle choices. The ketogenic diet (KD) has emerged as a dietary regime that offers positive outcomes on mood and health status. Psychological stress and elevated inflammation are common features of neuropsychiatric disorders such as certain types of major depressive disorder. KD has been attributed anti-inflammatory properties that could underlie its beneficial consequences on the brain and behavior. Microglia are the main drivers of inflammation in the central nervous system. They are known to respond to both dietary changes and psychological stress, notably by modifying their production of cytokines and relationships among the brain parenchyma. To assess the interactions between KD and the stress response, including effects on microglia, we examined adult male mice on control diet (CD) versus KD that underwent 10 days of repeated social defeat (RSD) or remained non-stressed (controls; CTRLs). Through a social interaction test, stressed mice were classified as susceptible (SUS) or resistant (RES) to RSD. The mouse population fed a KD tended to have a higher proportion of individuals classified as RES following RSD. Microglial morphology and ultrastructure were then analyzed in the ventral hippocampus CA1, a brain region known to present structural alterations as a response to psychological stress. Distinct changes in microglial soma and arborization linked to the KD, SUS and RES phenotypes were revealed. Ultrastructural analysis by electron microscopy showed a clear reduction of cellular stress markers in microglia from KD fed animals. Furthermore, ultrastructural analysis showed that microglial contacts with synaptic elements were reduced in the SUS compared to the RES and CTRL groups. Hippocampal lipidomic analyses lastly identified a distinct lipid profile in SUS animals compared to CTRLs. These key differences, combined with the distinct microglial responses to diet and stress, indicate that unique metabolic changes may underlie the stress susceptibility phenotypes. Altogether, our results reveal novel mechanisms by which a KD might improve the resistance to psychological stress.
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Affiliation(s)
- Fernando González Ibáñez
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada; Département de Médecine Moléculaire, Université Laval, Québec, Quebec, Canada; Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Torin Halvorson
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada; Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kaushik Sharma
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada; Département de Médecine Moléculaire, Université Laval, Québec, Quebec, Canada; Department of Chemistry, Purdue University, West Lafayette, Indiana, United States
| | - Chloe Grace McKee
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Micaël Carrier
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada; Département de Médecine Moléculaire, Université Laval, Québec, Quebec, Canada; Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Katherine Picard
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada; Département de Médecine Moléculaire, Université Laval, Québec, Quebec, Canada; Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Nathalie Vernoux
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada
| | - Kanchan Bisht
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada; Département de Médecine Moléculaire, Université Laval, Québec, Quebec, Canada; Department of Chemistry, Purdue University, West Lafayette, Indiana, United States
| | | | - Maciej Lalowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland; Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, Quebec, Canada; Département de Médecine Moléculaire, Université Laval, Québec, Quebec, Canada; Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada; Neurology and Neurosurgery Department, McGill University, Montréal, Quebec, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada; Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, British Columbia, Canada.
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10
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Jain M, Dhariwal R, Patil N, Ojha S, Tendulkar R, Tendulkar M, Dhanda PS, Yadav A, Kaushik P. Unveiling the Molecular Footprint: Proteome-Based Biomarkers for Alzheimer's Disease. Proteomes 2023; 11:33. [PMID: 37873875 PMCID: PMC10594437 DOI: 10.3390/proteomes11040033] [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: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by progressive cognitive decline and memory loss. Early and accurate diagnosis of AD is crucial for implementing timely interventions and developing effective therapeutic strategies. Proteome-based biomarkers have emerged as promising tools for AD diagnosis and prognosis due to their ability to reflect disease-specific molecular alterations. There is of great significance for biomarkers in AD diagnosis and management. It emphasizes the limitations of existing diagnostic approaches and the need for reliable and accessible biomarkers. Proteomics, a field that comprehensively analyzes the entire protein complement of cells, tissues, or bio fluids, is presented as a powerful tool for identifying AD biomarkers. There is a diverse range of proteomic approaches employed in AD research, including mass spectrometry, two-dimensional gel electrophoresis, and protein microarrays. The challenges associated with identifying reliable biomarkers, such as sample heterogeneity and the dynamic nature of the disease. There are well-known proteins implicated in AD pathogenesis, such as amyloid-beta peptides, tau protein, Apo lipoprotein E, and clusterin, as well as inflammatory markers and complement proteins. Validation and clinical utility of proteome-based biomarkers are addressing the challenges involved in validation studies and the diagnostic accuracy of these biomarkers. There is great potential in monitoring disease progression and response to treatment, thereby aiding in personalized medicine approaches for AD patients. There is a great role for bioinformatics and data analysis in proteomics for AD biomarker research and the importance of data preprocessing, statistical analysis, pathway analysis, and integration of multi-omics data for a comprehensive understanding of AD pathophysiology. In conclusion, proteome-based biomarkers hold great promise in the field of AD research. They provide valuable insights into disease mechanisms, aid in early diagnosis, and facilitate personalized treatment strategies. However, further research and validation studies are necessary to harness the full potential of proteome-based biomarkers in clinical practice.
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Affiliation(s)
- Mukul Jain
- Cell and Developmental Biology Laboratory, Research and Development Cell, Parul University, Vadodara 391760, India; (R.D.); (N.P.)
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Vadodara 391760, India;
| | - Rupal Dhariwal
- Cell and Developmental Biology Laboratory, Research and Development Cell, Parul University, Vadodara 391760, India; (R.D.); (N.P.)
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Vadodara 391760, India;
| | - Nil Patil
- Cell and Developmental Biology Laboratory, Research and Development Cell, Parul University, Vadodara 391760, India; (R.D.); (N.P.)
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Vadodara 391760, India;
| | - Sandhya Ojha
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Vadodara 391760, India;
| | - Reshma Tendulkar
- Vivekanand Education Society, College of Pharmacy, Chembur, Mumbai 400071, India;
| | - Mugdha Tendulkar
- Sardar Vallabhbhai Patel College of Science, Mira Rd (East), Thane 400071, India;
| | | | - Alpa Yadav
- Department of Botany, Indira Gandhi University, Meerpur, Rewari 122502, India;
| | - Prashant Kaushik
- Instituto de Conservacióny Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
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11
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Pysz PM, Hoskins JK, Zou M, Stenken JA. 3D Printed Customizable Microsampling Devices for Neuroscience Applications. ACS Chem Neurosci 2023; 14:3278-3287. [PMID: 37646856 DOI: 10.1021/acschemneuro.3c00166] [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: 09/01/2023] Open
Abstract
Multifunctional devices that incorporate chemical or physical measurements combined with ways to manipulate brain tissue via drug delivery, electrical stimulation, or light for optogenetics are desired by neuroscientists. The next generation in vivo brain devices will likely utilize the extensive flexibility and rapid processing of 3D printing. This Perspective demonstrates how close we are to this reality for advanced neuroscience measurements. 3D printing provides the opportunity to improve microsampling-based devices in ways that have not been previously available. Not only can 3D printing be used for actual device creation, but it can also allow printing of peripheral objects necessary to assemble functional devices. The most probable 3D printing set up for microsampling devices with appropriate nm to μm feature size will likely require 2-photon polymerization-based printers. This Perspective describes the advantages and challenges for 3D printing of microsampling devices as an initial step to meet the next generation device needs of neuroscientists.
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Affiliation(s)
- Patrick M Pysz
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Julia K Hoskins
- Department of Mechanical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Center for Advanced Surface Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Min Zou
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Department of Mechanical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Center for Advanced Surface Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Julie A Stenken
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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12
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González Ibáñez F, Halvorson T, Sharma K, McKee C, Carrier M, Picard K, Vernoux N, Bisht K, Deslauriers J, Lalowski M, Tremblay MÈ. Ketogenic diet alters microglial morphology and changes the hippocampal lipidomic profile distinctively in stress susceptible versus resistant male mice upon repeated social defeat. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555135. [PMID: 37693370 PMCID: PMC10491121 DOI: 10.1101/2023.08.28.555135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Psychological stress confers an increased risk for several diseases including psychiatric conditions. The susceptibility to psychological stress is modulated by various factors, many of them being modifiable lifestyle choices. The ketogenic diet (KD) has emerged as a dietary regime that offers positive outcomes on mood and health status. Psychological stress and elevated inflammation are common features of neuropsychiatric disorders such as certain types of major depressive disorder. KD has been attributed anti-inflammatory properties that could underlie its beneficial consequences on the brain and behavior. Microglia are the main drivers of inflammation in the central nervous system. They are known to respond to both dietary changes and psychological stress, notably by modifying their production of cytokines and relationships among the brain parenchyma. To assess the interactions between KD and the stress response, including effects on microglia, we examined adult male mice on control diet (CD) versus KD that underwent 10 days of repeated social defeat (RSD) or remained non-stressed (controls; CTRLs). Through a social interaction test, stressed mice were classified as susceptible (SUS) or resistant (RES) to RSD. The mouse population fed a KD tended to have a higher proportion of individuals classified as RES following RSD. Microglial morphology and ultrastructure were then analyzed in the ventral hippocampus CA1, a brain region known to present structural alterations as a response to psychological stress. Distinct changes in microglial soma and arborization linked to the KD, SUS and RES phenotypes were revealed. Ultrastructural analysis by electron microscopy showed a clear reduction of cellular stress markers in microglia from KD fed animals. Furthermore, ultrastructural analysis showed that microglial contacts with synaptic elements were reduced in the SUS compared to the RES and CTRL groups. Hippocampal lipidomic analyses lastly identified a distinct lipid profile in SUS animals compared to CTRLs. These key differences, combined with the distinct microglial responses to diet and stress, indicate that unique metabolic changes may underlie the stress susceptibility phenotypes. Altogether, our results reveal novel mechanisms by which a KD might improve the resistance to psychological stress.
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Affiliation(s)
- Fernando González Ibáñez
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de médecine moléculaire, Université Laval, Québec City, QC, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Torin Halvorson
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kaushik Sharma
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de médecine moléculaire, Université Laval, Québec City, QC, Canada
- Department of Chemistry, Purdue University, West Lafayette, IN, United States of America
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Micaël Carrier
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de médecine moléculaire, Université Laval, Québec City, QC, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Katherine Picard
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de médecine moléculaire, Université Laval, Québec City, QC, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Nathalie Vernoux
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Kanchan Bisht
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de médecine moléculaire, Université Laval, Québec City, QC, Canada
- Department of Chemistry, Purdue University, West Lafayette, IN, United States of America
| | | | - Maciej Lalowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Biochemistry/Developmental Biology, Meilahti Clinical Proteomics Core Facility, University of Helsinki, Finland
| | - Marie-Ève Tremblay
- Axe neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Département de médecine moléculaire, Université Laval, Québec City, QC, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Neurology and Neurosurgery Department, McGill University, Montréal, QC, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, BC, Canada
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13
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Montero-Calle A, Coronel R, Garranzo-Asensio M, Solís-Fernández G, Rábano A, de Los Ríos V, Fernández-Aceñero MJ, Mendes ML, Martínez-Useros J, Megías D, Moreno-Casbas MT, Peláez-García A, Liste I, Barderas R. Proteomics analysis of prefrontal cortex of Alzheimer's disease patients revealed dysregulated proteins in the disease and novel proteins associated with amyloid-β pathology. Cell Mol Life Sci 2023; 80:141. [PMID: 37149819 PMCID: PMC11073180 DOI: 10.1007/s00018-023-04791-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 04/06/2023] [Accepted: 04/25/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a progressive, chronic, and neurodegenerative disease, and the most common cause of dementia worldwide. Currently, the mechanisms underlying the disease are far from being elucidated. Thus, the study of proteins involved in its pathogenesis would allow getting further insights into the disease and identifying new markers for AD diagnosis. METHODS We aimed here to analyze protein dysregulation in AD brain by quantitative proteomics to identify novel proteins associated with the disease. 10-plex TMT (tandem mass tags)-based quantitative proteomics experiments were performed using frozen tissue samples from the left prefrontal cortex of AD patients and healthy individuals and vascular dementia (VD) and frontotemporal dementia (FTD) patients as controls (CT). LC-MS/MS analyses were performed using a Q Exactive mass spectrometer. RESULTS In total, 3281 proteins were identified and quantified using MaxQuant. Among them, after statistical analysis with Perseus (p value < 0.05), 16 and 155 proteins were defined as upregulated and downregulated, respectively, in AD compared to CT (Healthy, FTD and VD) with an expression ratio ≥ 1.5 (upregulated) or ≤ 0.67 (downregulated). After bioinformatics analysis, ten dysregulated proteins were selected as more prone to be associated with AD, and their dysregulation in the disease was verified by qPCR, WB, immunohistochemistry (IHC), immunofluorescence (IF), pull-down, and/or ELISA, using tissue and plasma samples of AD patients, patients with other dementias, and healthy individuals. CONCLUSIONS We identified and validated novel AD-associated proteins in brain tissue that should be of further interest for the study of the disease. Remarkably, PMP2 and SCRN3 were found to bind to amyloid-β (Aβ) fibers in vitro, and PMP2 to associate with Aβ plaques by IF, whereas HECTD1 and SLC12A5 were identified as new potential blood-based biomarkers of the disease.
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Affiliation(s)
- Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220, Madrid, Spain
| | - Raquel Coronel
- Unidad de Regeneración Neural, Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - María Garranzo-Asensio
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220, Madrid, Spain
| | - Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220, Madrid, Spain
- Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Celestijnenlaan 200F, Heverlee, 3001, Louvain, Belgium
| | - Alberto Rábano
- Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, E-28031, Madrid, Spain
| | | | | | - Marta L Mendes
- Department of Infection and Immunity, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Health Research Institute-University Hospital Fundación Jiménez Díaz-Universidad Autónoma de Madrid, E-28040, Madrid, Spain
- Area of Physiology, Department of Basic Health Sciences, Faculty of Health Sciences, Rey Juan Carlos University, E-28922, Madrid, Spain
| | - Diego Megías
- Advanced Optical Microscopy Unit, UCCTs, Instituto de Salud Carlos III (ISCIII), E-28220, Majadahonda, Madrid, Spain
| | | | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), E-28046, Madrid, Spain
| | - Isabel Liste
- Unidad de Regeneración Neural, Unidad Funcional de Investigación de Enfermedades Crónicas, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220, Madrid, Spain.
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14
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Thanou E, Koopmans F, Pita-Illobre D, Klaassen RV, Özer B, Charalampopoulos I, Smit AB, Li KW. Suspension TRAPping Filter (sTRAP) Sample Preparation for Quantitative Proteomics in the Low µg Input Range Using a Plasmid DNA Micro-Spin Column: Analysis of the Hippocampus from the 5xFAD Alzheimer's Disease Mouse Model. Cells 2023; 12:cells12091242. [PMID: 37174641 PMCID: PMC10177283 DOI: 10.3390/cells12091242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Suspension TRAPping filter (sTRAP) is an attractive sample preparation method for proteomics studies. The sTRAP protocol uses 5% SDS that maximizes protein solubilization. Proteins are trapped on a borosilicate glass membrane filter, where SDS is subsequently removed from the filter. After trypsin digestion, peptides are analyzed directly by LC-MS. Here, we demonstrated the use of a low-cost plasmid DNA micro-spin column for the sTRAP sample preparation of a dilution series of a synapse-enriched sample with a range of 10-0.3 µg. With 120 ng tryptic peptides loaded onto the Evosep LC system coupled to timsTOF Pro 2 mass spectrometer, we identified 5700 protein groups with 4% coefficient of variation (CoV). Comparing other sample preparation protocols, such as the in-gel digestion and the commercial Protifi S-TRAP with the plasmid DNA micro-spin column, the last is superior in both protein and peptide identification numbers and CoV. We applied sTRAP for the analysis of the hippocampal proteome from the 5xFAD mouse model of Alzheimer's disease and their wildtype littermates, and revealed 121 up- and 54 down-regulated proteins. Protein changes in the mutant mice point to the alteration of processes related to the immune system and Amyloid aggregation, which correlates well with the known major Alzheimer's-disease-related pathology. Data are available via ProteomeXchange with the identifier PXD041045.
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Affiliation(s)
- Evangelia Thanou
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Débora Pita-Illobre
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Remco V Klaassen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Berna Özer
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ioannis Charalampopoulos
- Pharmacology Department, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 71003 Heraklion, Greece
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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15
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Quality Control—A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome. Biomolecules 2023; 13:biom13030491. [PMID: 36979426 PMCID: PMC10046854 DOI: 10.3390/biom13030491] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/08/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Proteomic studies using mass spectrometry (MS)-based quantification are a main approach to the discovery of new biomarkers. However, a number of analytical conditions in front and during MS data acquisition can affect the accuracy of the obtained outcome. Therefore, comprehensive quality assessment of the acquired data plays a central role in quantitative proteomics, though, due to the immense complexity of MS data, it is often neglected. Here, we address practically the quality assessment of quantitative MS data, describing key steps for the evaluation, including the levels of raw data, identification and quantification. With this, four independent datasets from cerebrospinal fluid, an important biofluid for neurodegenerative disease biomarker studies, were assessed, demonstrating that sample processing-based differences are already reflected at all three levels but with varying impacts on the quality of the quantitative data. Specifically, we provide guidance to critically interpret the quality of MS data for quantitative proteomics. Moreover, we provide the free and open source quality control tool MaCProQC, enabling systematic, rapid and uncomplicated data comparison of raw data, identification and feature detection levels through defined quality metrics and a step-by-step quality control workflow.
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16
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Direct and Indirect Effects of Filamin A on Tau Pathology in Neuronal Cells. Mol Neurobiol 2023; 60:1021-1039. [PMID: 36399251 PMCID: PMC9849303 DOI: 10.1007/s12035-022-03121-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
In Alzheimer disease (AD), Tau, an axonal microtubule-associated protein, becomes hyperphosphorylated, detaches from microtubules, accumulates, and self-aggregates in the somatodendritic (SD) compartment. The accumulation of hyperphosphorylated and aggregated Tau is also seen in other neurodegenerative diseases such as frontotemporal lobar degeneration (FTLD-Tau). Previous studies reported a link between filamin A (FLNA), an actin-binding protein found in the SD compartment, and Tau pathology. In the present study, we further explored this link. We confirmed the interaction of Tau with FLNA in neuroblastoma 2a (N2a) cells. This interaction was mediated by a domain located between the 157 and 383 amino acids (a.a.) of Tau. Our results also revealed that the overexpression of FLNA resulted in an intracellular accumulation of wild-type Tau and Tau mutants (P301L, V337M, and R406W) in N2a cells. Tau phosphorylation and cleavage by caspase-3 but not its aggregation were increased upon FLNA overexpression in N2a cells. In the parietal cortex of AD brain, insoluble FLNA was increased compared to control brain, but it did not correlate with Tau pathology. Interestingly, Tau binding to microtubules and F-actin was preserved upon FLNA overexpression in N2a cells. Lastly, our results revealed that FLNA also induced the accumulation of annexin A2, a Tau interacting partner involved in its axonal localization. Collectively, our data indicated that in Tauopathies, FLNA could contribute to Tau pathology by acting on Tau and annexin A2.
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17
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From protein biomarkers to proteomics in dementia with Lewy Bodies. Ageing Res Rev 2023; 83:101771. [PMID: 36328346 DOI: 10.1016/j.arr.2022.101771] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/15/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative dementia. Despite considerable research progress, there remain gaps in our understanding of the pathophysiology and there is no disease-modifying treatment. Proteomics is a powerful tool to elucidate complex biological pathways across heterogenous conditions. This review summarizes the widely used proteomic methods and presents evidence for protein dysregulation in the brain and peripheral tissues in DLB. Proteomics of post-mortem brain tissue shows that DLB shares common features with other dementias, such as synaptic dysfunction, but retains a unique protein signature. Promising diagnostic biomarkers are being identified in cerebrospinal fluid (CSF), blood, and peripheral tissues, such as serum Heart-type fatty acid binding protein. Research is needed to track these changes from the prodromal stage to established dementia, with standardized workflows to ensure replicability. Identifying novel protein targets in causative biological pathways could lead to the development of new targeted therapeutics or the stratification of participants for clinical trials.
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Proteomics of the dentate gyrus reveals semantic dementia specific molecular pathology. Acta Neuropathol Commun 2022; 10:190. [PMID: 36578035 PMCID: PMC9795759 DOI: 10.1186/s40478-022-01499-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Semantic dementia (SD) is a clinical subtype of frontotemporal dementia consistent with the neuropathological diagnosis frontotemporal lobar degeneration (FTLD) TDP type C, with characteristic round TDP-43 protein inclusions in the dentate gyrus. Despite this striking clinicopathological concordance, the pathogenic mechanisms are largely unexplained forestalling the development of targeted therapeutics. To address this, we carried out laser capture microdissection of the dentate gyrus of 15 SD patients and 17 non-demented controls, and assessed relative protein abundance changes by label-free quantitative mass spectrometry. To identify SD specific proteins, we compared our results to eight other FTLD and Alzheimer's disease (AD) proteomic datasets of cortical brain tissue, parallel with functional enrichment analyses and protein-protein interactions (PPI). Of the total 5,354 quantified proteins, 151 showed differential abundance in SD patients (adjusted P-value < 0.01). Seventy-nine proteins were considered potentially SD specific as these were not detected, or demonstrated insignificant or opposite change in FTLD/AD. Functional enrichment indicated an overrepresentation of pathways related to the immune response, metabolic processes, and cell-junction assembly. PPI analysis highlighted a cluster of interacting proteins associated with adherens junction and cadherin binding, the cadherin-catenin complex. Multiple proteins in this complex showed significant upregulation in SD, including β-catenin (CTNNB1), γ-catenin (JUP), and N-cadherin (CDH2), which were not observed in other neurodegenerative proteomic studies, and hence may resemble SD specific involvement. A trend of upregulation of all three proteins was observed by immunoblotting of whole hippocampus tissue, albeit only significant for N-cadherin. In summary, we discovered a specific increase of cell adhesion proteins in SD constituting the cadherin-catenin complex at the synaptic membrane, essential for synaptic signaling. Although further investigation and validation are warranted, we anticipate that these findings will help unravel the disease processes underlying SD.
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Xin C, Guan X, Wang L, Liu J. Integrative Multi-Omics Research in Cerebral Palsy: Current Progress and Future Prospects. Neurochem Res 2022; 48:1269-1279. [PMID: 36512293 DOI: 10.1007/s11064-022-03839-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/10/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Cerebral palsy (CP) describes a heterogeneous group of non-progressive neurodevelopmental disorders affecting movement and posture. The etiology and diagnostic biomarkers of CP are a hot topic in clinical research. Recent advances in omics techniques, including genomics, epigenomics, transcriptomics, metabolomics and proteomics, have offered new insights to further understand the pathophysiology of CP and have allowed for identification of diagnostic biomarkers of CP. In present study, we reviewed the latest multi-omics investigations of CP and provided an in-depth summary of current research progress in CP. This review will offer the basis and recommendations for future fundamental research on the pathogenesis of CP, identification of diagnostic biomarkers, and prevention strategies for CP.
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Affiliation(s)
- Chengqi Xin
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, No. 193, Lianhe Road, Shahekou District, 116011, Dalian City, Liaoning Province, P.R. China
- Dalian Innovation Institute of Stem Cell and Precision Medicine, No. 57, Xinda Street, Dalian High-Tech Park, 116023, Dalian City, Liaoning Province, P.R. China
| | - Xin Guan
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, No. 193, Lianhe Road, Shahekou District, 116011, Dalian City, Liaoning Province, P.R. China
- Dalian Innovation Institute of Stem Cell and Precision Medicine, No. 57, Xinda Street, Dalian High-Tech Park, 116023, Dalian City, Liaoning Province, P.R. China
| | - Liang Wang
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, No. 193, Lianhe Road, Shahekou District, 116011, Dalian City, Liaoning Province, P.R. China
- Dalian Innovation Institute of Stem Cell and Precision Medicine, No. 57, Xinda Street, Dalian High-Tech Park, 116023, Dalian City, Liaoning Province, P.R. China
| | - Jing Liu
- Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, No. 193, Lianhe Road, Shahekou District, 116011, Dalian City, Liaoning Province, P.R. China.
- Dalian Innovation Institute of Stem Cell and Precision Medicine, No. 57, Xinda Street, Dalian High-Tech Park, 116023, Dalian City, Liaoning Province, P.R. China.
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Yoon JH, Seo Y, Jo YS, Lee S, Cho E, Cazenave-Gassiot A, Shin YS, Moon MH, An HJ, Wenk MR, Suh PG. Brain lipidomics: From functional landscape to clinical significance. SCIENCE ADVANCES 2022; 8:eadc9317. [PMID: 36112688 PMCID: PMC9481132 DOI: 10.1126/sciadv.adc9317] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 05/23/2023]
Abstract
Lipids are crucial components of cellular function owing to their role in membrane formation, intercellular signaling, energy storage, and homeostasis maintenance. In the brain, lipid dysregulations have been associated with the etiology and progression of neurodegeneration and other neurological pathologies. Hence, brain lipids are emerging as important potential targets for the early diagnosis and prognosis of neurological diseases. This review aims to highlight the significance and usefulness of lipidomics in diagnosing and treating brain diseases. We explored lipid alterations associated with brain diseases, paying attention to organ-specific characteristics and the functions of brain lipids. As the recent advances in brain lipidomics would have been impossible without advances in analytical techniques, we provide up-to-date information on mass spectrometric approaches and integrative analysis with other omic approaches. Last, we present the potential applications of lipidomics combined with artificial intelligence techniques and interdisciplinary collaborative research for treating brain diseases with clinical heterogeneities.
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Affiliation(s)
- Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Yeon Suk Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
- Department of Brain Sciences, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Seulah Lee
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Eunji Cho
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
| | - Yong-Seung Shin
- Laboratory Solutions Sales, Agilent Technologies Korea Ltd., Seoul, 06621, Republic of Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore
| | - Pann-Ghill Suh
- Korea Brain Research Institute, Daegu 41062, Republic of Korea
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21
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Inoue Y, Tasaki M, Masuda T, Misumi Y, Nomura T, Ando Y, Ueda M. α-Enolase reduces cerebrovascular Aβ deposits by protecting Aβ amyloid formation. Cell Mol Life Sci 2022; 79:462. [PMID: 35916996 PMCID: PMC11072596 DOI: 10.1007/s00018-022-04493-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: 02/17/2022] [Revised: 06/29/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
Cerebral amyloid angiopathy (CAA) is characterized by cerebrovascular amyloid β (Aβ) deposits and causes dementia and cerebral hemorrhage. Although α-enolase (ENO1) was shown to possess multifunctional roles, its exact functions in CAA pathogenesis have not been determined. In this study, we focused on ENO1, a well-known glycolytic enzyme, which was previously identified via a proteomic approach as an upregulated protein in brain samples from patients with Alzheimer's disease (AD). We utilized the thioflavin T fluorescence assay and transmission electron microscopy to monitor the effects of ENO1 on amyloid formation by Aβ peptides. We also cultured murine primary cerebrovascular smooth muscle cells to determine the effects of ENO1 on Aβ cytotoxicity. To investigate the effects of ENO1 in vivo, we infused ENO1 or a vehicle control into the brains of APP23 mice, a transgenic model of AD/CAA, using a continuous infusion system, followed by a cognitive test and pathological and biochemical analyses. We found that novel functions of ENO1 included interacting with Aβ and inhibiting its fibril formation, disrupting Aβ fibrils, and weakening the cytotoxic effects of these fibrils via proteolytic degradation of Aβ peptide. We also demonstrated that infusion of ENO1 into APP23 mouse brains reduced cerebrovascular Aβ deposits and improved cognitive impairment. In addition, we found that enzymatically inactivated ENO1 failed to inhibit Aβ fibril formation and fibril disruption. The proteolytic activity of ENO1 may thus underlie the enzyme's cytoprotective effect and clearance of Aβ from the brain, and ENO1 may be a therapeutic target in CAA.
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Affiliation(s)
- Yasuteru Inoue
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1, Chuo-ku, Honjo, Kumamoto, Kumamoto, 860-8556, Japan.
| | - Masayoshi Tasaki
- Department of Biomedical Laboratory Sciences, Graduate School of Health Sciences, Kumamoto University, Kumamoto, Japan
| | - Teruaki Masuda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1, Chuo-ku, Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Yohei Misumi
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1, Chuo-ku, Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Toshiya Nomura
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1, Chuo-ku, Honjo, Kumamoto, Kumamoto, 860-8556, Japan
| | - Yukio Ando
- Department of Amyloidosis Research, Nagasaki International University, Sasebo, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1, Chuo-ku, Honjo, Kumamoto, Kumamoto, 860-8556, Japan
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22
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Kluever V, Russo B, Mandad S, Kumar NH, Alevra M, Ori A, Rizzoli SO, Urlaub H, Schneider A, Fornasiero EF. Protein lifetimes in aged brains reveal a proteostatic adaptation linking physiological aging to neurodegeneration. SCIENCE ADVANCES 2022; 8:eabn4437. [PMID: 35594347 PMCID: PMC9122331 DOI: 10.1126/sciadv.abn4437] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/07/2022] [Indexed: 05/27/2023]
Abstract
Aging is a prominent risk factor for neurodegenerative disorders (NDDs); however, the molecular mechanisms rendering the aged brain particularly susceptible to neurodegeneration remain unclear. Here, we aim to determine the link between physiological aging and NDDs by exploring protein turnover using metabolic labeling and quantitative pulse-SILAC proteomics. By comparing protein lifetimes between physiologically aged and young adult mice, we found that in aged brains protein lifetimes are increased by ~20% and that aging affects distinct pathways linked to NDDs. Specifically, a set of neuroprotective proteins are longer-lived in aged brains, while some mitochondrial proteins linked to neurodegeneration are shorter-lived. Strikingly, we observed a previously unknown alteration in proteostasis that correlates to parsimonious turnover of proteins with high biosynthetic costs, revealing an overall metabolic adaptation that preludes neurodegeneration. Our findings suggest that future therapeutic paradigms, aimed at addressing these metabolic adaptations, might be able to delay NDD onset.
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Affiliation(s)
- Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Belisa Russo
- German Center for Neurodegenerative Diseases, DZNE Bonn, Venusberg Campus 1, 53127 Bonn, Germany
| | - Sunit Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Nisha Hemandhar Kumar
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mihai Alevra
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Silvio O. Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Anja Schneider
- German Center for Neurodegenerative Diseases, DZNE Bonn, Venusberg Campus 1, 53127 Bonn, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany
| | - Eugenio F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
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23
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Analysis of human brain tissue derived from DBS surgery. Transl Neurodegener 2022; 11:22. [PMID: 35418104 PMCID: PMC9006459 DOI: 10.1186/s40035-022-00297-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the postmortem interval can affect the transcriptomic and proteomic profiles. Therefore, fresh brain tissue samples from living patients represent a valuable resource of metabolically intact tissue. Implantation of deep brain stimulation (DBS) electrodes into the human brain is a neurosurgical treatment for, e.g., movement disorders. Here, we describe an improved approach to collecting brain tissues from surgical instruments used in implantation of DBS device for transcriptomics and proteomics analyses. Methods Samples were extracted from guide tubes and recording electrodes used in routine DBS implantation procedure to treat patients with Parkinson’s disease, genetic dystonia and tremor. RNA sequencing was performed in tissues extracted from the recording microelectrodes and liquid chromatography-mass spectrometry (LC-MS) performed in tissues from guide tubes. To assess the performance of the current approach, the obtained datasets were compared with previously published datasets representing brain tissues. Results Altogether, 32,034 RNA transcripts representing the unique Ensembl gene identifiers were detected from eight samples representing both hemispheres of four patients. By using LC-MS, we identified 734 unique proteins from 31 samples collected from 14 patients. The datasets are available in the BioStudies database (accession number S-BSST667). Our results indicate that surgical instruments used in DBS installation retain brain material sufficient for protein and gene expression studies. Comparison with previously published datasets obtained with similar approach proved the robustness and reproducibility of the protocol. Conclusions The instruments used during routine DBS surgery are a useful source for obtaining fresh brain tissues from living patients. This approach overcomes the issues that arise from using postmortem tissues, such as the effect of postmortem interval on transcriptomic and proteomic landscape of the brain, and can be used for studying molecular aspects of DBS-treatable diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-022-00297-y.
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24
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Kwon DH, Hwang JS, Kim SG, Jang YE, Shin TH, Lee G. Cerebrospinal Fluid Metabolome in Parkinson's Disease and Multiple System Atrophy. Int J Mol Sci 2022; 23:ijms23031879. [PMID: 35163800 PMCID: PMC8836409 DOI: 10.3390/ijms23031879] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Parkinson’s disease (PD) and multiple system atrophy (MSA) belong to the neurodegenerative group of synucleinopathies; differential diagnosis between PD and MSA is difficult, especially at early stages, owing to their clinical and biological similarities. Thus, there is a pressing need to identify metabolic biomarkers for these diseases. The metabolic profile of the cerebrospinal fluid (CSF) is reported to be altered in PD and MSA; however, the altered metabolites remain unclear. We created a single network with altered metabolites in PD and MSA based on the literature and assessed biological functions, including metabolic disorders of the nervous system, inflammation, concentration of ATP, and neurological disorder, through bioinformatics methods. Our in-silico prediction-based metabolic networks are consistent with Parkinsonism events. Although metabolomics approaches provide a more quantitative understanding of biochemical events underlying the symptoms of PD and MSA, limitations persist in covering molecules related to neurodegenerative disease pathways. Thus, omics data, such as proteomics and microRNA, help understand the altered metabolomes mechanism. In particular, integrated omics and machine learning approaches will be helpful to elucidate the pathological mechanisms of PD and MSA. This review discusses the altered metabolites between PD and MSA in the CSF and omics approaches to discover diagnostic biomarkers.
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Affiliation(s)
- Do Hyeon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Ji Su Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Seok Gi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Yong Eun Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
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25
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Agrawal I, Tripathi P, Biswas S. Mass Spectrometry Based Protein Biomarkers and Drug Target Discovery and Clinical Diagnosis in Age-Related Progressing Neurodegenerative Diseases. Drug Metab Rev 2022; 54:22-36. [PMID: 35038284 DOI: 10.1080/03602532.2022.2029475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Neurodegenerative diseases correspond to overly complex health disorders that are driven by intersecting pathophysiology that are often trapped in vicious cycles of degeneration and cognitive decline. The usual diagnostic route of these diseases is based on postmortem examination that involves identifying pathology that is specific to the disease in the brain. However, in such cases, accurate diagnosis of the specific disease is limited because clinical disease presentations are often complex that do not easily allow to discriminate patient's cognitive, behavioral, and functional impairment profiles. Additionally, an early identification and therapeutic intervention of these diseases is pivotal to slow the progression of neurodegeneration and extend healthy life span. Mass spectrometry-based techniques have proven to be hugely promising in biological sample analysis and discovery of biomarkers including protein and peptide biomarkers for potential drug target discovery. Recent studies on these biomarkers have demonstrated their potential for applications in early diagnostics and identifying therapeutic targets to battle against neurodegenerative diseases. In this review, we have presented principles of mass spectrometry (MS) and the associated workflows in analyzing and imaging biological samples for discovery of biomarkers. We have especially focused on age- related progressing neurodegenerative diseases such as Alzheimer's (AD) and Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD) and the related MS-based biomarkers developments for these diseases. Finally, we present a future perspective discussing the potential research directions ahead.
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Affiliation(s)
- Ishita Agrawal
- Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Pallavi Tripathi
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shyamasri Biswas
- USA Prime Biotech LLC, 1330 NW 6th St., Suite A-2, Gainesville, FL 32601, USA
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26
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Beker MC, Caglayan AB, Altunay S, Ozbay E, Ates N, Kelestemur T, Caglayan B, Kilic U, Doeppner TR, Hermann DM, Kilic E. Phosphodiesterase 10A Is a Critical Target for Neuroprotection in a Mouse Model of Ischemic Stroke. Mol Neurobiol 2021; 59:574-589. [PMID: 34735672 DOI: 10.1007/s12035-021-02621-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022]
Abstract
Phosphodiesterase 10A (PDE10A) hydrolyzes adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP). It is highly expressed in the striatum. Recent evidence implied that PDE10A may be involved in the inflammatory processes following injury, such as ischemic stroke. Its role in ischemic injury was unknown. Herein, we exposed mice to 90 or 30-min middle cerebral artery occlusion, followed by the delivery of the highly selective PDE10A inhibitor TAK-063 (0.3 mg/kg or 3 mg/kg) immediately after reperfusion. Animals were sacrificed after 24 or 72 h, respectively. Both TAK-063 doses enhanced neurological function, reduced infarct volume, increased neuronal survival, reduced brain edema, and increased blood-brain barrier integrity, alongside cerebral microcirculation improvements. Post-ischemic neuroprotection was associated with increased phosphorylation (i.e., activation) of pro-survival Akt, Erk-1/2, GSK-3α/β and anti-apoptotic Bcl-xL abundance, decreased phosphorylation of pro-survival mTOR, and HIF-1α, MMP-9 and pro-apoptotic Bax abundance. Interestingly, PDE10A inhibition reduced inflammatory cytokines/chemokines, including IFN-γ and TNF-α, analyzed by planar surface immunoassay. In addition, liquid chromatography-tandem mass spectrometry revealed 40 proteins were significantly altered by TAK-063. Our study established PDE10A as a target for ischemic stroke therapy.
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Affiliation(s)
- Mustafa C Beker
- Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey. .,Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.
| | - Ahmet B Caglayan
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Serdar Altunay
- Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Elif Ozbay
- Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Nilay Ates
- Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Taha Kelestemur
- Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Berrak Caglayan
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Genetics, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ulkan Kilic
- Department of Medical Biology, International School of Medicine, University of Health Sciences Turkey, Istanbul, Turkey
| | - Thorsten R Doeppner
- Department of Neurology, University Medicine Göttingen, University of Göttingen, Göttingen, Germany
| | - Dirk M Hermann
- Department of Neurology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ertugrul Kilic
- Department of Physiology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
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27
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Molecular Pathways Involved in Frontotemporal Lobar Degeneration with TDP-43 Proteinopathy: What Can We Learn from Proteomics? Int J Mol Sci 2021; 22:ijms221910298. [PMID: 34638637 PMCID: PMC8508653 DOI: 10.3390/ijms221910298] [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: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) is a neurodegenerative disorder clinically characterized by behavioral, language, and motor symptoms, with major impact on the lives of patients and their families. TDP-43 proteinopathy is the underlying neuropathological substrate in the majority of cases, referred to as FTLD-TDP. Several genetic causes have been identified, which have revealed some components of its pathophysiology. However, the exact mechanisms driving FTLD-TDP remain largely unknown, forestalling the development of therapies. Proteomic approaches, in particular high-throughput mass spectrometry, hold promise to help elucidate the pathogenic molecular and cellular alterations. In this review, we describe the main findings of the proteomic profiling studies performed on human FTLD-TDP brain tissue. Subsequently, we address the major biological pathways implicated in FTLD-TDP, by reviewing these data together with knowledge derived from genomic and transcriptomic literature. We illustrate that an integrated perspective, encompassing both proteomic, genetic, and transcriptomic discoveries, is vital to unravel core disease processes, and to enable the identification of disease biomarkers and therapeutic targets for this devastating disorder.
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28
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Abyadeh M, Gupta V, Chitranshi N, Gupta V, Wu Y, Saks D, Wander Wall R, Fitzhenry MJ, Basavarajappa D, You Y, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. Mitochondrial dysfunction in Alzheimer's disease - a proteomics perspective. Expert Rev Proteomics 2021; 18:295-304. [PMID: 33874826 DOI: 10.1080/14789450.2021.1918550] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is involved in Alzheimer's disease (AD) pathogenesis. Mitochondria have their own genetic material; however, most of their proteins (∼99%) are synthesized as precursors on cytosolic ribosomes, and then imported into the mitochondria. Therefore, exploring proteome changes in these organelles can yield valuable information and shed light on the molecular mechanisms underlying mitochondrial dysfunction in AD. Here, we review AD-associated mitochondrial changes including the effects of amyloid beta and tau protein accumulation on the mitochondrial proteome. We also discuss the relationship of ApoE genetic polymorphism with mitochondrial changes, and present a meta-analysis of various differentially expressed proteins in the mitochondria in AD.Area covered: Proteomics studies and their contribution to our understanding of mitochondrial dysfunction in AD pathogenesis.Expert opinion: Proteomics has proven to be an efficient tool to uncover various aspects of this complex organelle, which will broaden our understanding of mitochondrial dysfunction in AD. Evidently, mitochondrial dysfunction is an early biochemical event that might play a central role in driving AD pathogenesis.
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Affiliation(s)
- Morteza Abyadeh
- Cell Science Research Center, Department of Molecular Systems Biology, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran Iran
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Nitin Chitranshi
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Veer Gupta
- School of Medicine, Deakin University, VIC, Australia
| | - Yunqi Wu
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW Australia
| | - Danit Saks
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Roshana Wander Wall
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Matthew J Fitzhenry
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW Australia
| | - Devaraj Basavarajappa
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Yuyi You
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Ghasem H Salekdeh
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Stuart L Graham
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
| | - Mehdi Mirzaei
- Department of Clinical Medicine, Macquarie University, Macquarie Park, NSW, Australia
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29
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Perrone F, Cacace R, van der Zee J, Van Broeckhoven C. Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases. Genome Med 2021; 13:59. [PMID: 33853652 PMCID: PMC8048219 DOI: 10.1186/s13073-021-00878-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the molecular etiology of neurodegenerative brain diseases (NBD) has substantially increased over the past three decades. Early genetic studies of NBD families identified rare and highly penetrant deleterious mutations in causal genes that segregate with disease. Large genome-wide association studies uncovered common genetic variants that influenced disease risk. Major developments in next-generation sequencing (NGS) technologies accelerated gene discoveries at an unprecedented rate and revealed novel pathways underlying NBD pathogenesis. NGS technology exposed large numbers of rare genetic variants of uncertain significance (VUS) in coding regions, highlighting the genetic complexity of NBD. Since experimental studies of these coding rare VUS are largely lacking, the potential contributions of VUS to NBD etiology remain unknown. In this review, we summarize novel findings in NBD genetic etiology driven by NGS and the impact of rare VUS on NBD etiology. We consider different mechanisms by which rare VUS can act and influence NBD pathophysiology and discuss why a better understanding of rare VUS is instrumental for deriving novel insights into the molecular complexity and heterogeneity of NBD. New knowledge might open avenues for effective personalized therapies.
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Affiliation(s)
- Federica Perrone
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
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30
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Du X, Shi Q, Zhao Y, Xie Y, Li X, Liu Q, Iqbal J, Zhang H, Liu X, Shen L. Se-Methylselenocysteine (SMC) Improves Cognitive Deficits by Attenuating Synaptic and Metabolic Abnormalities in Alzheimer's Mice Model: A Proteomic Study. ACS Chem Neurosci 2021; 12:1112-1132. [PMID: 33689275 DOI: 10.1021/acschemneuro.0c00549] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Se-methylselenocysteine (SMC) is a major selenocompound in selenium (Se) enriched plants and has been found to ameliorate neuropathology and cognitive deficits in triple-transgenic mice model of Alzheimer's disease (3 × Tg-AD mice). To explore the underlying molecular mechanisms, the present study is designed to elucidate the protein changes in the cortex of SMC-treated 3 × Tg-AD mice. After SMC supplementation, proteomic analysis revealed that 181, 271, and 41 proteins were identified as differentially expressed proteins (DEPs) between 3 × Tg-AD mice vs wild type (AD/WT group), SMC-treated AD mice vs AD (AD + SMC/AD), and AD + SMC/WT group, respectively. Among these, 138 proteins in the diseased group were reversed by SMC treatment. The DEPs in AD/WT group and AD + SMC/AD group were mainly related to metabolism, synapses, and antioxidant proteins, while their levels were decreased in AD mice but up-regulated after treating with SMC. In addition, we found reduced ATP levels and destroyed synaptic structures in the AD mice brains, which were significantly ameliorated upon SMC treatment. Our study suggests that energy metabolism disorders, abnormal amino acid metabolism, synaptic dysfunction, and oxidative stress may be the key pathogenic phenomena of AD. SMC reversed the expression of proteins associated with them, which might be the main mechanism of its intervention in AD.
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Affiliation(s)
- Xiubo Du
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Qingqing Shi
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Yuxi Zhao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Yongli Xie
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Xuexia Li
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Javed Iqbal
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
| | - Huajie Zhang
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
- Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
| | - Xukun Liu
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, P. R. China
| | - Liming Shen
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, P. R. China
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Proteomic Profiling of Cerebrum Mitochondria, Myelin Sheath, and Synaptosome Revealed Mitochondrial Damage and Synaptic Impairments in Association with 3 × Tg-AD Mice Model. Cell Mol Neurobiol 2021; 42:1745-1763. [PMID: 33560469 DOI: 10.1007/s10571-021-01052-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/29/2021] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) is the most common age-associated dementia with complex pathological hallmarks. Mitochondrion, synaptosome, and myelin sheath appear to be vulnerable and play a key role in the pathogenesis of AD. To clarify the early mechanism associated with AD, followed by subcellular components separation, we performed iTRAQ (isobaric tags for relative and absolute quantification)-based proteomics analysis to simultaneously investigate the differentially expressed proteins (DEPs) within the mitochondria, synaptosome, and myelin sheath in the cerebrum of the 6-month-old triple transgenic AD (3 × Tg-AD) and 6-month-old wild-type (WT) mice. A large number of DEPs between the AD and WT mice were identified. Most of them are related to mitochondria and synaptic dysfunction and cytoskeletal protein change. Differential expressions of Lrpprc, Nefl, and Sirpa were verified by Western blot analysis. The results suggest that decreased energy metabolism, impaired amino acid metabolism and neurotransmitter synthesis, increase compensatory fatty acid metabolism, up-regulated cytoskeletal protein expression, and oxidative stress are the early events of AD. Among these, mitochondrial damage, synaptic dysfunction, decreased energy metabolism, and abnormal amino acid metabolism are the most significant events. The results indicate that it is feasible to separate and simultaneously perform proteomics analysis on the three subcellular components.
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Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.
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Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
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Holm KN, Herren AW, Taylor SL, Randol JL, Kim K, Espinal G, Martiínez-Cerdeño V, Pessah IN, Hagerman RJ, Hagerman PJ. Human Cerebral Cortex Proteome of Fragile X-Associated Tremor/Ataxia Syndrome. Front Mol Biosci 2021; 7:600840. [PMID: 33585555 PMCID: PMC7879451 DOI: 10.3389/fmolb.2020.600840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/27/2020] [Indexed: 01/10/2023] Open
Abstract
Background: Fragile X-associated tremor/ataxia syndrome (FXTAS) is an adult-onset neurodegenerative disorder associated with premutation CGG-repeat expansions (55–200 repeats) in the 5′ non-coding portion of the fragile X mental retardation 1 (FMR1) gene. Core features of FXTAS include progressive tremor/ataxia, cognitive decline, variable brain volume loss, and white matter disease. The principal histopathological feature of FXTAS is the presence of central nervous system (CNS) and non-CNS intranuclear inclusions. Objective: To further elucidate the molecular underpinnings of FXTAS through the proteomic characterization of human FXTAS cortexes. Results: Proteomic analysis of FXTAS brain cortical tissue (n = 8) identified minor differences in protein abundance compared to control brains (n = 6). Significant differences in FXTAS relative to control brain predominantly involved decreased abundance of proteins, with the greatest decreases observed for tenascin-C (TNC), cluster of differentiation 38 (CD38), and phosphoserine aminotransferase 1 (PSAT1); proteins typically increased in other neurodegenerative diseases. Proteins with the greatest increased abundance include potentially novel neurodegeneration-related proteins and small ubiquitin-like modifier 1/2 (SUMO1/2). The FMRpolyG peptide, proposed in models of FXTAS pathogenesis but only identified in trace amounts in the earlier study of FXTAS inclusions, was not identified in any of the FXTAS or control brains in the current study. Discussion: The observed proteomic shifts, while generally relatively modest, do show a bias toward decreased protein abundance with FXTAS. Such shifts in protein abundance also suggest altered RNA binding as well as loss of cell–cell adhesion/structural integrity. Unlike other neurodegenerative diseases, the proteome of end-stage FXTAS does not suggest a strong inflammation-mediated degenerative response.
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Affiliation(s)
- Katharine Nichole Holm
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Anthony W Herren
- Mass Spectrometry Research Core, University of California Davis, Davis, CA, United States
| | - Sandra L Taylor
- Department of Public Health Sciences, Division of Biostatistics, University of California Davis School of Medicine, Davis, CA, United States
| | - Jamie L Randol
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Kyoungmi Kim
- Department of Public Health Sciences, Division of Biostatistics, University of California Davis School of Medicine, Davis, CA, United States.,Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States
| | - Glenda Espinal
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Verónica Martiínez-Cerdeño
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States.,Department of Pathology and Laboratory Medicine, University of California Davis School of Medicine, Davis, CA, United States
| | - Isaac N Pessah
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States.,Department of Molecular Biosciences, University of California Davis School of Veterinary Medicine, Davis, CA, United States
| | - Randi J Hagerman
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States.,Department of Pediatrics, University of California Davis School of Medicine, Davis, CA, United States
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA, United States.,Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis School of Medicine, Davis, CA, United States
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do Canto AM, Donatti A, Geraldis JC, Godoi AB, da Rosa DC, Lopes-Cendes I. Neuroproteomics in Epilepsy: What Do We Know so Far? Front Mol Neurosci 2021; 13:604158. [PMID: 33488359 PMCID: PMC7817846 DOI: 10.3389/fnmol.2020.604158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Epilepsies are chronic neurological diseases that affect approximately 2% of the world population. In addition to being one of the most frequent neurological disorders, treatment for patients with epilepsy remains a challenge, because a proportion of patients do not respond to the antiseizure medications that are currently available. This results in a severe economic and social burden for patients, families, and the healthcare system. A characteristic common to all forms of epilepsy is the occurrence of epileptic seizures that are caused by abnormal neuronal discharges, leading to a clinical manifestation that is dependent on the affected brain region. It is generally accepted that an imbalance between neuronal excitation and inhibition generates the synchronic electrical activity leading to seizures. However, it is still unclear how a normal neural circuit becomes susceptible to the generation of seizures or how epileptogenesis is induced. Herein, we review the results of recent proteomic studies applied to investigate the underlying mechanisms leading to epilepsies and how these findings may impact research and treatment for these disorders.
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Affiliation(s)
- Amanda M. do Canto
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Amanda Donatti
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Jaqueline C. Geraldis
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Alexandre B. Godoi
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Douglas C. da Rosa
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
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Seshagiri DV, Huddar A, Nashi S, Ray S, Ramaswamy P, Oommen AT, Chawla T, Yadav S, Annapureddy J, Jankar R, Polavarapu K, Vengalil S, Preethish-Kumar V, Warrier M, Thomas PT, Shingavi L, Arunachal G, Yadav R, Nalini A. Altered REM sleep architecture in patients with Myotonic dystrophy type 1: is related to sleep apnea? Sleep Med 2021; 79:48-54. [PMID: 33472130 DOI: 10.1016/j.sleep.2020.12.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To determine the sleep architecture and sleep respiratory abnormalities and to correlate with sleep symptoms in patients with Myotonic dystrophy type 1 (DM1). METHODS We recruited a cohort of genetically confirmed patients with DM1, who attended the Neuromuscular clinic between July 2016 and December 2019. Clinical, sleep and whole night polysomnography data were collected. The analysis of sleep architecture, sleep respiratory parameters and comparison with healthy controls (HC) was performed in our sleep laboratory. RESULTS A total of 59 patients with DM1 underwent sleep evaluation. Hypersomnolence in 42 (77.8%), ESS>10 in 23 (39%), and PSQI>5 in 18 (30.5%) were found in patients with DM1. Thirty-one (68.89%) patients with DM1 and 22 (95.65%) HC had more than 4-h of total sleep time (TST). More than 4 h of TST was taken to compare respiratory and sleep architecture parameters. Patients with DM1 had reduced sleep efficiency, reduced N2 sleep, and increase in N1 sleep, wake index, stage shift index, nocturnal sleep-onset REM periods compared to HC. AHI>15 was found in 16 (51.61%) DM1 and in 3 HC (13.64%). AHI had positive correlation with BMI, but not with age, ESS or disease progression (MIRS). All DM1 with AHI>15; 8(80%) and 1(33.33%) in AHI5to15, and AHI<5 groups, respectively had hypersomnolence. CONCLUSION In this first study on Indian cohort, daytime hypersomnolence, poor nocturnal sleep quality, sleep architecture irregularities are identified to be common in patients with DM1. These abnormalities may be explained by sleep-related breathing disorders that are highly prevalent in these patients.
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Affiliation(s)
| | - Akshata Huddar
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Somdattaa Ray
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Palanyswamy Ramaswamy
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Abel Thomas Oommen
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Tanushree Chawla
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Srikanth Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Jagadish Annapureddy
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Rahul Jankar
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Manjusha Warrier
- Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Priya Treesa Thomas
- Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Leena Shingavi
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Gautham Arunachal
- Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India.
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Li KW, Gonzalez-Lozano MA, Koopmans F, Smit AB. Recent Developments in Data Independent Acquisition (DIA) Mass Spectrometry: Application of Quantitative Analysis of the Brain Proteome. Front Mol Neurosci 2020; 13:564446. [PMID: 33424549 PMCID: PMC7793698 DOI: 10.3389/fnmol.2020.564446] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is the driving force behind current brain proteome analysis. In a typical proteomics approach, a protein isolate is digested into tryptic peptides and then analyzed by liquid chromatography–mass spectrometry. The recent advancements in data independent acquisition (DIA) mass spectrometry provide higher sensitivity and protein coverage than the classic data dependent acquisition. DIA cycles through a pre-defined set of peptide precursor isolation windows stepping through 400–1,200 m/z across the whole liquid chromatography gradient. All peptides within an isolation window are fragmented simultaneously and detected by tandem mass spectrometry. Peptides are identified by matching the ion peaks in a mass spectrum to a spectral library that contains information of the peptide fragment ions' pattern and its chromatography elution time. Currently, there are several reports on DIA in brain research, in particular the quantitative analysis of cellular and synaptic proteomes to reveal the spatial and/or temporal changes of proteins that underlie neuronal plasticity and disease mechanisms. Protocols in DIA are continuously improving in both acquisition and data analysis. The depth of analysis is currently approaching proteome-wide coverage, while maintaining high reproducibility in a stable and standardisable MS environment. DIA can be positioned as the method of choice for routine proteome analysis in basic brain research and clinical applications.
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Affiliation(s)
- Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Miguel A Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Caillaud M, Msheik Z, Ndong-Ntoutoume GMA, Vignaud L, Richard L, Favreau F, Faye PA, Sturtz F, Granet R, Vallat JM, Sol V, Desmoulière A, Billet F. Curcumin-cyclodextrin/cellulose nanocrystals improve the phenotype of Charcot-Marie-Tooth-1A transgenic rats through the reduction of oxidative stress. Free Radic Biol Med 2020; 161:246-262. [PMID: 32980538 DOI: 10.1016/j.freeradbiomed.2020.09.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/09/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022]
Abstract
The most prevalent form of Charcot-Marie-Tooth disease (CMT type 1A) is characterized by duplication of the PMP22 gene, peripheral dysmyelination and decreased nerve conduction velocities leading to muscle weakness. Recently, oxidative stress was reported as a feature in CMT1A patients. Curcumin exhibits antioxidant activities and has shown beneficial properties on peripheral nerves. However, curcumin presents unfavorable pharmacokinetics. We developed curcumin-cyclodextrin/cellulose nanocrystals (Nano-Cur) to bypass this limitation. The present study investigated the therapeutic potential of Nano-Cur in vitro in Schwann cells (SCs) and in vivo in the transgenic CMT1A rat model. In vitro, Nano-Cur treatment (0.01 μM for 8 h) reduced reactive oxygen species and improved mitochondrial membrane potential in CMT1A SCs. Moreover, Nano-Cur treatment (0.01 μM for 1 week) increased the expression of myelin basic protein in SC/neuron co-cultures. Preliminary in vivo experiments carried out in WT rats showed that intraperitoneal (i.p.) injection of Nano-Cur treatment containing 0.2 mg/kg of curcumin strongly enhanced the bioavailability of curcumin. Afterwards, in 1-month-old male CMT1A rats, Nano-Cur treatment (0.2 mg/kg/day, i.p. for 8 weeks) significantly improved sensori-motor functions (grip strength, balance performance, and mechanical and thermal sensitivities). Importantly, sensory and motor nerve conduction velocities were improved. Further histological and biochemical analyses indicated that myelin sheath thickness and myelin protein expression (myelin protein zero and PMP22) were increased. In addition, oxidative stress markers were decreased in the sciatic nerve and gastrocnemius muscle. Finally, Nrf2 expression and some major antioxidant enzymes were increased in sciatic nerve. Therefore, Nano-Cur significantly improved cellular, electrophysiological, and functional features of CMT1A rats.
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Affiliation(s)
- Martial Caillaud
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France; Department of Pharmacology and Toxicology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA, USA
| | - Zeina Msheik
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France
| | - Gautier M-A Ndong-Ntoutoume
- EA7500, PEIRENE Laboratory, Faculty of Science and Technology, University of Limoges, F-87000, Limoges, France
| | - Laetitia Vignaud
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France
| | - Laurence Richard
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France; Reference Center for Rare Peripheral Neuropathies, Department of Neurology, University Hospital of Limoges, F-87000, Limoges, France
| | - Frédéric Favreau
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France; Department of Biochemistry, University Hospital of Limoges, F-87000, Limoges, France
| | - Pierre-Antoine Faye
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France; Department of Biochemistry, University Hospital of Limoges, F-87000, Limoges, France
| | - Franck Sturtz
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France; Department of Biochemistry, University Hospital of Limoges, F-87000, Limoges, France
| | - Robert Granet
- EA7500, PEIRENE Laboratory, Faculty of Science and Technology, University of Limoges, F-87000, Limoges, France
| | - Jean-Michel Vallat
- Reference Center for Rare Peripheral Neuropathies, Department of Neurology, University Hospital of Limoges, F-87000, Limoges, France
| | - Vincent Sol
- EA7500, PEIRENE Laboratory, Faculty of Science and Technology, University of Limoges, F-87000, Limoges, France
| | - Alexis Desmoulière
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France
| | - Fabrice Billet
- EA6309, Myelin Maintenance and Peripheral Neuropathies, University of Limoges, Faculties of Medicine and Pharmacy, F-87000, Limoges, France.
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Venkatachalam N, Bakavayev S, Engel D, Barak Z, Engel S. Primate differential redoxome (PDR) - A paradigm for understanding neurodegenerative diseases. Redox Biol 2020; 36:101683. [PMID: 32829254 PMCID: PMC7451816 DOI: 10.1016/j.redox.2020.101683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/18/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Despite different phenotypic manifestations, mounting evidence points to similarities in the molecular basis of major neurodegenerative diseases (ND). CNS has evolved to be robust against hazard of ROS, a common perturbation aerobic organisms are confronted with. The trade-off of robustness is system's fragility against rare and unexpected perturbations. Identifying the points of CNS fragility is key for understanding etiology of ND. We postulated that the 'primate differential redoxome' (PDR), an assembly of proteins that contain cysteine residues present only in the primate orthologues of mammals, is likely to associate with an added level of regulatory functionalities that enhanced CNS robustness against ROS and facilitated evolution. The PDR contains multiple deterministic and susceptibility factors of major ND, which cluster to form coordinated redox networks regulating various cellular processes. The PDR analysis revealed a potential CNS fragility point, which appears to associates with a non-redundant PINK1-PRKN-SQSTM1(p62) axis coordinating protein homeostasis and mitophagy.
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Affiliation(s)
- Nachiyappan Venkatachalam
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shamchal Bakavayev
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Engel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Zeev Barak
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Proukakis C. Somatic mutations in neurodegeneration: An update. Neurobiol Dis 2020; 144:105021. [PMID: 32712267 DOI: 10.1016/j.nbd.2020.105021] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/12/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
Mosaicism, the presence of genomic differences between cells due to post-zygotic somatic mutations, is widespread in the human body, including within the brain. A role for this in neurodegenerative diseases has long been hypothesised, and technical developments are now allowing the question to be addressed in detail. The rapidly accumulating evidence is discussed in this review, with a focus on recent developments. Somatic mutations of numerous types may occur, including single nucleotide variants (SNVs), copy number variants (CNVs), and retrotransposon insertions. They could act as initiators or risk factors, especially if they arise in development, although they could also result from the disease process, potentially contributing to progression. In common sporadic neurodegenerative disorders, relevant mutations have been reported in synucleinopathies, comprising somatic gains of SNCA in Parkinson's disease and multiple system atrophy, and in Alzheimer's disease, where a novel recombination mechanism leading to somatic variants of APP, as well as an excess of somatic SNVs affecting tau phosphorylation, have been reported. In Mendelian repeat expansion disorders, mosaicism due to somatic instability, first detected 25 years ago, has come to the forefront. Brain somatic SNVs occur in DNA repair disorders, and there is evidence for a role of several ALS genes in DNA repair. While numerous challenges, and need for further validation, remain, this new, or perhaps rediscovered, area of research has the potential to transform our understanding of neurodegeneration.
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Affiliation(s)
- Christos Proukakis
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK.
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Cogliati S, Clementi V, Francisco M, Crespo C, Argañaraz F, Grau R. Bacillus Subtilis Delays Neurodegeneration and Behavioral Impairment in the Alzheimer’s Disease Model Caenorhabditis Elegans. J Alzheimers Dis 2020; 73:1035-1052. [DOI: 10.3233/jad-190837] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sebastián Cogliati
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET – Rosario, Argentina
| | - Victoria Clementi
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET – Rosario, Argentina
| | - Marcos Francisco
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET – Rosario, Argentina
| | - Cira Crespo
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET – Rosario, Argentina
| | - Federico Argañaraz
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET – Rosario, Argentina
| | - Roberto Grau
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET – Rosario, Argentina
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Cookson MR. Proteomics: techniques and applications in neuroscience. J Neurochem 2019; 151:394-396. [PMID: 31625157 PMCID: PMC6856389 DOI: 10.1111/jnc.14867] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/25/2019] [Indexed: 12/20/2022]
Abstract
This Preface introduces the articles of the special issue on 'Proteomics' where we survey these powerful techniques specifically in the context of applications in neurosciences. Proteomics as used here is a catch-all term for approaches where a broad survey of all protein content of a cell or tissue is performed in parallel. In the special issue, various experts outline applications as diverse as finding disease biomarkers in human samples, including living participants or post-mortem brain, as well as application of protein technologies to model systems such as animals and cells. Collectively, these articles outline the utility of current technologies for proteome interrogation and identify enhancements that will shape applications to future studies. This is the Preface for the special issue "Proteomics". Cover Image for this issue: doi: 10.1111/jnc.14530.
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Affiliation(s)
- Mark R Cookson
- Laboratory of Neurogenetics, Cell Biology and Gene Expression Section, National Institute on Aging, Bethesda, Maryland, USA
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Liu W, Song Q, Cao Y, Zhao Y, Huo H, Wang Y, Song Y, Li J, Tu P. Advanced liquid chromatography-mass spectrometry enables merging widely targeted metabolomics and proteomics. Anal Chim Acta 2019; 1069:89-97. [DOI: 10.1016/j.aca.2019.04.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
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Alachkar A, Khan N, Łażewska D, Kieć-Kononowicz K, Sadek B. Histamine H3 receptor antagonist E177 attenuates amnesia induced by dizocilpine without modulation of anxiety-like behaviors in rats. Neuropsychiatr Dis Treat 2019; 15:531-542. [PMID: 30863075 PMCID: PMC6388968 DOI: 10.2147/ndt.s193125] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Alzheimer disease (AD) is the main cause of dementia in elderly people. The potential of histamine H3 receptor (H3R) antagonists as a pharmacological treatment of several neuropsychiatric diseases is well established. METHODS The novel non-imidazole-based H3R antagonist E177 was screened for its pro-cognitive effects on the inhibitory avoidance paradigm (IAP) and novel object recognition (NOR) task in a dizocilpine (DIZ)-induced model of amnesia in male Wistar rats. Donepezil, an acetylcholine esterase inhibitor, was used as the reference drug. RESULTS Acute systemic treatment with E177 (1.25, 2.5, 5, and 10 mg/kg intraperitoneally [i.p.]) significantly attenuated the cognitive impairments induced by DIZ in the IAP (all P-values <0.05, n=7), and the protective effect of the most promising dose of E177 (5 mg/kg) was abrogated when H3R agonist R-(α)-methylhistamine (RAMH; 10 mg/kg i.p.) was co-administered (P=0.281 for DIZ-amnesia group vs DIZ + E177 + RAMH group, n=7). The discrimination index calculated for E177 (5 mg/kg, i.p.) showed a significant memory-enhancing effect on DIZ-induced short-term memory impairment in the NOR task (P<0.05, n=6), with the enhancement nullified when animals were co-administered RAMH (10 mg/kg). Moreover, the results revealed that E177 (5 and 10 mg/kg, i.p.) did not alter the anxiety levels and locomotor activity of animals naïve to the open-field test (all P-values >0.05, n=8) or the elevated plus maze test (all P-values >0.05, n=6-8), which indicated that the E177-induced enhancement of memory performance in the IAP or NOR task was unrelated to changes in emotional response or in spontaneous locomotor activity. CONCLUSION The observed results suggested a possible contribution of H3Rs in the alteration of brain neurotransmitters that accompany neurodegenerative diseases, such as AD.
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Affiliation(s)
- Alaa Alachkar
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates,
| | - Nadia Khan
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates,
| | - Dorota Łażewska
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Katarzyna Kieć-Kononowicz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Bassem Sadek
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates,
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