1
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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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2
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Sadick JS, O'Dea MR, Hasel P, Dykstra T, Faustin A, Liddelow SA. Astrocytes and oligodendrocytes undergo subtype-specific transcriptional changes in Alzheimer's disease. Neuron 2022; 110:1788-1805.e10. [PMID: 35381189 PMCID: PMC9167747 DOI: 10.1016/j.neuron.2022.03.008] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 01/24/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022]
Abstract
Resolving glial contributions to Alzheimer's disease (AD) is necessary because changes in neuronal function, such as reduced synaptic density, altered electrophysiological properties, and degeneration, are not entirely cell autonomous. To improve understanding of transcriptomic heterogeneity in glia during AD, we used single-nuclei RNA sequencing (snRNA-seq) to characterize astrocytes and oligodendrocytes from apolipoprotein (APOE) Ɛ2/3 human AD and age- and genotype-matched non-symptomatic (NS) brains. We enriched astrocytes before sequencing and characterized pathology from the same location as the sequenced material. We characterized baseline heterogeneity in both astrocytes and oligodendrocytes and identified global and subtype-specific transcriptomic changes between AD and NS astrocytes and oligodendrocytes. We also took advantage of recent human and mouse spatial transcriptomics resources to localize heterogeneous astrocyte subtypes to specific regions in the healthy and inflamed brain. Finally, we integrated our data with published AD snRNA-seq datasets, highlighting the power of combining datasets to resolve previously unidentifiable astrocyte subpopulations.
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Affiliation(s)
- Jessica S Sadick
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Michael R O'Dea
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Philip Hasel
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Taitea Dykstra
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Arline Faustin
- Center for Cognitive Neurology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA; Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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3
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Jurcau A. Insights into the Pathogenesis of Neurodegenerative Diseases: Focus on Mitochondrial Dysfunction and Oxidative Stress. Int J Mol Sci 2021; 22:11847. [PMID: 34769277 PMCID: PMC8584731 DOI: 10.3390/ijms222111847] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
As the population ages, the incidence of neurodegenerative diseases is increasing. Due to intensive research, important steps in the elucidation of pathogenetic cascades have been made and significantly implicated mitochondrial dysfunction and oxidative stress. However, the available treatment in Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis is mainly symptomatic, providing minor benefits and, at most, slowing down the progression of the disease. Although in preclinical setting, drugs targeting mitochondrial dysfunction and oxidative stress yielded encouraging results, clinical trials failed or had inconclusive results. It is likely that by the time of clinical diagnosis, the pathogenetic cascades are full-blown and significant numbers of neurons have already degenerated, making it impossible for mitochondria-targeted or antioxidant molecules to stop or reverse the process. Until further research will provide more efficient molecules, a healthy lifestyle, with plenty of dietary antioxidants and avoidance of exogenous oxidants may postpone the onset of neurodegeneration, while familial cases may benefit from genetic testing and aggressive therapy started in the preclinical stage.
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Affiliation(s)
- Anamaria Jurcau
- Department of Psycho-Neurosciences and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania;
- Neurology Ward, Clinical Municipal Hospital “dr. G. Curteanu” Oradea, 410154 Oradea, Romania
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4
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Jové M, Mota-Martorell N, Torres P, Ayala V, Portero-Otin M, Ferrer I, Pamplona R. The Causal Role of Lipoxidative Damage in Mitochondrial Bioenergetic Dysfunction Linked to Alzheimer's Disease Pathology. Life (Basel) 2021; 11:life11050388. [PMID: 33923074 PMCID: PMC8147054 DOI: 10.3390/life11050388] [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: 03/19/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 01/18/2023] Open
Abstract
Current shreds of evidence point to the entorhinal cortex (EC) as the origin of the Alzheimer’s disease (AD) pathology in the cerebrum. Compared with other cortical areas, the neurons from this brain region possess an inherent selective vulnerability derived from particular oxidative stress conditions that favor increased mitochondrial molecular damage with early bioenergetic involvement. This alteration of energy metabolism is the starting point for subsequent changes in a multitude of cell mechanisms, leading to neuronal dysfunction and, ultimately, cell death. These events are induced by changes that come with age, creating the substrate for the alteration of several neuronal pathways that will evolve toward neurodegeneration and, consequently, the development of AD pathology. In this context, the present review will focus on description of the biological mechanisms that confer vulnerability specifically to neurons of the entorhinal cortex, the changes induced by the aging process in this brain region, and the alterations at the mitochondrial level as the earliest mechanism for the development of AD pathology. Current findings allow us to propose the existence of an altered allostatic mechanism at the entorhinal cortex whose core is made up of mitochondrial oxidative stress, lipid metabolism, and energy production, and which, in a positive loop, evolves to neurodegeneration, laying the basis for the onset and progression of AD pathology.
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Affiliation(s)
- Mariona Jové
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Natàlia Mota-Martorell
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Pascual Torres
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Victoria Ayala
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Manuel Portero-Otin
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
| | - Isidro Ferrer
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Bellvitge University Hospital/Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), ISCIII, 28220 Madrid, Spain
- Correspondence: (I.F.); (R.P.)
| | - Reinald Pamplona
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), Lleida University (UdL), 25198 Lleida, Spain; (M.J.); (N.M.-M.); (P.T.); (V.A.); (M.P.-O.)
- Correspondence: (I.F.); (R.P.)
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5
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Harper CB, Smillie KJ. Current molecular approaches to investigate pre-synaptic dysfunction. J Neurochem 2021; 157:107-129. [PMID: 33544872 DOI: 10.1111/jnc.15316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Over the course of the last few decades it has become clear that many neurodevelopmental and neurodegenerative disorders have a synaptic defect, which contributes to pathogenicity. A rise in new techniques, and in particular '-omics'-based methods providing large datasets, has led to an increase in potential proteins and pathways implicated in synaptic function and related disorders. Additionally, advancements in imaging techniques have led to the recent discovery of alternative modes of synaptic vesicle recycling. This has resulted in a lack of clarity over the precise role of different pathways in maintaining synaptic function and whether these new pathways are dysfunctional in neurodevelopmental and neurodegenerative disorders. A greater understanding of the molecular detail of pre-synaptic function in health and disease is key to targeting new proteins and pathways for novel treatments and the variety of new techniques currently available provides an ideal opportunity to investigate these functions. This review focuses on techniques to interrogate pre-synaptic function, concentrating mainly on synaptic vesicle recycling. It further examines techniques to determine the underlying molecular mechanism of pre-synaptic dysfunction and discusses methods to identify molecular targets, along with protein-protein interactions and cellular localization. In combination, these techniques will provide an expanding and more complete picture of pre-synaptic function. With the application of recent technological advances, we are able to resolve events with higher spatial and temporal resolution, leading research towards a greater understanding of dysfunction at the presynapse and the role it plays in pathogenicity.
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Affiliation(s)
- Callista B Harper
- Centre for Discovery Brain Sciences, University of Edinburgh, Scotland, UK
| | - Karen J Smillie
- Centre for Discovery Brain Sciences, University of Edinburgh, Scotland, UK
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6
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Jain AP, Sathe G. Proteomics Landscape of Alzheimer's Disease. Proteomes 2021; 9:proteomes9010013. [PMID: 33801961 PMCID: PMC8005944 DOI: 10.3390/proteomes9010013] [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: 02/09/2021] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent form of dementia, and the numbers of AD patients are expected to increase as human life expectancy improves. Deposition of β-amyloid protein (Aβ) in the extracellular matrix and intracellular neurofibrillary tangles are molecular hallmarks of the disease. Since the precise pathophysiology of AD has not been elucidated yet, effective treatment is not available. Thus, understanding the disease pathology, as well as identification and development of valid biomarkers, is imperative for early diagnosis as well as for monitoring disease progression and therapeutic responses. Keeping this goal in mind several studies using quantitative proteomics platform have been carried out on both clinical specimens including the brain, cerebrospinal fluid (CSF), plasma and on animal models of AD. In this review, we summarize the mass spectrometry (MS)-based proteomics studies on AD and discuss the discovery as well as validation stages in brief to identify candidate biomarkers.
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Affiliation(s)
- Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Correspondence:
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7
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Enculescu C, Kerr ED, Yeo KYB, Schenk G, Fortes MRS, Schulz BL. Proteomics Reveals Profound Metabolic Changes in the Alcohol Use Disorder Brain. ACS Chem Neurosci 2019; 10:2364-2373. [PMID: 30807102 DOI: 10.1021/acschemneuro.8b00660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Changes in brain metabolism are a hallmark of alcohol use disorder (AUD). Determining how AUD changes the brain proteome is critical for understanding the effects of alcohol consumption on biochemical processes in the brain. We used data-independent acquisition mass spectrometry proteomics to study differences in the abundance of proteins associated with AUD in prefrontal lobe and motor cortex from autopsy brain. AUD had a substantial effect on the overall brain proteome exceeding the inherent differences between brain regions. Proteins associated with glycolysis, trafficking, the cytoskeleton, and excitotoxicity were altered in abundance in AUD. We observed extensive changes in the abundance of key metabolic enzymes, consistent with a switch from glucose to acetate utilization in the AUD brain. We propose that metabolic adaptations allowing efficient acetate utilization contribute to ethanol dependence in AUD.
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Affiliation(s)
- Charmaine Enculescu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Edward D. Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - K. Y. Benjamin Yeo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
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8
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Cilento EM, Jin L, Stewart T, Shi M, Sheng L, Zhang J. Mass spectrometry: A platform for biomarker discovery and validation for Alzheimer's and Parkinson's diseases. J Neurochem 2019; 151:397-416. [PMID: 30474862 DOI: 10.1111/jnc.14635] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022]
Abstract
Accurate, reliable, and objective biomarkers for Alzheimer's disease (AD), Parkinson's disease (PD), and related age-associated neurodegenerative disorders are urgently needed to assist in both diagnosis, particularly at early stages, and monitoring of disease progression. Technological advancements in protein detection platforms over the last few decades have resulted in a plethora of reported molecular biomarker candidates for both AD and PD; however, very few of these candidates are developed beyond the discovery phase of the biomarker development pipeline, a reflection of the current bottleneck within the field. In this review, the expanded use of selected reaction monitoring (SRM) targeted mass spectrometry will be discussed in detail as a platform for systematic verification of large panels of protein biomarker candidates prior to costly validation testing. We also advocate for the coupling of discovery-based proteomics with modern targeted MS-based approaches (e.g., SRM) within a single study in future workflows to expedite biomarker development and validation for AD and PD. It is our hope that improving the efficiency within the biomarker development process by use of an SRM pipeline may ultimately hasten the development of biomarkers that both decrease misdiagnosis of AD and PD and ultimately lead to detection at early stages of disease and objective assessment of disease progression. This article is part of the special issue "Proteomics".
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Affiliation(s)
- Eugene M Cilento
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lorrain Jin
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Tessandra Stewart
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Min Shi
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lifu Sheng
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Jing Zhang
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA.,Department of Pathology, School of Basic Medicine, Peking University Health Science Center, Peking University Third Hospital and Peking Key Laboratory for Early Diagnosis of Neurodegenerative Disorders, Beijing, China
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9
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Stepler KE, Robinson RAS. The Potential of ‘Omics to Link Lipid Metabolism and Genetic and Comorbidity Risk Factors of Alzheimer’s Disease in African Americans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:1-28. [DOI: 10.1007/978-3-030-05542-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Benito I, Casañas JJ, Montesinos ML. Proteomic Analysis of Synaptoneurosomes Highlights the Relevant Role of Local Translation in the Hippocampus. Proteomics 2018; 18:e1800005. [PMID: 29923338 DOI: 10.1002/pmic.201800005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Indexed: 11/12/2022]
Abstract
Several proteomic analyses have been performed on synaptic fractions isolated from cortex or even total brain, resulting in preparations with a high synaptic heterogeneity and complexity. Synaptoneurosomes (SNs) are subcellular membranous elements that contain sealed pre- and post-synaptic components. They are obtained by subcellular fractionation of brain homogenates and serve as a suitable model to study many aspects of the synapse physiology. Here the proteomic content of SNs isolated from hippocampus of adult mice, a brain region involved in memory that presents lower synaptic heterogeneity than cortex, is reported. Interestingly, in addition to pre- and post-synaptic proteins, proteins involved in RNA binding and translation are overrepresented in this preparation. These results validate the protocol previously reported for SNs isolation, and, as reported by other authors, highlight the relevance of local synaptic translation for hippocampal physiology.
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Affiliation(s)
- Itziar Benito
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, Sevilla, E-41009, Spain.,Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla,, Sevilla, E-41013, Spain.,Servicio de Animalario, Hospital Universitario Virgen Macarena (HUVM), Sevilla, E-41009, Spain
| | - Juan José Casañas
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, Sevilla, E-41009, Spain.,Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla,, Sevilla, E-41013, Spain
| | - María Luz Montesinos
- Departamento de Fisiología Médica y Biofísica, Universidad de Sevilla, Sevilla, E-41009, Spain.,Instituto de Biomedicina de Sevilla, IBIS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla,, Sevilla, E-41013, Spain
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11
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Zafar S, Shafiq M, Younas N, Schmitz M, Ferrer I, Zerr I. Prion Protein Interactome: Identifying Novel Targets in Slowly and Rapidly Progressive Forms of Alzheimer's Disease. J Alzheimers Dis 2018; 59:265-275. [PMID: 28671123 DOI: 10.3233/jad-170237] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rapidly progressive Alzheimer's disease (rpAD) is a variant of AD distinguished by a rapid decline in cognition and short disease duration from onset to death. While attempts to identify rpAD based on biomarker profile classifications have been initiated, the mechanisms which contribute to the rapid decline and prion mimicking heterogeneity in clinical signs are still largely unknown. In this study, we characterized prion protein (PrP) expression, localization, and interactome in rpAD, slow progressive AD, and in non-dementia controls. PrP along with its interacting proteins were affinity purified with magnetic Dynabeads Protein-G, and were identified using Q-TOF-ESI/MS analysis. Our data demonstrated a significant 1.2-fold decrease in di-glycosylated PrP isoforms specifically in rpAD patients. Fifteen proteins appeared to interact with PrP and only two proteins3/4histone H2B-type1-B and zinc alpha-2 protein3/4were specifically bound with PrP isoform isolated from rpAD cases. Our data suggest distinct PrP involvement in association with the altered PrP interacting protein in rpAD, though the pathophysiological significance of these interactions remains to be established.
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Affiliation(s)
- Saima Zafar
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Mohsin Shafiq
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Neelam Younas
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Matthias Schmitz
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Isidre Ferrer
- Institute of Neuropathology, IDIBELL-University Hospital Bellvitge, University of Barcelona, Hospitalet de Llobregat, Spain.,CIBERNED (Network center for biomedical research of neurodegenerative diseases), Institute Carlos III, Ministry of Health, Spain
| | - Inga Zerr
- Department of Neurology, Clinical Dementia Center and DZNE, Georg-August University, University Medical Center Göttingen (UMG), Göttingen, Germany
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12
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Smith R, Wang J, Seymour C, Fernandez-Palomo C, Fazzari J, Schültke E, Bräuer-Krisch E, Laissue J, Schroll C, Mothersill C. Homogenous and Microbeam X-Ray Radiation Induces Proteomic Changes in the Brains of Irradiated Rats and in the Brains of Nonirradiated Cage Mate Rats. Dose Response 2018; 16:1559325817750068. [PMID: 29383012 PMCID: PMC5784471 DOI: 10.1177/1559325817750068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 01/08/2023] Open
Abstract
To evaluate microbeam radiation therapy (MRT), for brain tumor treatment, the bystander effect in nonirradiated companion animals was investigated. Adult rats were irradiated with 35 or 350 Gy at the European Synchrotron Research Facility using homogenous irradiation (HR) or MRT to the right brain hemisphere. The irradiated rats were housed with nonirradiated rats. After 48 hours, all rats were euthanized and the frontal lobe proteome was analyzed using 2-dimensional electrophoresis and mass spectrometry. Proteome changes were determined by analysis of variance (P < .05). Homogenous irradiation increased serum albumin, heat shock protein 71 (HSP-71), triosephosphate isomerase (TPI), fructose bisphosphate aldolase (FBA), and prohibitin and decreased dihydrolipoyl dehydrogenase (DLD) and pyruvate kinase. Microbeam radiation therapy increased HSP-71, FBA, and prohibitin, and decreased aconitase, dihydropyrimidinase, TPI, tubulin DLD, and pyruvate kinase. Cage mates with HR irradiated rats showed increased HSP-71 and FBA and decreased pyruvate kinase, DLD, and aconitase. Cage mates with MRT irradiated rats showed increased HSP-71, prohibitin, and FBA and decreased aconitase and DLD. Homogenous irradiation proteome changes indicated tumorigenesis, while MRT proteome changes indicated an oxidative stress response. The bystander effect of proteome changes appeared antitumorigenic and inducing radioresistance. This investigation also supports the need for research into prohibitin interaction with HSP-70/71 chaperones and cancer therapy.
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Affiliation(s)
- Richard Smith
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jiaxi Wang
- Mass Spectrometry Facility, Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Colin Seymour
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cristian Fernandez-Palomo
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer Fazzari
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Elisabeth Schültke
- Department of Radio-oncology, Rostock University Medical Centre, Rostock, Germany
| | | | - Jean Laissue
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Christian Schroll
- Stereotactic Neurosurgery and Laboratory for Molecular Neurosurgery, Freiburg University Medical Centre, Freiburg, Germany
| | - Carmel Mothersill
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario, Canada
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Abstract
Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.
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Affiliation(s)
- Isidro Ferrer
- Pathologic Anatomy Service, Institute of Neuropathology, Bellvitge University Hospital; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona; and Network Center of Biomedical Research on Neurodegenerative Diseases, Institute Carlos III; Hospitalet de Llobregat, Llobregat, Spain.
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14
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Choi H, Kim HJ, Kim J, Kim S, Yang J, Lee W, Park Y, Hyeon SJ, Lee DS, Ryu H, Chung J, Mook-Jung I. Increased acetylation of Peroxiredoxin1 by HDAC6 inhibition leads to recovery of Aβ-induced impaired axonal transport. Mol Neurodegener 2017; 12:23. [PMID: 28241840 PMCID: PMC5330132 DOI: 10.1186/s13024-017-0164-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/22/2017] [Indexed: 02/07/2023] Open
Abstract
Background Reduction or inhibition of histone deacetylase 6 (HDAC6) has been shown to rescue memory in mouse models of Alzheimer’s disease (AD) and is recently being considered a possible therapeutic strategy. However, the restoring mechanism of HDAC6 inhibition has not been fully understood. Methods and results Here, we found that an anti-oxidant protein Peroxdiredoxin1 (Prx1), a substrate of HDAC6, malfunctions in Aβ treated cells, the brains of 5xFAD AD model mice and AD patients. Malfunctioning Prx1, caused by reduced Prx1 acetylation levels, was recovered by HDAC6 inhibition. Increasing acetylation levels of Prx1 by HDAC6 inhibition recovered elevated reactive oxygen species (ROS) levels, elevated Ca2+ levels and impaired mitochondrial axonal transport, sequentially, even in the presence of Aβ. Prx1 mutant studies on the K197 site for an acetylation mimic or silencing mutation support the results showing that HDAC6 inhibitor restores Aβ-induced disruption of ROS, Ca2+ and axonal transport. Conclusions Taken together, increasing acetylation of Prx1 by HDAC6 inhibition has several beneficial effects in AD pathology. Here, we present the novel mechanism by which elevated acetylation of Prx1 rescues mitochondrial axonal transport impaired by Aβ. Therefore, our results suggest that modulation of Prx1 acetylation by HDAC6 inhibition has great therapeutic potential for AD and has further therapeutic possibilities for other neurodegenerative diseases as well. Electronic supplementary material The online version of this article (doi:10.1186/s13024-017-0164-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heesun Choi
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Haeng Jun Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Jisoo Kim
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Soohyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University, College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jinhee Yang
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Wonik Lee
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea
| | - Yeonju Park
- Department of Biomedical Sciences, Laboratory of Immunology and Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Jae Hyeon
- Center for Neuromedicine, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Laboratory of Immunology and Cancer Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Hoon Ryu
- VA Boston Healthcare System, Boston University Alzheimer's Disease Center, and Department of Neurology, Boston University School of Medicine, Boston, MA02130, USA.,Center for Neuromedicine, Brain Science Institute, Korea Institute of Science and Technology, Seoul, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University, College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, Seoul, Korea.
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15
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Sethi S, Chourasia D, Parhar IS. Approaches for targeted proteomics and its potential applications in neuroscience. J Biosci 2016; 40:607-27. [PMID: 26333406 DOI: 10.1007/s12038-015-9537-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other 'omics' approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.
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Affiliation(s)
- Sumit Sethi
- Brain Research Institute, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor Darul Ehsan, Malaysia,
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16
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Sengupta MB, Chakrabarti A, Saha S, Mukhopadhyay D. Clinical proteomics of enervated neurons. Clin Proteomics 2016; 13:10. [PMID: 27152104 PMCID: PMC4857373 DOI: 10.1186/s12014-016-9112-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/18/2016] [Indexed: 11/16/2022] Open
Abstract
The dynamic field of neurosciences entails ever increasing search for molecular mechanisms of disease states, especially in the domain of neurodegenerative disorders. The previous century heralded the techniques in proteomics when indexing of the human proteomes relating to various disease conditions became important. Early stage research in certain diseases or pathological conditions requires a more holistic approach of first discovering the proteins of interest for the condition. Despite its limitations, proteomics is one of the most powerful techniques available to us today to dissect the molecular scenario in a particular disease situation. In this review we will discuss about the current clinical research in neurodegenerative disorders that employ proteomics techniques. We will specifically focus on our understanding of Alzheimer’s disease, traumatic spinal cord injury and neuromyelitis optica. Discussions will include ongoing worldwide research in these areas, research in India and specifically our laboratory in these domains of neurodegenerative conditions.
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Affiliation(s)
- Mohor Biplab Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
| | - Arunabha Chakrabarti
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
| | - Suparna Saha
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal 700064 India
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17
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de Wilde MC, Overk CR, Sijben JW, Masliah E. Meta-analysis of synaptic pathology in Alzheimer's disease reveals selective molecular vesicular machinery vulnerability. Alzheimers Dement 2016; 12:633-44. [PMID: 26776762 DOI: 10.1016/j.jalz.2015.12.005] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/02/2015] [Accepted: 12/04/2015] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Loss of synapses best correlates to cognitive deficits in Alzheimer's disease (AD) in which oligomeric neurotoxic species of amyloid-β appears to contribute synaptic pathology. Although a number of clinical pathologic studies have been performed with limited sample size, there are no systematic studies encompassing large samples. Therefore, we performed a meta-analysis study. METHODS We identified 417 publications reporting postmortem synapse and synaptic marker loss from AD patients. Two meta-analyses were performed using a single database of subselected publications and calculating the standard mean differences. RESULTS Meta-analysis confirmed synaptic loss in selected brain regions is an early event in AD pathogenesis. The second meta-analysis of 57 synaptic markers revealed that presynaptic makers were affected more than postsynaptic markers. DISCUSSION The present meta-analysis study showed a consistent synaptic loss across brain regions and that molecular machinery including endosomal pathways, vesicular assembly mechanisms, glutamate receptors, and axonal transport are often affected.
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Affiliation(s)
- Martijn C de Wilde
- Nutricia Advanced Medical Nutrition, Nutricia Research, Utrecht, The Netherlands
| | - Cassia R Overk
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - John W Sijben
- Nutricia Advanced Medical Nutrition, Nutricia Research, Utrecht, The Netherlands
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
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18
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Chang RYK, Etheridge N, Nouwens AS, Dodd PR. SWATH analysis of the synaptic proteome in Alzheimer's disease. Neurochem Int 2015; 87:1-12. [PMID: 25958317 DOI: 10.1016/j.neuint.2015.04.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
Abstract
Brain tissue from Alzheimer's disease patients exhibits synaptic degeneration in selected regions. Synaptic dysfunction occurs early in the disease and is a primary pathological target for treatment. The molecular mechanisms underlying this degeneration remain unknown. Quantifying the synaptic proteome in autopsy brain and comparing tissue from Alzheimer's disease cases and subjects with normal aging are critical to understanding the molecular mechanisms associated with Alzheimer pathology. We isolated synaptosomes from hippocampus and motor cortex so as to reduce sample complexity relative to whole-tissue homogenates. Synaptosomal extracts were subjected to strong cation exchange (SCX) fractionation to further partition sample complexity; each fraction received SWATH-based information-dependent acquisition to generate a comprehensive peptide-ion library. The expression of synaptic proteins from AD hippocampus and motor cortex was then compared between groups. A total of 2077 unique proteins were identified at a critical local false discovery rate <5%. Thirty of these, including 17 novel proteins, exhibited significant expression differences between cases and controls; these proteins are involved in cellular functions including structural maintenance, signal transduction, autophagy, oxidative stress, and proteasome activity, or they have synaptic-vesicle related or energy-related functions. Differentially expressed proteins were subjected to pathway analysis to identify protein-protein interactions. This revealed that the most perturbed molecular and cellular functions were cellular assembly and organization. Core analysis revealed RhoA signaling to be the top canonical pathway. Network analysis showed that differentially expressed proteins were related to cellular assembly and organization, and cellular function and maintenance. This is the first study to combine SCX fractionation with SWATH analysis. SWATH is a promising new technique that can greatly enhance protein identification in any proteome, and has many other benefits; however, there are limitations yet to be resolved.
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Affiliation(s)
| | - Naomi Etheridge
- School of Chemistry and Molecular Biosciences, University of Queensland, Australia
| | - Amanda S Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, Australia
| | - Peter R Dodd
- School of Chemistry and Molecular Biosciences, University of Queensland, Australia.
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19
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Brinkmalm A, Portelius E, Öhrfelt A, Brinkmalm G, Andreasson U, Gobom J, Blennow K, Zetterberg H. Explorative and targeted neuroproteomics in Alzheimer's disease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:769-78. [PMID: 25619854 DOI: 10.1016/j.bbapap.2015.01.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/23/2014] [Accepted: 01/16/2015] [Indexed: 01/08/2023]
Abstract
Alzheimer's disease (AD) is a progressive brain amyloidosis that injures brain regions involved in memory consolidation and other higher brain functions. Neuropathologically, the disease is characterized by accumulation of a 42 amino acid peptide called amyloid β (Aβ42) in extracellular senile plaques, intraneuronal inclusions of hyperphosphorylated tau protein in neurofibrillary tangles, and neuronal and axonal degeneration and loss. Biomarker assays capturing these pathologies have been developed for use on cerebrospinal fluid samples but there are additional molecular pathways that most likely contribute to the neurodegeneration and full clinical expression of AD. One way of learning more about AD pathogenesis is to identify novel biomarkers for these pathways and examine them in longitudinal studies of patients in different stages of the disease. Here, we discuss targeted proteomic approaches to study AD and AD-related pathologies in closer detail and explorative approaches to discover novel pathways that may contribute to the disease. This article is part of a Special Issue entitled: Neuroproteomics: Applications in neuroscience and neurology.
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Affiliation(s)
- Ann Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden.
| | - Erik Portelius
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Annika Öhrfelt
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Ulf Andreasson
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Johan Gobom
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, S-431 80 Mölndal, Sweden; UCL Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom.
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20
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The effects of endogenous non-peptide molecule isatin and hydrogen peroxide on proteomic profiling of rat brain amyloid-β binding proteins: relevance to Alzheimer's disease? Int J Mol Sci 2014; 16:476-95. [PMID: 25551598 PMCID: PMC4307257 DOI: 10.3390/ijms16010476] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/16/2014] [Indexed: 12/27/2022] Open
Abstract
The amyloid-β peptide is considered as a key player in the development and progression of Alzheimer’s disease (AD). Although good evidence exists that amyloid-β accumulates inside cells, intracellular brain amyloid-binding proteins remain poorly characterized. Proteomic profiling of rat brain homogenates, performed in this study, resulted in identification of 89 individual intracellular amyloid-binding proteins, and approximately 25% of them were proteins that we had previously identified as specifically binding to isatin, an endogenous neuroprotector molecule. A significant proportion of the amyloid-binding proteins (more than 30%) are differentially expressed or altered/oxidatively modified in AD patients. Incubation of brain homogenates with 70 µM hydrogen peroxide significantly influenced the profile of amyloid-β binding proteins and 0.1 mM isatin decreased the number of identified amyloid-β binding proteins both in control and hydrogen peroxide treated brain homogenates. The effects of hydrogen peroxide and isatin have been confirmed in optical biosensor experiments with purified glyceraldehyde-3-phosphate dehydrogenase, one of the known crucial amyloid-β binding proteins (also identified in this study). Data obtained suggest that isatin protects crucial intracellular protein targets against amyloid binding, and possibly favors intracellular degradation of this protein via preventing formation of amyloid-β oligomers described in the literature for some isatin derivatives.
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