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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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Davis E, Lloyd AF. The proteomic landscape of microglia in health and disease. Front Cell Neurosci 2024; 18:1379717. [PMID: 38560294 PMCID: PMC10978577 DOI: 10.3389/fncel.2024.1379717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Microglia are the resident immune cells of the central nervous system (CNS) and as such play crucial roles in regulating brain homeostasis. Their presence in neurodegenerative diseases is known, with neurodegeneration-associated risk genes heavily expressed in microglia, highlighting their importance in contributing to disease pathogenesis. Transcriptomics studies have uncovered the heterogeneous landscape of microglia in health and disease, identifying important disease-associated signatures such as DAM, and insight into both the regional and temporal diversity of microglia phenotypes. Quantitative mass spectrometry methods are ever increasing in the field of neurodegeneration, utilised as ways to identify disease biomarkers and to gain deeper understanding of disease pathology. Proteins are the main mechanistic indicators of cellular function, yet discordance between transcript and proteomic findings has highlighted the need for in-depth proteomic phenotypic and functional analysis to fully understand disease kinetics at the cellular and molecular level. This review details the current progress of using proteomics to define microglia biology, the relationship between gene and protein expression in microglia, and the future of proteomics and emerging methods aiming to resolve heterogeneous cell landscapes.
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Affiliation(s)
- Emma Davis
- The Francis Crick Institute, London, United Kingdom
- UK Dementia Research Institute at UCL, University College London, London, United Kingdom
| | - Amy F. Lloyd
- Cell Signalling and Immunology, University of Dundee, Dundee, United Kingdom
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3
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Ong RCS, Beros JL, Fuller K, Wood FM, Melton PE, Rodger J, Fear MW, Barrett L, Stevenson AW, Tang AD. Non-severe thermal burn injuries induce long-lasting downregulation of gene expression in cortical excitatory neurons and microglia. Front Mol Neurosci 2024; 17:1368905. [PMID: 38476460 PMCID: PMC10927825 DOI: 10.3389/fnmol.2024.1368905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Burn injuries are devastating traumas, often leading to life-long consequences that extend beyond the observable burn scar. In the context of the nervous system, burn injury patients commonly develop chronic neurological disorders and have been suggested to have impaired motor cortex function, but the long-lasting impact on neurons and glia in the brain is unknown. Using a mouse model of non-severe burn injury, excitatory and inhibitory neurons in the primary motor cortex were labelled with fluorescent proteins using adeno-associated viruses (AAVs). A total of 5 weeks following the burn injury, virus labelled excitatory and inhibitory neurons were isolated using fluorescence-activated cell sorting (FACS). In addition, microglia and astrocytes from the remaining cortical tissue caudal to the motor cortex were immunolabelled and isolated with FACS. Whole transcriptome RNA-sequencing was used to identify any long-lasting changes to gene expression in the different cell types. RNA-seq analysis showed changes to the expression of a small number of genes with known functions in excitatory neurons and microglia, but not in inhibitory neurons or astrocytes. Specifically, genes related to GABA-A receptors in excitatory neurons and several cellular functions in microglia were found to be downregulated in burn injured mice. These findings suggest that non-severe burn injuries lead to long lasting transcriptomic changes in the brain, but only in specific cell types. Our findings provide a broad overview of the long-lasting impact of burn injuries on the central nervous system which may help identify potential therapeutic targets to prevent neurological dysfunction in burn patients.
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Affiliation(s)
- Rebecca C. S. Ong
- Experimental and Regenerative Neuroscience, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, Australia
| | - Jamie L. Beros
- Experimental and Regenerative Neuroscience, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, Australia
| | - Kathy Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Fiona M. Wood
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Burn Injury Research Unit, The University of Western Australia, Crawley, WA, Australia
- Burns Service of Western Australia, WA Department of Health, Murdoch, WA, Australia
- Paediatric Burn Care, Telethon Kids Institute, Nedlands, WA, Australia
| | - Phillip E. Melton
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
- School of Global and Population Health, The University of Western Australia, Crawley, WA, Australia
| | - Jennifer Rodger
- Experimental and Regenerative Neuroscience, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, Australia
| | - Mark W. Fear
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lucy Barrett
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Burn Injury Research Unit, The University of Western Australia, Crawley, WA, Australia
- Burns Service of Western Australia, WA Department of Health, Murdoch, WA, Australia
| | - Andrew W. Stevenson
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Burn Injury Research Unit, The University of Western Australia, Crawley, WA, Australia
| | - Alexander D. Tang
- Experimental and Regenerative Neuroscience, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
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4
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Gudmundsdottir V, Frick E, Emilsson V, Jonmundsson T, Steindorsdottir A, Johnson ECB, Puerta R, Dammer E, Shantaraman A, Cano A, Boada M, Valero S, Garcia-Gonzalez P, Gudmundsson E, Gudjonsson A, Pitts R, Qiu X, Finkel N, Loureiro J, Orth A, Seyfried N, Levey A, Ruiz A, Aspelund T, Jennings L, Launer L, Gudnason V. Serum proteomics reveals APOE dependent and independent protein signatures in Alzheimer's disease. RESEARCH SQUARE 2024:rs.3.rs-3706206. [PMID: 38260284 PMCID: PMC10802738 DOI: 10.21203/rs.3.rs-3706206/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The current demand for early intervention, prevention, and treatment of late onset Alzheimer's disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n = 5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOAD independently of APOE-ε4 carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was strongly dependent on APOE-ε4 carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated by APOE-ε4 yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed upon APOE-ε4 genotype adjustment, a finding which we replicate in an external cohort (n = 719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent on APOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Merce Boada
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades-UIC, Barcelona
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lenore Launer
- National Institute on Aging, National Institutes of Health
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5
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Shaik SM, Cao Y, Gogola JV, Dodiya HB, Zhang X, Boutej H, Han W, Kriz J, Sisodia SS. Translational profiling identifies sex-specific metabolic and epigenetic reprogramming of cortical microglia/macrophages in APPPS1-21 mice with an antibiotic-perturbed-microbiome. Mol Neurodegener 2023; 18:95. [PMID: 38104136 PMCID: PMC10725591 DOI: 10.1186/s13024-023-00668-7] [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: 04/19/2023] [Accepted: 10/14/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Microglia, the brain-resident macrophages perform immune surveillance and engage with pathological processes resulting in phenotype changes necessary for maintaining homeostasis. In preceding studies, we showed that antibiotic-induced perturbations of the gut microbiome of APPPS1-21 mice resulted in significant attenuation in Aβ amyloidosis and altered microglial phenotypes that are specific to male mice. The molecular events underlying microglial phenotypic transitions remain unclear. Here, by generating 'APPPS1-21-CD11br' reporter mice, we investigated the translational state of microglial/macrophage ribosomes during their phenotypic transition and in a sex-specific manner. METHODS Six groups of mice that included WT-CD11br, antibiotic (ABX) or vehicle-treated APPPS1-21-CD11br males and females were sacrificed at 7-weeks of age (n = 15/group) and used for immunoprecipitation of microglial/macrophage polysomes from cortical homogenates using anti-FLAG antibody. Liquid chromatography coupled to tandem mass spectrometry and label-free quantification was used to identify newly synthesized peptides isolated from polysomes. RESULTS We show that ABX-treatment leads to decreased Aβ levels in male APPPS1-21-CD11br mice with no significant changes in females. We identified microglial/macrophage polypeptides involved in mitochondrial dysfunction and altered calcium signaling that are associated with Aβ-induced oxidative stress. Notably, female mice also showed downregulation of newly-synthesized ribosomal proteins. Furthermore, male mice showed an increase in newly-synthesized polypeptides involved in FcγR-mediated phagocytosis, while females showed an increase in newly-synthesized polypeptides responsible for actin organization associated with microglial activation. Next, we show that ABX-treatment resulted in substantial remodeling of the epigenetic landscape, leading to a metabolic shift that accommodates the increased bioenergetic and biosynthetic demands associated with microglial polarization in a sex-specific manner. While microglia in ABX-treated male mice exhibited a metabolic shift towards a neuroprotective phenotype that promotes Aβ clearance, microglia in ABX-treated female mice exhibited loss of energy homeostasis due to persistent mitochondrial dysfunction and impaired lysosomal clearance that was associated with inflammatory phenotypes. CONCLUSIONS Our studies provide the first snapshot of the translational state of microglial/macrophage cells in a mouse model of Aβ amyloidosis that was subject to ABX treatment. ABX-mediated changes resulted in metabolic reprogramming of microglial phenotypes to modulate immune responses and amyloid clearance in a sex-specific manner. This microglial plasticity to support neuro-energetic homeostasis for its function based on sex paves the path for therapeutic modulation of immunometabolism for neurodegeneration.
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Affiliation(s)
- Shabana M Shaik
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Yajun Cao
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Joseph V Gogola
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hemraj B Dodiya
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Xulun Zhang
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Hejer Boutej
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Laval University, Québec, QC, Canada
| | - Weinong Han
- Dept. of Neurobiology, The University of Chicago, Chicago, IL, USA
| | - Jasna Kriz
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Laval University, Québec, QC, Canada
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6
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Du Y, Bradshaw WJ, Leisner TM, Annor-Gyamfi JK, Qian K, Bashore FM, Sikdar A, Nwogbo FO, Ivanov AA, Frye SV, Gileadi O, Brennan PE, Levey AI, Axtman AD, Pearce KH, Fu H, Katis VL. Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease. J Biol Chem 2023; 299:105382. [PMID: 37866628 PMCID: PMC10692723 DOI: 10.1016/j.jbc.2023.105382] [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: 05/22/2023] [Revised: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Proteomic studies have identified moesin (MSN), a protein containing a four-point-one, ezrin, radixin, moesin (FERM) domain, and the receptor CD44 as hub proteins found within a coexpression module strongly linked to Alzheimer's disease (AD) traits and microglia. These proteins are more abundant in Alzheimer's patient brains, and their levels are positively correlated with cognitive decline, amyloid plaque deposition, and neurofibrillary tangle burden. The MSN FERM domain interacts with the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) and the cytoplasmic tail of CD44. Inhibiting the MSN-CD44 interaction may help limit AD-associated neuronal damage. Here, we investigated the feasibility of developing inhibitors that target this protein-protein interaction. We have employed structural, mutational, and phage-display studies to examine how CD44 binds to the FERM domain of MSN. Interestingly, we have identified an allosteric site located close to the PIP2 binding pocket that influences CD44 binding. These findings suggest a mechanism in which PIP2 binding to the FERM domain stimulates CD44 binding through an allosteric effect, leading to the formation of a neighboring pocket capable of accommodating a receptor tail. Furthermore, high-throughput screening of a chemical library identified two compounds that disrupt the MSN-CD44 interaction. One compound series was further optimized for biochemical activity, specificity, and solubility. Our results suggest that the FERM domain holds potential as a drug development target. Small molecule preliminary leads generated from this study could serve as a foundation for additional medicinal chemistry efforts with the goal of controlling microglial activity in AD by modifying the MSN-CD44 interaction.
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Affiliation(s)
- Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - William J Bradshaw
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK
| | - Tina M Leisner
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Joel K Annor-Gyamfi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Structural Genomics Consortium, Chapel Hill, North Carolina, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Frances M Bashore
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Structural Genomics Consortium, Chapel Hill, North Carolina, USA
| | - Arunima Sikdar
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Felix O Nwogbo
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephen V Frye
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA
| | - Opher Gileadi
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK
| | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK
| | - Allan I Levey
- Department of Neurology, Emory Goizueta Alzheimer's Disease Research Center, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Alison D Axtman
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Structural Genomics Consortium, Chapel Hill, North Carolina, USA.
| | - Kenneth H Pearce
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, North Carolina, USA.
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia, USA.
| | - Vittorio L Katis
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, University of Oxford, Oxford, UK.
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7
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Frick EA, Emilsson V, Jonmundsson T, Steindorsdottir AE, Johnson ECB, Puerta R, Dammer EB, Shantaraman A, Cano A, Boada M, Valero S, García-González P, Gudmundsson EF, Gudjonsson A, Loureiro JJ, Orth AP, Seyfried NT, Levey AI, Ruiz A, Aspelund T, Jennings LL, Launer LJ, Gudmundsdottir V, Gudnason V. Serum proteomics reveals APOE dependent and independent protein signatures in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.08.23298251. [PMID: 37986771 PMCID: PMC10659486 DOI: 10.1101/2023.11.08.23298251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The current demand for early intervention, prevention, and treatment of late onset Alzheimer's disease (LOAD) warrants deeper understanding of the underlying molecular processes which could contribute to biomarker and drug target discovery. Utilizing high-throughput proteomic measurements in serum from a prospective population-based cohort of older adults (n=5,294), we identified 303 unique proteins associated with incident LOAD (median follow-up 12.8 years). Over 40% of these proteins were associated with LOAD independently of APOE-ε4 carrier status. These proteins were implicated in neuronal processes and overlapped with protein signatures of LOAD in brain and cerebrospinal fluid. We found 17 proteins which LOAD-association was strongly dependent on APOE-ε4 carrier status. Most of them showed consistent associations with LOAD in cerebrospinal fluid and a third had brain-specific gene expression. Remarkably, four proteins in this group (TBCA, ARL2, S100A13 and IRF6) were downregulated by APOE-ε4 yet upregulated as a consequence of LOAD as determined in a bi-directional Mendelian randomization analysis, reflecting a potential response to the disease onset. Accordingly, the direct association of these proteins to LOAD was reversed upon APOE-ε4 genotype adjustment, a finding which we replicate in an external cohort (n=719). Our findings provide an insight into the dysregulated pathways that may lead to the development and early detection of LOAD, including those both independent and dependent on APOE-ε4. Importantly, many of the LOAD-associated proteins we find in the circulation have been found to be expressed - and have a direct link with AD - in brain tissue. Thus, the proteins identified here, and their upstream modulating pathways, provide a new source of circulating biomarker and therapeutic target candidates for LOAD.
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Affiliation(s)
| | - Valur Emilsson
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | | | | | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Raquel Puerta
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Anantharaman Shantaraman
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Amanda Cano
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Mercè Boada
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Sergi Valero
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Pablo García-González
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | | | | | | | | | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, 30329, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, 30329, GA, USA
| | - Agustin Ruiz
- Research Center and Memory Clinic. Ace Alzheimer Center Barcelona - Universitat Internacional de Catalunya, Barcelona, 08028, Spain, Barcelona
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, 28029, Spain
| | - Thor Aspelund
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | | | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, Intramural Research Program, National Institute on Aging, Bethesda, 20892, MD, USA
| | - Valborg Gudmundsdottir
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, 200, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
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8
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Goettemoeller AM, Banks E, McCann KE, Kumar P, South K, Olah VJ, Ramelow CC, Duong DM, Seyfried NT, Rangaraju S, Weinshenker D, Rowan MJM. Entorhinal cortex vulnerability to human APP expression promotes hyperexcitability and tau pathology. RESEARCH SQUARE 2023:rs.3.rs-3370607. [PMID: 37987015 PMCID: PMC10659529 DOI: 10.21203/rs.3.rs-3370607/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Preventative treatment for Alzheimer's Disease is of dire importance, and yet, cellular mechanisms underlying early regional vulnerability in Alzheimer's Disease remain unknown. In human patients with Alzheimer's Disease, one of the earliest observed pathophysiological correlates to cognitive decline is hyperexcitability1. In mouse models, early hyperexcitability has been shown in the entorhinal cortex, the first cortical region impacted by Alzheimer's Disease2-4. The origin of hyperexcitability in early-stage disease and why it preferentially emerges in specific regions is unclear. Using cortical-region and cell-type- specific proteomics and patch-clamp electrophysiology, we uncovered differential susceptibility to human-specific amyloid precursor protein (hAPP) in a model of sporadic Alzheimer's. Unexpectedly, our findings reveal that early entorhinal hyperexcitability may result from intrinsic vulnerability of parvalbumin interneurons, rather than the suspected layer II excitatory neurons. This vulnerability of entorhinal PV interneurons is specific to hAPP, as it could not be recapitulated with increased murine APP expression. Furthermore, the Somatosensory Cortex showed no such vulnerability to adult-onset hAPP expression, likely resulting from PV-interneuron variability between the two regions based on physiological and proteomic evaluations. Interestingly, entorhinal hAPP-induced hyperexcitability was quelled by co-expression of human Tau at the expense of increased pathological tau species. This study suggests early disease interventions targeting non-excitatory cell types may protect regions with early vulnerability to pathological symptoms of Alzheimer's Disease and downstream cognitive decline.
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Affiliation(s)
- Annie M Goettemoeller
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322
- GDBBS Graduate Program, Laney Graduate School, Emory University
| | - Emmie Banks
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322
- GDBBS Graduate Program, Laney Graduate School, Emory University
| | | | - Prateek Kumar
- Department of Neurology, Emory University School of Medicine
| | - Kelly South
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322
- GDBBS Graduate Program, Laney Graduate School, Emory University
| | - Viktor J Olah
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322
| | - Christina C Ramelow
- Department of Neurology, Emory University School of Medicine
- GDBBS Graduate Program, Laney Graduate School, Emory University
| | - Duc M Duong
- Department of Neurology, Emory University School of Medicine
- Department of Biochemistry, Emory University
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine
- Department of Biochemistry, Emory University
- Center for Neurodegenerative Disease, Emory University School of Medicine
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine
- GDBBS Graduate Program, Laney Graduate School, Emory University
| | | | - Matthew JM Rowan
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322
- Center for Neurodegenerative Disease, Emory University School of Medicine
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9
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Ochandarena NE, Niehaus JK, Tassou A, Scherrer G. Cell-type specific molecular architecture for mu opioid receptor function in pain and addiction circuits. Neuropharmacology 2023; 238:109597. [PMID: 37271281 PMCID: PMC10494323 DOI: 10.1016/j.neuropharm.2023.109597] [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: 04/12/2023] [Accepted: 05/13/2023] [Indexed: 06/06/2023]
Abstract
Opioids are potent analgesics broadly used for pain management; however, they can produce dangerous side effects including addiction and respiratory depression. These harmful effects have led to an epidemic of opioid abuse and overdose deaths, creating an urgent need for the development of both safer pain medications and treatments for opioid use disorders. Both the analgesic and addictive properties of opioids are mediated by the mu opioid receptor (MOR), making resolution of the cell types and neural circuits responsible for each of the effects of opioids a critical research goal. Single-cell RNA sequencing (scRNA-seq) technology is enabling the identification of MOR-expressing cell types throughout the nervous system, creating new opportunities for mapping distinct opioid effects onto newly discovered cell types. Here, we describe molecularly defined MOR-expressing neuronal cell types throughout the peripheral and central nervous systems and their potential contributions to opioid analgesia and addiction.
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Affiliation(s)
- Nicole E Ochandarena
- Neuroscience Curriculum, Biological and Biomedical Sciences Program, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Jesse K Niehaus
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adrien Tassou
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Grégory Scherrer
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; New York Stem Cell Foundation - Robertson Investigator, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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10
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Palumbo MC, Gautam M, Sonneborn A, Kim K, Wilmarth PA, Reddy AP, Shi X, Marks DL, Sahay G, Abbas AI, Janowsky A. MicroRNA137-loaded lipid nanoparticles regulate synaptic proteins in the prefrontal cortex. Mol Ther 2023; 31:2975-2990. [PMID: 37644723 PMCID: PMC10556225 DOI: 10.1016/j.ymthe.2023.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/20/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023] Open
Abstract
Genome-wide association studies indicate that allele variants in MIR137, the host gene of microRNA137 (miR137), confer an increased risk of schizophrenia (SCZ). Aberrant expression of miR137 and its targets, many of which regulate synaptic functioning, are also associated with an increased risk of SCZ. Thus, miR137 represents an attractive target aimed at correcting the molecular basis for synaptic dysfunction in individuals with high genetic risk for SCZ. Advancements in nanotechnology utilize lipid nanoparticles (LNPs) to transport and deliver therapeutic RNA. However, there remains a gap in using LNPs to regulate gene and protein expression in the brain. To study the delivery of nucleic acids by LNPs to the brain, we found that LNPs released miR137 cargo and inhibited target transcripts of interest in neuroblastoma cells. Biodistribution of LNPs loaded with firefly luciferase mRNA remained localized to the mouse prefrontal cortex (PFC) injection site without circulating to off-target organs. LNPs encapsulating Cre mRNA preferentially co-expressed in neuronal over microglial or astrocytic cells. Using quantitative proteomics, we found miR137 modulated glutamatergic synaptic protein networks that are commonly dysregulated in SCZ. These studies support engineering the next generation of brain-specific LNPs to deliver RNA therapeutics and improve symptoms of central nervous system disorders.
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Affiliation(s)
- Michelle C Palumbo
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Milan Gautam
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Alex Sonneborn
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kilsun Kim
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiao Shi
- Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel L Marks
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, Portland, OR 97239, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Atheir I Abbas
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA; Research Service, Veterans Affairs Portland Health Care System, Portland, OR 97239, USA
| | - Aaron Janowsky
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA; Research Service, Veterans Affairs Portland Health Care System, Portland, OR 97239, USA.
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11
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Chakrabarti S, Gorai S, Pahan K. A simple protocol for isolating microglia from adult mouse brain. NEUROIMMUNE PHARMACOLOGY AND THERAPEUTICS 2023; 2:293-300. [PMID: 37885917 PMCID: PMC10474378 DOI: 10.1515/nipt-2023-0014] [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: 07/02/2023] [Accepted: 07/20/2023] [Indexed: 10/28/2023]
Abstract
Objectives Although microglia are activated in adult and aged brains resulting in neurodegenerative and neuroinflammatory disorders, most of the cell culture studies on microglia deal with neonatal microglia because of ease of isolation. Microglia could be isolated from adult brains, but it requires separation by density gradient centrifugation, magnetic beads, etc. Here, we describe a simple protocol of isolating highly purified microglia from adult mouse brains. Methods Our protocol involves dilution with sterile PBS or media, regular centrifugation, and plating on poly-D-lysine-coated flasks. Results These adult microglia expressed the inducible nitric oxide synthase in response to preformed α-syn fibril, an etiological reagent of Parkinson's disease, and bacterial lipopolysaccharides, one of the prototype proinflammatory stimuli. Moreover, these adult microglia exhibited phagocytosis, which was stimulated by LPS treatment. Conclusions These results suggest that adult microglia isolated by our procedure are functional and that these adult microglia could be used for studies related to neurodegenerative disorders.
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Affiliation(s)
- Sudipta Chakrabarti
- Department of Neurological Sciences, Rush University Medical Center, Chicago, USA
| | - Sukhamoy Gorai
- Department of Neurological Sciences, Rush University Medical Center, Chicago, USA
| | - Kalipada Pahan
- Department of Neurological Sciences, Rush University Medical Center, Chicago, USA
- Division of Research and Development, Jesse Brown Veterans Affairs Medical Center, Chicago, USA
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12
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Sunna S, Bowen CA, Ramelow CC, Santiago JV, Kumar P, Rangaraju S. Advances in proteomic phenotyping of microglia in neurodegeneration. Proteomics 2023; 23:e2200183. [PMID: 37060300 PMCID: PMC10528430 DOI: 10.1002/pmic.202200183] [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: 11/21/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/16/2023]
Abstract
Microglia are dynamic resident immune cells of the central nervous system (CNS) that sense, survey, and respond to changes in their environment. In disease states, microglia transform from homeostatic to diverse molecular phenotypic states that play complex and causal roles in neurologic disease pathogenesis, as evidenced by the identification of microglial genes as genetic risk factors for neurodegenerative disease. While advances in transcriptomic profiling of microglia from the CNS of humans and animal models have provided transformative insights, the transcriptome is only modestly reflective of the proteome. Proteomic profiling of microglia is therefore more likely to provide functionally and therapeutically relevant targets. In this review, we discuss molecular insights gained from transcriptomic studies of microglia in the context of Alzheimer's disease as a prototypic neurodegenerative disease, and highlight existing and emerging approaches for proteomic profiling of microglia derived from in vivo model systems and human brain.
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Christine A. Bowen
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Christina C. Ramelow
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Juliet V. Santiago
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Prateek Kumar
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
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13
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Kim JH, Afridi R, Lee WH, Suk K. Analyzing the glial proteome in Alzheimer's disease. Expert Rev Proteomics 2023; 20:197-209. [PMID: 37724426 DOI: 10.1080/14789450.2023.2260955] [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: 06/09/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence indicates that dysfunction of glial cells, including astrocytes, microglia, and oligodendrocytes, may contribute to the development and progression of AD. Large-scale analysis of glial proteins sheds light on their roles in cellular processes and diseases. In AD, glial proteomics has been utilized to understand glia-based pathophysiology and identify potential biomarkers and therapeutic targets. AREA COVERED In this review, we provide an updated overview of proteomic analysis of glia in the context of AD. Additionally, we discuss current challenges in the field, involving glial complexity and heterogeneity, and describe some cutting-edge proteomic technologies to address them. EXPERT OPINION Unbiased comprehensive analysis of glial proteomes aids our understanding of the molecular and cellular mechanisms of AD pathogenesis. These investigations highlight the crucial role of glial cells and provide novel insights into the mechanisms of AD pathology. A deeper understanding of the AD-related glial proteome could offer a repertoire of potential biomarkers and therapeutics. Further technical advancement of glial proteomics will enable us to identify proteins within individual cells and specific cell types, thus significantly enhancing our comprehension of AD pathogenesis.
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Affiliation(s)
- Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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14
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Yim YY, Nestler EJ. Cell-Type-Specific Neuroproteomics of Synapses. Biomolecules 2023; 13:998. [PMID: 37371578 PMCID: PMC10296650 DOI: 10.3390/biom13060998] [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: 05/11/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders.
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Affiliation(s)
- Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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15
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Sunna S, Bowen C, Zeng H, Rayaprolu S, Kumar P, Bagchi P, Dammer EB, Guo Q, Duong DM, Bitarafan S, Natu A, Wood L, Seyfried NT, Rangaraju S. Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines. Mol Cell Proteomics 2023; 22:100546. [PMID: 37061046 PMCID: PMC10205547 DOI: 10.1016/j.mcpro.2023.100546] [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: 10/12/2022] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023] Open
Abstract
Different brain cell types play distinct roles in brain development and disease. Molecular characterization of cell-specific mechanisms using cell type-specific approaches at the protein (proteomic) level can provide biological and therapeutic insights. To overcome the barriers of conventional isolation-based methods for cell type-specific proteomics, in vivo proteomic labeling with proximity-dependent biotinylation of cytosolic proteins using biotin ligase TurboID, coupled with mass spectrometry (MS) of labeled proteins, emerged as a powerful strategy for cell type-specific proteomics in the native state of cells without the need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID approach are representative of the whole-cell proteome and capture cellular responses to stimuli without disruption of cellular processes. To address this, we generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing cytosolic TurboID to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under homeostatic conditions. TurboID labeled endolysosome, translation, vesicle, and signaling proteins in BV2 microglia and synaptic, neuron projection, and microtubule proteins in N2A neurons. TurboID expression and biotinylation minimally impacted homeostatic cellular proteomes of BV2 and N2A cells and did not affect lipopolysaccharide-mediated cytokine production or resting cellular respiration in BV2 cells. MS analysis of the microglial biotin-labeled proteins captured the impact of lipopolysaccharide treatment (>500 differentially abundant proteins) including increased canonical proinflammatory proteins (Il1a, Irg1, and Oasl1) and decreased anti-inflammatory proteins (Arg1 and Mgl2).
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Christine Bowen
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Hollis Zeng
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Eric B Dammer
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Qi Guo
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA
| | - Sara Bitarafan
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Aditya Natu
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA
| | - Levi Wood
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA; Department of Biochemistry, Emory University, Atlanta, Georgia, USA; Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta Georgia, USA; Center for Neurodegenerative Diseases, Emory University, Atlanta, Georgia, USA.
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16
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Du Y, Bradshaw WJ, Leisner TM, Annor-Gyamfi JK, Qian K, Bashore FM, Sikdar A, Nwogbo FO, Ivanov AA, Frye SV, Gileadi O, Brennan PE, Levey AI, Axtman AD, Pearce KH, Fu H, Katis VL. Development of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic strategy for Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541727. [PMID: 37292860 PMCID: PMC10245921 DOI: 10.1101/2023.05.22.541727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent genome-wide association studies have revealed genetic risk factors for Alzheimer's disease (AD) that are exclusively expressed in microglia within the brain. A proteomics approach identified moesin (MSN), a FERM (four-point-one ezrin radixin moesin) domain protein, and the receptor CD44 as hub proteins found within a co-expression module strongly linked to AD clinical and pathological traits as well as microglia. The FERM domain of MSN interacts with the phospholipid PIP2 and the cytoplasmic tails of receptors such as CD44. This study explored the feasibility of developing protein-protein interaction inhibitors that target the MSN-CD44 interaction. Structural and mutational analyses revealed that the FERM domain of MSN binds to CD44 by incorporating a beta strand within the F3 lobe. Phage-display studies identified an allosteric site located close to the PIP2 binding site in the FERM domain that affects CD44 binding within the F3 lobe. These findings support a model in which PIP2 binding to the FERM domain stimulates receptor tail binding through an allosteric mechanism that causes the F3 lobe to adopt an open conformation permissive for binding. High-throughput screening of a chemical library identified two compounds that disrupt the MSN-CD44 interaction, and one compound series was further optimized for biochemical activity, specificity, and solubility. The results suggest that the FERM domain holds potential as a drug development target. The small molecule preliminary leads generated from the study could serve as a foundation for additional medicinal chemistry effort with the goal of controlling microglial activity in AD by modifying the MSN-CD44 interaction.
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Affiliation(s)
- Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - William J. Bradshaw
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
| | - Tina M. Leisner
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Joel K. Annor-Gyamfi
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, Chapel Hill, NC 27599, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Current address: Chemical Biology Consortium Sweden, Division of Chemical Biology and Genome Engineering, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Solna, Sweden
| | - Frances M. Bashore
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, Chapel Hill, NC 27599, USA
| | - Arunima Sikdar
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Felix O. Nwogbo
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Andrey A. Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen V. Frye
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Opher Gileadi
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
- Current address: Structural Genomics Consortium, Department of Medicine, Karolinska Hospital and Karolinska Institute, 171 76 Stockholm, Sweden
| | - Paul E. Brennan
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
| | - Allan I. Levey
- Department of Neurology, Emory Goizueta Alzheimer’s Disease Research Center, Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Alison D. Axtman
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Structural Genomics Consortium, Chapel Hill, NC 27599, USA
| | - Kenneth H. Pearce
- UNC Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Chapel Hill, NC 27599, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Vittorio L. Katis
- Alzheimer’s Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford, OX3 7FZ, UK
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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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18
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Tiwari V, Shukla S. Lipidomics and proteomics: An integrative approach for early diagnosis of dementia and Alzheimer's disease. Front Genet 2023; 14:1057068. [PMID: 36845373 PMCID: PMC9946989 DOI: 10.3389/fgene.2023.1057068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder and considered to be responsible for majority of worldwide prevalent dementia cases. The number of patients suffering from dementia are estimated to increase up to 115.4 million cases worldwide in 2050. Hence, AD is contemplated to be one of the major healthcare challenge in current era. This disorder is characterized by impairment in various signaling molecules at cellular and nuclear level including aggregation of Aβ protein, tau hyper phosphorylation altered lipid metabolism, metabolites dysregulation, protein intensity alteration etc. Being heterogeneous and multifactorial in nature, the disease do not has any cure or any confirmed diagnosis before the onset of clinical manifestations. Hence, there is a requisite for early diagnosis of AD in order to downturn the progression/risk of the disorder and utilization of newer technologies developed in this field are aimed to provide an extraordinary assistance towards the same. The lipidomics and proteomics constitute large scale study of cellular lipids and proteomes in biological matrices at normal stage or any stage of a disease. The study involves high throughput quantification and detection techniques such as mass spectrometry, liquid chromatography, nuclear mass resonance spectroscopy, fluorescence spectroscopy etc. The early detection of altered levels of lipids and proteins in blood or any other biological matrices could aid in preventing the progression of AD and dementia. Therefore, the present review is designed to focus on the recent techniques and early diagnostic criteria for AD, revealing the role of lipids and proteins in this disease and their assessment through different techniques.
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Affiliation(s)
- Virendra Tiwari
- Division of Neuroscience and Ageing Biology, CSIR- Central Drug Research Institute, Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shubha Shukla
- Division of Neuroscience and Ageing Biology, CSIR- Central Drug Research Institute, Lucknow, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Shubha Shukla,
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19
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Lue LF, Walker DG, Beh ST, Beach TG. Isolation of Human Microglia from Neuropathologically Diagnosed Cases in the Single-Cell Era. Methods Mol Biol 2023; 2561:43-62. [PMID: 36399264 DOI: 10.1007/978-1-0716-2655-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter describes the core procedures that we have developed over the last two decades to isolate routinely the microglia from postmortem human brains. The method is suitable for brain slices consisting of both gray and white matter.The ability to concomitantly isolate vascular cells with glial cells provides the opportunity to investigate multiple cell types originating from the same donor. This represents a novel approach for -omics research, with the potential for discovering the shared or distinct molecular features among the glia and vascular cells from the same individual.
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Affiliation(s)
- Lih-Fen Lue
- Human Cell Core for Translational Research, Banner Sun Health Research Institute, Sun City, AZ, USA.
| | - Douglas G Walker
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Shiga, Otsu, Japan
| | - Suet Theng Beh
- Human Cell Core for Translational Research, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Civin Neuropathology Laboratory, Banner Sun Health Research Institute, Sun City, AZ, USA
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20
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Aerqin Q, Wang ZT, Wu KM, He XY, Dong Q, Yu JT. Omics-based biomarkers discovery for Alzheimer's disease. Cell Mol Life Sci 2022; 79:585. [PMID: 36348101 DOI: 10.1007/s00018-022-04614-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorders presenting with the pathological hallmarks of amyloid plaques and tau tangles. Over the past few years, great efforts have been made to explore reliable biomarkers of AD. High-throughput omics are a technology driven by multiple levels of unbiased data to detect the complex etiology of AD, and it provides us with new opportunities to better understand the pathophysiology of AD and thereby identify potential biomarkers. Through revealing the interaction networks between different molecular levels, the ultimate goal of multi-omics is to improve the diagnosis and treatment of AD. In this review, based on the current AD pathology and the current status of AD diagnostic biomarkers, we summarize how genomics, transcriptomics, proteomics and metabolomics are all conducing to the discovery of reliable AD biomarkers that could be developed and used in clinical AD management.
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Affiliation(s)
- Qiaolifan Aerqin
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Kai-Min Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao-Yu He
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qiang Dong
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Jin-Tai Yu
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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21
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Hsieh YC, Negri J, He A, Pearse RV, Liu L, Duong DM, Chibnik LB, Bennett DA, Seyfried NT, Young-Pearse TL. Elevated ganglioside GM2 activator (GM2A) in human brain tissue reduces neurite integrity and spontaneous neuronal activity. Mol Neurodegener 2022; 17:61. [PMID: 36131294 PMCID: PMC9494921 DOI: 10.1186/s13024-022-00558-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alzheimer's Disease (AD) affects millions globally, but therapy development is lagging. New experimental systems that monitor neuronal functions in conditions approximating the AD brain may be beneficial for identifying new therapeutic strategies. METHODS We expose cultured neurons to aqueous-soluble human brain extract from 43 individuals across a spectrum of AD pathology. Multi-electrode arrays (MEAs) and live-cell imaging were used to assess neuronal firing and neurite integrity (NI), respectively, following treatments of rat cortical neurons (MEA) and human iPSC-derived neurons (iN) with human brain extracts. RESULTS We observe associations between spontaneous activity and Aβ42:40 levels, between neurite integrity and oligomeric Aβ, and between neurite integrity and tau levels present in the brain extracts. However, these associations with Aβ and tau do not fully account for the effects observed. Proteomic profiling of the brain extracts revealed additional candidates correlated with neuronal structure and activity. Neurotoxicity in MEA and NI assays was associated with proteins implicated in lysosomal storage disorders, while neuroprotection was associated with proteins of the WAVE regulatory complex controlling actin cytoskeleton dynamics. Elevated ganglioside GM2 activator (GM2A) associates with reductions in both NI and MEA activity, and cell-derived GM2A alone is sufficient to induce a loss of neurite integrity and a reduction in neuronal firing. CONCLUSIONS The techniques and data herein introduce a system for modeling neuronal vulnerability in response to factors in the human brain and provide insights into proteins potentially contributing to AD pathogenesis.
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Affiliation(s)
- Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA 02115 USA
| | - Joseph Negri
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA 02115 USA
| | - Amy He
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA 02115 USA
| | - Richard V. Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA 02115 USA
| | - Lei Liu
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA 02115 USA
| | - Duc M. Duong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd NE, Atlanta, GA 30322 USA
| | - Lori B. Chibnik
- Department of Neurology, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114 USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA 02115 USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, 600 S. Paulina St, Chicago, IL 60612 USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd NE, Atlanta, GA 30322 USA
- Department of Neurology, Emory University School of Medicine, 100 Woodruff Circle, Atlanta, GA 30322 USA
| | - Tracy L. Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, 60 Fenwood Rd, Boston, MA 02115 USA
- Harvard Stem Cell Institute, Harvard University, 7 Divinity Ave, Cambridge, MA 02138 USA
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22
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Gao C, Shen X, Tan Y, Chen S. Pathogenesis, therapeutic strategies and biomarker development based on "omics" analysis related to microglia in Alzheimer's disease. J Neuroinflammation 2022; 19:215. [PMID: 36058959 PMCID: PMC9441025 DOI: 10.1186/s12974-022-02580-1] [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: 05/31/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and the most common cause of dementia. Among various pathophysiological aspects, microglia are considered to play important roles in the pathogenesis of AD. Genome wide association studies (GWAS) showed that the majority of AD risk genes are highly or exclusively expressed in microglia, underscoring the critical roles of microglia in AD pathogenesis. Recently, omics technologies have greatly advanced our knowledge of microglia biology in AD. Omics approaches, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics/lipidomics, present remarkable opportunities to delineate the underlying mechanisms, discover novel diagnostic biomarkers, monitor disease progression, and shape therapeutic strategies for diseases. In this review, we summarized research based on microglial "omics" analysis in AD, especially the recent research advances in the identification of AD-associated microglial subsets. This review reinforces the important role of microglia in AD and advances our understanding of the mechanism of microglia in AD pathogenesis. Moreover, we proposed the value of microglia-based omics in the development of therapeutic strategies and biomarkers for AD.
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Affiliation(s)
- Chao Gao
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuyan Tan
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Shengdi Chen
- Department of Neurology and Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Lab for Translational Research of Neurodegenerative Diseases, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), Shanghai Tech University, Shanghai, 201210, China.
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23
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Tsumagari K, Sato Y, Shimozawa A, Aoyagi H, Okano H, Kuromitsu J. Co-expression network analysis of human tau-transgenic mice reveals protein modules associated with tau-induced pathologies. iScience 2022; 25:104832. [PMID: 35992067 PMCID: PMC9382322 DOI: 10.1016/j.isci.2022.104832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/03/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Abnormally accumulated tau protein aggregates are one of the hallmarks of neurodegenerative diseases, including Alzheimer’s disease (AD). In order to investigate proteomic alteration driven by tau aggregates, we implemented quantitative proteomics to analyze disease model mice expressing human MAPTP301S transgene (hTau-Tg) and quantified more than 9,000 proteins in total. We applied the weighted gene co-expression analysis (WGCNA) algorithm to the datasets and explored protein co-expression modules that were associated with the accumulation of tau aggregates and were preserved in proteomes of AD brains. This led us to identify four modules with functions related to neuroinflammatory responses, mitochondrial energy production processes (including the tricarboxylic acid cycle and oxidative phosphorylation), cholesterol biosynthesis, and postsynaptic density. Furthermore, a phosphoproteomics study uncovered phosphorylation sites that were highly correlated with these modules. Our datasets represent resources for understanding the molecular basis of tau-induced neurodegeneration, including AD. Large-scale proteome datasets of tauopathy model mice Protein co-expression network constructed Four co-expression modules associated with tau-induced pathologies Identification of phosphorylation sites correlated with the modules
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24
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Nelson RS, Dammer EB, Santiago JV, Seyfried NT, Rangaraju S. Brain Cell Type-Specific Nuclear Proteomics Is Imperative to Resolve Neurodegenerative Disease Mechanisms. Front Neurosci 2022; 16:902146. [PMID: 35784845 PMCID: PMC9243337 DOI: 10.3389/fnins.2022.902146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 01/19/2023] Open
Abstract
Neurodegenerative diseases (NDs) involve complex cellular mechanisms that are incompletely understood. Emerging findings have revealed that disruption of nuclear processes play key roles in ND pathogenesis. The nucleus is a nexus for gene regulation and cellular processes that together, may underlie pathomechanisms of NDs. Furthermore, many genetic risk factors for NDs encode proteins that are either present in the nucleus or are involved in nuclear processes (for example, RNA binding proteins, epigenetic regulators, or nuclear-cytoplasmic transport proteins). While recent advances in nuclear transcriptomics have been significant, studies of the nuclear proteome in brain have been relatively limited. We propose that a comprehensive analysis of nuclear proteomic alterations of various brain cell types in NDs may provide novel biological and therapeutic insights. This may be feasible because emerging technical advances allow isolation and investigation of intact nuclei from post-mortem frozen human brain tissue with cell type-specific and single-cell resolution. Accordingly, nuclei of various brain cell types harbor unique protein markers which can be used to isolate cell-type specific nuclei followed by down-stream proteomics by mass spectrometry. Here we review the literature providing a rationale for investigating proteomic changes occurring in nuclei in NDs and then highlight the potential for brain cell type-specific nuclear proteomics to enhance our understanding of distinct cellular mechanisms that drive ND pathogenesis.
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Affiliation(s)
- Ruth S. Nelson
- Department of Neurology, Emory University, Atlanta, GA, United States
| | - Eric B. Dammer
- Department of Biochemistry, Emory University, Atlanta, GA, United States
| | | | | | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, United States,*Correspondence: Srikant Rangaraju
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25
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Rayaprolu S, Bitarafan S, Santiago JV, Betarbet R, Sunna S, Cheng L, Xiao H, Nelson RS, Kumar P, Bagchi P, Duong DM, Goettemoeller AM, Oláh VJ, Rowan M, Levey AI, Wood LB, Seyfried NT, Rangaraju S. Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain. Nat Commun 2022; 13:2927. [PMID: 35614064 PMCID: PMC9132937 DOI: 10.1038/s41467-022-30623-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/06/2022] [Indexed: 01/19/2023] Open
Abstract
Proteomic profiling of brain cell types using isolation-based strategies pose limitations in resolving cellular phenotypes representative of their native state. We describe a mouse line for cell type-specific expression of biotin ligase TurboID, for in vivo biotinylation of proteins. Using adenoviral and transgenic approaches to label neurons, we show robust protein biotinylation in neuronal soma and axons throughout the brain, allowing quantitation of over 2000 neuron-derived proteins spanning synaptic proteins, transporters, ion channels and disease-relevant druggable targets. Next, we contrast Camk2a-neuron and Aldh1l1-astrocyte proteomes and identify brain region-specific proteomic differences within both cell types, some of which might potentially underlie the selective vulnerability to neurological diseases. Leveraging the cellular specificity of proteomic labeling, we apply an antibody-based approach to uncover differences in neuron and astrocyte-derived signaling phospho-proteins and cytokines. This approach will facilitate the characterization of cell-type specific proteomes in a diverse number of tissues under both physiological and pathological states.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Sara Bitarafan
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Ranjita Betarbet
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Sydney Sunna
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Hailian Xiao
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Ruth S Nelson
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Prateek Kumar
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | | | - Viktor János Oláh
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matt Rowan
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
- Emory Integrated Proteomics Core, Emory University, Atlanta, GA, 30322, USA.
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, 30322, USA.
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26
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Sudwarts A, Ramesha S, Gao T, Ponnusamy M, Wang S, Hansen M, Kozlova A, Bitarafan S, Kumar P, Beaulieu-Abdelahad D, Zhang X, Collier L, Szekeres C, Wood LB, Duan J, Thinakaran G, Rangaraju S. BIN1 is a key regulator of proinflammatory and neurodegeneration-related activation in microglia. Mol Neurodegener 2022; 17:33. [PMID: 35526014 PMCID: PMC9077874 DOI: 10.1186/s13024-022-00535-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/30/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The BIN1 locus contains the second-most significant genetic risk factor for late-onset Alzheimer's disease. BIN1 undergoes alternate splicing to generate tissue- and cell-type-specific BIN1 isoforms, which regulate membrane dynamics in a range of crucial cellular processes. Whilst the expression of BIN1 in the brain has been characterized in neurons and oligodendrocytes in detail, information regarding microglial BIN1 expression is mainly limited to large-scale transcriptomic and proteomic data. Notably, BIN1 protein expression and its functional roles in microglia, a cell type most relevant to Alzheimer's disease, have not been examined in depth. METHODS Microglial BIN1 expression was analyzed by immunostaining mouse and human brain, as well as by immunoblot and RT-PCR assays of isolated microglia or human iPSC-derived microglial cells. Bin1 expression was ablated by siRNA knockdown in primary microglial cultures in vitro and Cre-lox mediated conditional deletion in adult mouse brain microglia in vivo. Regulation of neuroinflammatory microglial signatures by BIN1 in vitro and in vivo was characterized using NanoString gene panels and flow cytometry methods. The transcriptome data was explored by in silico pathway analysis and validated by complementary molecular approaches. RESULTS Here, we characterized microglial BIN1 expression in vitro and in vivo and ascertained microglia expressed BIN1 isoforms. By silencing Bin1 expression in primary microglial cultures, we demonstrate that BIN1 regulates the activation of proinflammatory and disease-associated responses in microglia as measured by gene expression and cytokine production. Our transcriptomic profiling revealed key homeostatic and lipopolysaccharide (LPS)-induced inflammatory response pathways, as well as transcription factors PU.1 and IRF1 that are regulated by BIN1. Microglia-specific Bin1 conditional knockout in vivo revealed novel roles of BIN1 in regulating the expression of disease-associated genes while counteracting CX3CR1 signaling. The consensus from in vitro and in vivo findings showed that loss of Bin1 impaired the ability of microglia to mount type 1 interferon responses to proinflammatory challenge, particularly the upregulation of a critical type 1 immune response gene, Ifitm3. CONCLUSIONS Our convergent findings provide novel insights into microglial BIN1 function and demonstrate an essential role of microglial BIN1 in regulating brain inflammatory response and microglial phenotypic changes. Moreover, for the first time, our study shows a regulatory relationship between Bin1 and Ifitm3, two Alzheimer's disease-related genes in microglia. The requirement for BIN1 to regulate Ifitm3 upregulation during inflammation has important implications for inflammatory responses during the pathogenesis and progression of many neurodegenerative diseases.
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Affiliation(s)
- Ari Sudwarts
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Supriya Ramesha
- grid.189967.80000 0001 0941 6502Department of Neurology, Emory University, Atlanta, GA 30322 USA
| | - Tianwen Gao
- grid.189967.80000 0001 0941 6502Department of Neurology, Emory University, Atlanta, GA 30322 USA
| | - Moorthi Ponnusamy
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Shuai Wang
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Mitchell Hansen
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Alena Kozlova
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, North Shore University Health System, Evanston, IL 60201 USA
| | - Sara Bitarafan
- grid.213917.f0000 0001 2097 4943Parker H. Petit Institute for Bioengineering and Bioscience, Wallace H. Coulter Department of Biomedical Engineering, and Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Prateek Kumar
- grid.189967.80000 0001 0941 6502Department of Neurology, Emory University, Atlanta, GA 30322 USA
| | - David Beaulieu-Abdelahad
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Xiaolin Zhang
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Lisa Collier
- grid.170693.a0000 0001 2353 285XByrd Alzheimer’s Center and Research Institute, University of South Florida, Tampa, FL 33613 USA ,grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Charles Szekeres
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620 USA
| | - Levi B. Wood
- grid.213917.f0000 0001 2097 4943Parker H. Petit Institute for Bioengineering and Bioscience, Wallace H. Coulter Department of Biomedical Engineering, and Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Jubao Duan
- grid.240372.00000 0004 0400 4439Center for Psychiatric Genetics, North Shore University Health System, Evanston, IL 60201 USA ,grid.170205.10000 0004 1936 7822Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637 USA
| | - Gopal Thinakaran
- Byrd Alzheimer's Center and Research Institute, University of South Florida, Tampa, FL, 33613, USA. .,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA.
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27
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Yurduseven K, Babal YK, Celik E, Kerman BE, Kurnaz IA. Multiple Sclerosis Biomarker Candidates Revealed by Cell-Type-Specific Interactome Analysis. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:305-317. [PMID: 35483054 DOI: 10.1089/omi.2022.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multiple sclerosis (MS) is a demyelinating disorder that affects multiple regions of the central nervous system such as the brain, spinal cord, and optic nerves. Susceptibility to MS, as well as disease progression rates, displays marked patient-to-patient variability. To date, biomarkers that forecast differences in clinical phenotypes and outcomes have been limited. In this context, cell-type-specific interactome analyses offer important prospects and hope for novel diagnostics and therapeutics. We report here an original study using bioinformatic analysis of MS data sets that revealed interaction profiles as well as specific hub proteins in white matter (WM) and gray matter (GM) that appear critical for disease mechanisms. First, cell-type-specific interactome analyses suggested that while interactions within the WM were focused on oligodendrocytes, interactions within the GM were mostly neuron centric. Second, hub proteins such as APP, EGLN3, PTEN, and LRRK2 were identified to be differentially regulated in MS data sets. Lastly, a comparison of the brain and peripheral blood samples identified biomarker candidates such as NRGN, CRTC1, CDC42, and IFITM3 to be differentially expressed in different types of MS. These findings offer a unique cell-type-specific cell-to-cell interaction network in MS and identify potential biomarkers by comparative analysis of the brain and the blood transcriptomics. From a study design and methodology perspective, we suggest that the cell-type-specific interactome analysis is an important systems science frontier that might offer new insights on other neurodegenerative and brain disorders as well.
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Affiliation(s)
- Kübra Yurduseven
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Yigit Koray Babal
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Esref Celik
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Bilal Ersen Kerman
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Işıl Aksan Kurnaz
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
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Drummond E, Kavanagh T, Pires G, Marta-Ariza M, Kanshin E, Nayak S, Faustin A, Berdah V, Ueberheide B, Wisniewski T. The amyloid plaque proteome in early onset Alzheimer's disease and Down syndrome. Acta Neuropathol Commun 2022; 10:53. [PMID: 35418158 PMCID: PMC9008934 DOI: 10.1186/s40478-022-01356-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloid plaques contain many proteins in addition to beta amyloid (Aβ). Previous studies examining plaque-associated proteins have shown these additional proteins are important; they provide insight into the factors that drive amyloid plaque development and are potential biomarkers or therapeutic targets for Alzheimer's disease (AD). The aim of this study was to comprehensively identify proteins that are enriched in amyloid plaques using unbiased proteomics in two subtypes of early onset AD: sporadic early onset AD (EOAD) and Down Syndrome (DS) with AD. We focused our study on early onset AD as the drivers of the more aggressive pathology development in these cases is unknown and it is unclear whether amyloid-plaque enriched proteins differ between subtypes of early onset AD. Amyloid plaques and neighbouring non-plaque tissue were microdissected from human brain sections using laser capture microdissection and label-free LC-MS was used to quantify the proteins present. 48 proteins were consistently enriched in amyloid plaques in EOAD and DS. Many of these proteins were more significantly enriched in amyloid plaques than Aβ. The most enriched proteins in amyloid plaques in both EOAD and DS were: COL25A1, SMOC1, MDK, NTN1, OLFML3 and HTRA1. Endosomal/lysosomal proteins were particularly highly enriched in amyloid plaques. Fluorescent immunohistochemistry was used to validate the enrichment of four proteins in amyloid plaques (moesin, ezrin, ARL8B and SMOC1) and to compare the amount of total Aβ, Aβ40, Aβ42, phosphorylated Aβ, pyroglutamate Aβ species and oligomeric species in EOAD and DS. These studies showed that phosphorylated Aβ, pyroglutamate Aβ species and SMOC1 were significantly higher in DS plaques, while oligomers were significantly higher in EOAD. Overall, we observed that amyloid plaques in EOAD and DS largely contained the same proteins, however the amount of enrichment of some proteins was different in EOAD and DS. Our study highlights the significant enrichment of many proteins in amyloid plaques, many of which may be potential therapeutic targets and/or biomarkers for AD.
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Affiliation(s)
- Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, Australia.
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA.
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, 94 Mallett Street, Camperdown, NSW, Australia
| | - Geoffrey Pires
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Mitchell Marta-Ariza
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
| | - Shruti Nayak
- Merck & Co., Inc, Computational & Structural Chemistry, Kenilworth, NJ, USA
| | - Arline Faustin
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Valentin Berdah
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
| | - Beatrix Ueberheide
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Centre for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, Science Building, Rm 1017, 435 East 30th Street, New York, NY, 10016, USA.
- Departments of Pathology and Psychiatry, Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
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A human tau seeded neuronal cell model recapitulates molecular responses associated with Alzheimer's disease. Sci Rep 2022; 12:2673. [PMID: 35177665 PMCID: PMC8854741 DOI: 10.1038/s41598-022-06411-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022] Open
Abstract
Cellular models recapitulating features of tauopathies are useful tools to investigate the causes and consequences of tau aggregation and the identification of novel treatments. We seeded rat primary cortical neurons with tau isolated from Alzheimer’s disease brains to induce a time-dependent increase in endogenous tau inclusions. Transcriptomics of seeded and control cells identified 1075 differentially expressed genes (including 26 altered at two time points). These were enriched for lipid/steroid metabolism and neuronal/glial cell development genes. 50 genes were correlated with tau inclusion formation at both transcriptomic and proteomic levels, including several microtubule and cytoskeleton-related proteins such as Tubb2a, Tubb4a, Nefl and Snca. Several genes (such as Fyn kinase and PTBP1, a tau exon 10 repressor) interact directly with or regulate tau. We conclude that this neuronal model may be a suitable platform for high-throughput screens for target or hit compound identification and validation.
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Carrier M, Šimončičová E, St-Pierre MK, McKee C, Tremblay MÈ. Psychological Stress as a Risk Factor for Accelerated Cellular Aging and Cognitive Decline: The Involvement of Microglia-Neuron Crosstalk. Front Mol Neurosci 2021; 14:749737. [PMID: 34803607 PMCID: PMC8599581 DOI: 10.3389/fnmol.2021.749737] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
The relationship between the central nervous system (CNS) and microglia is lifelong. Microglia originate in the embryonic yolk sac during development and populate the CNS before the blood-brain barrier forms. In the CNS, they constitute a self-renewing population. Although they represent up to 10% of all brain cells, we are only beginning to understand how much brain homeostasis relies on their physiological functions. Often compared to a double-edged sword, microglia hold the potential to exert neuroprotective roles that can also exacerbate neurodegeneration once compromised. Microglia can promote synaptic growth in addition to eliminating synapses that are less active. Synaptic loss, which is considered one of the best pathological correlates of cognitive decline, is a distinctive feature of major depressive disorder (MDD) and cognitive aging. Long-term psychological stress accelerates cellular aging and predisposes to various diseases, including MDD, and cognitive decline. Among the underlying mechanisms, stress-induced neuroinflammation alters microglial interactions with the surrounding parenchymal cells and exacerbates oxidative burden and cellular damage, hence inducing changes in microglia and neurons typical of cognitive aging. Focusing on microglial interactions with neurons and their synapses, this review discusses the disrupted communication between these cells, notably involving fractalkine signaling and the triggering receptor expressed on myeloid cells (TREM). Overall, chronic stress emerges as a key player in cellular aging by altering the microglial sensome, notably via fractalkine signaling deficiency. To study cellular aging, novel positron emission tomography radiotracers for TREM and the purinergic family of receptors show interest for human study.
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Affiliation(s)
- Micaël Carrier
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada.,Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Eva Šimončičová
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Kim St-Pierre
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Department of Molecular Medicine, Université Laval, Québec City, QC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada.,Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Department of Molecular Medicine, Université Laval, Québec City, QC, Canada.,Neurology and Neurosurgery Department, McGill University, Montreal, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
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31
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Cao C, Prado MA, Sun L, Rockowitz S, Sliz P, Paulo JA, Finley D, Fleming MD. Maternal Iron Deficiency Modulates Placental Transcriptome and Proteome in Mid-Gestation of Mouse Pregnancy. J Nutr 2021; 151:1073-1083. [PMID: 33693820 PMCID: PMC8112763 DOI: 10.1093/jn/nxab005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Maternal iron deficiency (ID) is associated with poor pregnancy and fetal outcomes. The effect is thought to be mediated by the placenta but there is no comprehensive assessment of placental responses to maternal ID. Additionally, whether the influence of maternal ID on the placenta differs by fetal sex is unknown. OBJECTIVES To identify gene and protein signatures of ID mouse placentas at mid-gestation. A secondary objective was to profile the expression of iron genes in mouse placentas across gestation. METHODS We used a real-time PCR-based array to determine the mRNA expression of all known iron genes in mouse placentas at embryonic day (E) 12.5, E14.5, E16.5, and E19.5 (n = 3 placentas/time point). To determine the effect of maternal ID, we performed RNA sequencing and proteomics in male and female placentas from ID and iron-adequate mice at E12.5 (n = 8 dams/diet). RESULTS In female placentas, 6 genes, including transferrin receptor (Tfrc) and solute carrier family 11 member 2, were significantly changed by maternal ID. An additional 154 genes were altered in male ID placentas. A proteomic analysis quantified 7662 proteins in the placenta. Proteins translated from iron-responsive element (IRE)-containing mRNA were altered in abundance; ferritin and ferroportin 1 decreased, while TFRC increased in ID placentas. Less than 4% of the significantly altered genes in ID placentas occurred both at the transcriptional and translational levels. CONCLUSIONS Our data demonstrate that the impact of maternal ID on placental gene expression in mice is limited in scope and magnitude at mid-gestation. We provide strong evidence for IRE-based transcriptional and translational coordination of iron gene expression in the mouse placenta. Finally, we discover sexually dimorphic effects of maternal ID on placental gene expression, with more genes and pathways altered in male compared with female mouse placentas.
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Affiliation(s)
- Chang Cao
- Address correspondence to CC (e-mail: )
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Liang Sun
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Piotr Sliz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA,Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
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32
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Li G, Luo W, Wang B, Qian C, Ye Y, Li Y, Zhang S. HMGA1 Induction of miR-103/107 Forms a Negative Feedback Loop to Regulate Autophagy in MPTP Model of Parkinson's Disease. Front Cell Neurosci 2021; 14:620020. [PMID: 33536877 PMCID: PMC7847849 DOI: 10.3389/fncel.2020.620020] [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: 10/21/2020] [Accepted: 12/09/2020] [Indexed: 11/18/2022] Open
Abstract
Autophagy dysfunction has been directly linked with the onset and progression of Parkinson’s disease (PD), but the underlying mechanisms are not well understood. High-mobility group A1 (HMGA1), well-known chromatin remodeling proteins, play pivotal roles in diverse biological processes and diseases. Their function in neural cell death in PD, however, have not yet been fully elucidated. Here, we report that HMGA1 is highly induced during dopaminergic cell death in vitro and mice models of PD in vivo. Functional studies using genetic knockdown of endogenous HMGA1 show that HMGA1 signaling inhibition accelerates neural cell death, at least partially through aggravating MPP+-induced autophagic flux reduction resulting from partial block in autophagic flux at the terminal stages, indicating a novel potential neuroprotective role for HMGA1 in dopaminergic neurons death. MicroRNA-103/107 (miR-103/107) family, which is highly expressed in neuron, coordinately ensures proper end-stage autophagy. We further illustrate that MPP+/1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced HMGA1 elevation counterparts the effect of miR-103/107 downregulation by directly binding to their promoters, respectively, sustaining their expression in MPP+-damaged MN9D cells and modulates autophagy through CDK5R1/CDK5 signaling pathway. We also find that HMGA1 is a direct target of miR-103/107 family. Thus, our results suggest that HMGA1 forms a negative feedback loop with miR-103/107-CDK5R1/CDK5 signaling to regulate the MPP+/MPTP-induced autophagy impairment and neural cell death. Collectively, we identify a paradigm for compensatory neuroprotective HMGA1 signaling in dopaminergic neurons that could have important therapeutic implications for PD.
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Affiliation(s)
- Gehui Li
- Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The National Key Clinical Specialty, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Wanxian Luo
- Department of Medicine Ultrasonics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Baoyan Wang
- Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The National Key Clinical Specialty, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chen Qian
- Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The National Key Clinical Specialty, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yongyi Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuantao Li
- Department of Anesthesiology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Shizhong Zhang
- Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The National Key Clinical Specialty, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Vitek MP, Araujo JA, Fossel M, Greenberg BD, Howell GR, Rizzo SJS, Seyfried NT, Tenner AJ, Territo PR, Windisch M, Bain LJ, Ross A, Carrillo MC, Lamb BT, Edelmayer RM. Translational animal models for Alzheimer's disease: An Alzheimer's Association Business Consortium Think Tank. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2021; 6:e12114. [PMID: 33457489 PMCID: PMC7798310 DOI: 10.1002/trc2.12114] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022]
Abstract
Over 5 million Americans and 50 million individuals worldwide are living with Alzheimer's disease (AD). The progressive dementia associated with AD currently has no cure. Although clinical trials in patients are ultimately required to find safe and effective drugs, animal models of AD permit the integration of brain pathologies with learning and memory deficits that are the first step in developing these new drugs. The purpose of the Alzheimer's Association Business Consortium Think Tank meeting was to address the unmet need to improve the discovery and successful development of Alzheimer's therapies. We hypothesize that positive responses to new therapies observed in validated models of AD will provide predictive evidence for positive responses to these same therapies in AD patients. To achieve this goal, we convened a meeting of experts to explore the current state of AD animal models, identify knowledge gaps, and recommend actions for development of next-generation models with better predictability. Among our findings, we all recognize that models reflecting only single aspects of AD pathogenesis do not mimic AD. Models or combinations of new models are needed that incorporate genetics with environmental interactions, timing of disease development, heterogeneous mechanisms and pathways, comorbidities, and other pathologies that lead to AD and related dementias. Selection of the best models requires us to address the following: (1) which animal species, strains, and genetic backgrounds are most appropriate; (2) which models permit efficient use throughout the drug development pipeline; (3) the translatability of behavioral-cognitive assays from animals to patients; and (4) how to match potential AD therapeutics with particular models. Best practice guidelines to improve reproducibility also need to be developed for consistent use of these models in different research settings. To enhance translational predictability, we discuss a multi-model evaluation strategy to de-risk the successful transition of pre-clinical drug assets to the clinic.
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Affiliation(s)
| | | | | | | | | | | | - Nicholas T. Seyfried
- Departments of Biochemistry and NeurologyEmory School of MedicineAtlantaGeorgiaUSA
| | - Andrea J. Tenner
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA
| | | | | | - Lisa J. Bain
- Independent Science and Medical WriterElversonPennsylvaniaUSA
| | - April Ross
- Former Alzheimer's Association EmployeeChicagoIllinoisUSA
| | | | - Bruce T. Lamb
- Indiana University School of MedicineStark Neurosciences Research InstituteIndianapolisIndianaUSA
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Abstract
Due to the growing number of chronic traumatic encephalopathy (CTE) cases in the military and contact sports, defining the cellular and molecular substrate of this disorder is crucial. Most classic neuropathological investigations describe cortical tau and, to a lesser extent, amyloid lesions, which may underlie the clinical sequela associated with CTE. The application of modern molecular biologic technology to postmortem human brain tissue has made it possible to evaluate the genetic signature of specific neuronal phenotypes at different stages of CTE pathology. Most recently, molecular pathobiology has been used in the field of CTE, with an emphasis on the cholinergic neurons located within the nucleus basalis of Meynert, which develop tau pathology and are associated with cognitive dysfunction similar to that found in Alzheimer's disease (AD). Quantitative findings derived from single-cell transcript investigations provide clues to our understanding of the selective vulnerability of neurons containing AD-like tau pathology at different stages of CTE. Since human tissue-based studies provide a gold standard for the field of CTE, continued molecular pathological studies are needed to reveal novel drug targets for the treatment of this disorder.
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35
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Rayaprolu S, Higginbotham L, Bagchi P, Watson CM, Zhang T, Levey AI, Rangaraju S, Seyfried NT. Systems-based proteomics to resolve the biology of Alzheimer's disease beyond amyloid and tau. Neuropsychopharmacology 2021; 46:98-115. [PMID: 32898852 PMCID: PMC7689445 DOI: 10.1038/s41386-020-00840-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/05/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
The repeated failures of amyloid-targeting therapies have challenged our narrow understanding of Alzheimer's disease (AD) pathogenesis and inspired wide-ranging investigations into the underlying mechanisms of disease. Increasing evidence indicates that AD develops from an intricate web of biochemical and cellular processes that extend far beyond amyloid and tau accumulation. This growing recognition surrounding the diversity of AD pathophysiology underscores the need for holistic systems-based approaches to explore AD pathogenesis. Here we describe how network-based proteomics has emerged as a powerful tool and how its application to the AD brain has provided an informative framework for the complex protein pathophysiology underlying the disease. Furthermore, we outline how the AD brain network proteome can be leveraged to advance additional scientific and translational efforts, including the discovery of novel protein biomarkers of disease.
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Affiliation(s)
- Sruti Rayaprolu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lenora Higginbotham
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Pritha Bagchi
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Caroline M Watson
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tian Zhang
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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36
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Roussarie JP, Rodriguez-Rodriguez P. Deciphering cell-type specific signal transduction in the brain: Challenges and promises. ADVANCES IN PHARMACOLOGY 2020; 90:145-171. [PMID: 33706931 DOI: 10.1016/bs.apha.2020.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Signal transduction designates the set of molecular events that take place within a cell upon extracellular stimulation to mediate a functional outcome. Decades after the discovery that dopamine triggers opposing signaling pathways in D1- and D2-expressing medium spiny neurons, it is now clear that there are as many different flavors of signaling pathways in the brain as there are neuron types. One of the biggest challenges in molecular neuroscience is to elucidate cell-type specific signaling, in order to understand neurological diseases with regional vulnerability, but also to identify targets for precision drugs devoid of off-target effects. Here, we make a case for the importance of the study of neuron-type specific molecular characteristics. We then review the technologies that exist to study neurons in their full diversity and highlight their disease-relevant idiosyncrasies.
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Affiliation(s)
- Jean-Pierre Roussarie
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, United States.
| | - Patricia Rodriguez-Rodriguez
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, United States; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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