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Ma Y, Shi W, Dong Y, Sun Y, Jin Q. Spatial Multi-Omics in Alzheimer's Disease: A Multi-Dimensional Approach to Understanding Pathology and Progression. Curr Issues Mol Biol 2024; 46:4968-4990. [PMID: 38785566 PMCID: PMC11119029 DOI: 10.3390/cimb46050298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Alzheimer's Disease (AD) presents a complex neuropathological landscape characterized by hallmark amyloid plaques and neurofibrillary tangles, leading to progressive cognitive decline. Despite extensive research, the molecular intricacies contributing to AD pathogenesis are inadequately understood. While single-cell omics technology holds great promise for application in AD, particularly in deciphering the understanding of different cell types and analyzing rare cell types and transcriptomic expression changes, it is unable to provide spatial distribution information, which is crucial for understanding the pathological processes of AD. In contrast, spatial multi-omics research emerges as a promising and comprehensive approach to analyzing tissue cells, potentially better suited for addressing these issues in AD. This article focuses on the latest advancements in spatial multi-omics technology and compares various techniques. Additionally, we provide an overview of current spatial omics-based research results in AD. These technologies play a crucial role in facilitating new discoveries and advancing translational AD research in the future. Despite challenges such as balancing resolution, increasing throughput, and data analysis, the application of spatial multi-omics holds immense potential in revolutionizing our understanding of human disease processes and identifying new biomarkers and therapeutic targets, thereby potentially contributing to the advancement of AD research.
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Affiliation(s)
| | | | | | | | - Qiguan Jin
- College of Physical Education, Yangzhou University, Yangzhou 225127, China; (Y.M.); (W.S.); (Y.D.); (Y.S.)
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2
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Chen X, Song Y, Song W, Han J, Cao H, Xu X, Li S, Fu Y, Ding C, Lin F, Shi Y, Li J. Multi-omics reveal neuroprotection of Acer truncatum Bunge Seed extract on hypoxic-ischemia encephalopathy rats under high-altitude. Commun Biol 2023; 6:1001. [PMID: 37783835 PMCID: PMC10545756 DOI: 10.1038/s42003-023-05341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Abstract
Hypoxic-ischemic encephalopathy (HIE) at high-altitudes leads to neonatal mortality and long-term neurological complications without effective treatment. Acer truncatum Bunge Seed extract (ASO) is reported to have effect on cognitive improvement, but its molecular mechanisms on HIE are unclear. In this study, ASO administration contributed to reduced neuronal cell edema and improved motor ability in HIE rats at a simulated 4500-meter altitude. Transcriptomics and WGCNA analysis showed genes associated with lipid biosynthesis, redox homeostasis, neuronal growth, and synaptic plasticity regulated in the ASO group. Targeted and untargeted-lipidomics revealed decreased free fatty acids and increased phospholipids with favorable ω-3/ω-6/ω-9 fatty acid ratios, as well as reduced oxidized glycerophospholipids (OxGPs) in the ASO group. Combining multi-omics analysis demonstrated FA to FA-CoA, phospholipids metabolism, and lipid peroxidation were regulated by ASO treatment. Our results illuminated preliminary metabolism mechanism of ASO ingesting in rats, implying ASO administration as potential intervention strategy for HIE under high-altitude.
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Affiliation(s)
- Xianyang Chen
- Bao Feng Key Laboratory of Genetics and Metabolism, Beijing, China
| | - Yige Song
- Bao Feng Key Laboratory of Genetics and Metabolism, Beijing, China
| | - Wangting Song
- Bao Feng Key Laboratory of Genetics and Metabolism, Beijing, China
| | - Jiarui Han
- Bao Feng Key Laboratory of Genetics and Metabolism, Beijing, China
| | - Hongli Cao
- Department of Respiratory, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Xiao Xu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Plateau Medical Research Center of China Medical University, Shenyang, China
| | - Shujia Li
- Department of Pediatrics, Shengjing Hospital of China Medical University, Plateau Medical Research Center of China Medical University, Shenyang, China
| | - Yanmin Fu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Plateau Medical Research Center of China Medical University, Shenyang, China
| | - Chunguang Ding
- National Center for Occupational Safety and Health, Beijing, China
| | - Feng Lin
- Department of Neurology, Sanming First Hospital Affiliated to Fujian Medical University, Sanming, Fujian, China
| | - Yuan Shi
- Department of Neonatology, Children's Hospital Affiliated Chongqing Medical University, Chongqing, China
| | - Jiujun Li
- Department of Pediatrics, Shengjing Hospital of China Medical University, Plateau Medical Research Center of China Medical University, Shenyang, China.
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3
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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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4
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Larsson JNK, Nyström S, Hammarström P. HSP10 as a Chaperone for Neurodegenerative Amyloid Fibrils. Front Neurosci 2022; 16:902600. [PMID: 35769706 PMCID: PMC9234269 DOI: 10.3389/fnins.2022.902600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022] Open
Abstract
Neurodegenerative diseases (NDs) are associated with accumulated misfolded proteins (MPs). MPs oligomerize and form multiple forms of amyloid fibril polymorphs that dictate fibril propagation and cellular dysfunction. Protein misfolding processes that impair protein homeostasis are implicated in onset and progression of NDs. A wide variety of molecular chaperones safeguard the cell from MP accumulation. A rather overlooked molecular chaperone is HSP10, known as a co-chaperone for HSP60. Due to the ubiquitous presence in human tissues and protein overabundance compared with HSP60, we studied how HSP10 alone influences fibril formation in vitro of Alzheimer’s disease-associated Aβ1–42. At sub-stoichiometric concentrations, eukaryotic HSP10s (human and Drosophila) significantly influenced the fibril formation process and the fibril structure of Aβ1–42, more so than the prokaryotic HSP10 GroES. Similar effects were observed for prion disease-associated prion protein HuPrP90–231. Paradoxically, for a chaperone, low concentrations of HSP10 appeared to promote fibril nucleation by shortened lag-phases, which were chaperone and substrate dependent. Higher concentrations of chaperone while still sub-stoichiometric extended the nucleation and/or the elongation phase. We hypothesized that HSP10 by means of its seven mobile loops provides the chaperone with high avidity binding to amyloid fibril ends. The preserved sequence of the edge of the mobile loop GGIM(V)L (29–33 human numbering) normally dock to the HSP60 apical domain. Interestingly, this segment shows sequence similarity to amyloidogenic core segments of Aβ1–42, GGVVI (37–41), and HuPrP90-231 GGYML (126–130) likely allowing efficient competitive binding to fibrillar conformations of these MPs. Our results propose that HSP10 can function as an important molecular chaperone in human proteostasis in NDs.
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Sasaguri H, Hashimoto S, Watamura N, Sato K, Takamura R, Nagata K, Tsubuki S, Ohshima T, Yoshiki A, Sato K, Kumita W, Sasaki E, Kitazume S, Nilsson P, Winblad B, Saito T, Iwata N, Saido TC. Recent Advances in the Modeling of Alzheimer's Disease. Front Neurosci 2022; 16:807473. [PMID: 35431779 PMCID: PMC9009508 DOI: 10.3389/fnins.2022.807473] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
Since 1995, more than 100 transgenic (Tg) mouse models of Alzheimer's disease (AD) have been generated in which mutant amyloid precursor protein (APP) or APP/presenilin 1 (PS1) cDNA is overexpressed ( 1st generation models ). Although many of these models successfully recapitulate major pathological hallmarks of the disease such as amyloid β peptide (Aβ) deposition and neuroinflammation, they have suffered from artificial phenotypes in the form of overproduced or mislocalized APP/PS1 and their functional fragments, as well as calpastatin deficiency-induced early lethality, calpain activation, neuronal cell death without tau pathology, endoplasmic reticulum stresses, and inflammasome involvement. Such artifacts bring two important uncertainties into play, these being (1) why the artifacts arise, and (2) how they affect the interpretation of experimental results. In addition, destruction of endogenous gene loci in some Tg lines by transgenes has been reported. To overcome these concerns, single App knock-in mouse models harboring the Swedish and Beyreuther/Iberian mutations with or without the Arctic mutation (AppNL-G-F and AppNL-F mice) were developed ( 2nd generation models ). While these models are interesting given that they exhibit Aβ pathology, neuroinflammation, and cognitive impairment in an age-dependent manner, the model with the Artic mutation, which exhibits an extensive pathology as early as 6 months of age, is not suitable for investigating Aβ metabolism and clearance because the Aβ in this model is resistant to proteolytic degradation and is therefore prone to aggregation. Moreover, it cannot be used for preclinical immunotherapy studies owing to the discrete affinity it shows for anti-Aβ antibodies. The weakness of the latter model (without the Arctic mutation) is that the pathology may require up to 18 months before it becomes sufficiently apparent for experimental investigation. Nevertheless, this model was successfully applied to modulating Aβ pathology by genome editing, to revealing the differential roles of neprilysin and insulin-degrading enzyme in Aβ metabolism, and to identifying somatostatin receptor subtypes involved in Aβ degradation by neprilysin. In addition to discussing these issues, we also provide here a technical guide for the application of App knock-in mice to AD research. Subsequently, a new double knock-in line carrying the AppNL-F and Psen1 P117L/WT mutations was generated, the pathogenic effect of which was found to be synergistic. A characteristic of this 3rd generation model is that it exhibits more cored plaque pathology and neuroinflammation than the AppNL-G-F line, and thus is more suitable for preclinical studies of disease-modifying medications targeting Aβ. Furthermore, a derivative AppG-F line devoid of Swedish mutations which can be utilized for preclinical studies of β-secretase modifier(s) was recently created. In addition, we introduce a new model of cerebral amyloid angiopathy that may be useful for analyzing amyloid-related imaging abnormalities that can be caused by anti-Aβ immunotherapy. Use of the App knock-in mice also led to identification of the α-endosulfine-K ATP channel pathway as components of the somatostatin-evoked physiological mechanisms that reduce Aβ deposition via the activation of neprilysin. Such advances have provided new insights for the prevention and treatment of preclinical AD. Because tau pathology plays an essential role in AD pathogenesis, knock-in mice with human tau wherein the entire murine Mapt gene has been humanized were generated. Using these mice, the carboxy-terminal PDZ ligand of neuronal nitric oxide synthase (CAPON) was discovered as a mediator linking tau pathology to neurodegeneration and showed that tau humanization promoted pathological tau propagation. Finally, we describe and discuss the current status of mutant human tau knock-in mice and a non-human primate model of AD that we have successfully created.
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Affiliation(s)
- Hiroki Sasaguri
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Shoko Hashimoto
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Naoto Watamura
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Kaori Sato
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
- Laboratory for Molecular Brain Science, Department of Life Science and Medical Bioscience, Waseda University, Shinjuku City, Japan
| | - Risa Takamura
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
- Laboratory for Molecular Brain Science, Department of Life Science and Medical Bioscience, Waseda University, Shinjuku City, Japan
| | - Kenichi Nagata
- Department of Functional Anatomy and Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Tsubuki
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Toshio Ohshima
- Laboratory for Molecular Brain Science, Department of Life Science and Medical Bioscience, Waseda University, Shinjuku City, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Kenya Sato
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Wakako Kumita
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Erika Sasaki
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Japan
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako, Japan
| | - Shinobu Kitazume
- Department of Clinical Laboratory Sciences, School of Health Sciences, Fukushima Medical University, Fukushima, Japan
| | - Per Nilsson
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Winblad
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Nobuhisa Iwata
- Department of Genome-Based Drug Discovery and Leading Medical Research Core Unit, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Takaomi C. Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
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Sandebring-Matton A, Axenhus M, Bogdanovic N, Winblad B, Schedin-Weiss S, Nilsson P, Tjernberg LO. Microdissected Pyramidal Cell Proteomics of Alzheimer Brain Reveals Alterations in Creatine Kinase B-Type, 14-3-3-γ, and Heat Shock Cognate 71. Front Aging Neurosci 2021; 13:735334. [PMID: 34867272 PMCID: PMC8641652 DOI: 10.3389/fnagi.2021.735334] [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: 07/02/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Novel insights on proteins involved in Alzheimer’s disease (AD) are needed. Since multiple cell types and matrix components are altered in AD, bulk analysis of brain tissue maybe difficult to interpret. In the current study, we isolated pyramidal cells from the cornu ammonis 1 (CA1) region of the hippocampus from five AD and five neurologically healthy donors using laser capture microdissection (LCM). The samples were analyzed by proteomics using 18O-labeled internal standard and nano-high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) for relative quantification. Fold change between AD and control was calculated for the proteins that were identified in at least two individual proteomes from each group. From the 10 cases analyzed, 62 proteins were identified in at least two AD cases and two control cases. Creatine kinase B-type (CKB), 14-3-3-γ, and heat shock cognate 71 (Hsc71), which have not been extensively studied in the context of the human AD brain previously, were selected for further studies by immunohistochemistry (IHC). In hippocampus, semi-quantitative measures of IHC staining of the three proteins confirmed the findings from our proteomic analysis. Studies of the same proteins in the frontal cortex revealed that the alterations remained for CKB and 14-3-3-γ but not for Hsc71. Protein upregulation in CA1 neurons of final stage AD is either a result of detrimental, pathological effects, or from cell-specific protective response mechanisms in surviving neurons. Based on previous findings from experimental studies, CKB and Hsc71 likely exhibit protective effects, whereas 14-3-3-γ may represent a detrimental pathway. These new players could reflect pathways of importance for the development of new therapeutic strategies.
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Affiliation(s)
- Anna Sandebring-Matton
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, United Kingdom
| | - Michael Axenhus
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Theme Inflammation and Aging, Karolinska University Hospital, Huddinge, Sweden
| | - Nenad Bogdanovic
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Theme Inflammation and Aging, Karolinska University Hospital, Huddinge, Sweden
| | - Bengt Winblad
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Per Nilsson
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden.,Clinical Chemistry, Karolinska University Hospital, Solna, Sweden
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7
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Haytural H, Benfeitas R, Schedin-Weiss S, Bereczki E, Rezeli M, Unwin RD, Wang X, Dammer EB, Johnson ECB, Seyfried NT, Winblad B, Tijms BM, Visser PJ, Frykman S, Tjernberg LO. Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis. Sci Data 2021; 8:312. [PMID: 34862388 PMCID: PMC8642431 DOI: 10.1038/s41597-021-01090-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
Mass spectrometry (MS)-based proteomics is a powerful tool to explore pathogenic changes of a disease in an unbiased manner and has been used extensively in Alzheimer disease (AD) research. Here, by performing a meta-analysis of high-quality proteomic studies, we address which pathological changes are observed consistently and therefore most likely are of great importance for AD pathogenesis. We retrieved datasets, comprising a total of 21,588 distinct proteins identified across 857 postmortem human samples, from ten studies using labeled or label-free MS approaches. Our meta-analysis findings showed significant alterations of 757 and 1,195 proteins in AD in the labeled and label-free datasets, respectively. Only 33 proteins, some of which were associated with synaptic signaling, had the same directional change across the individual studies. However, despite alterations in individual proteins being different between the labeled and the label-free datasets, several pathways related to synaptic signaling, oxidative phosphorylation, immune response and extracellular matrix were commonly dysregulated in AD. These pathways represent robust changes in the human AD brain and warrant further investigation.
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Affiliation(s)
- Hazal Haytural
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden.
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, S-10691, Stockholm, Sweden
| | - Sophia Schedin-Weiss
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Erika Bereczki
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Melinda Rezeli
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre, and Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Sciences Centre, CityLabs 1.0, Nelson Street, Manchester, M13 9NQ, UK
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
- Karolinska University Hospital, Theme of Inflammation and Aging, Huddinge, Sweden
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Pieter Jelle Visser
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
- Alzheimer Center Limburg, School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Susanne Frykman
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden
| | - Lars O Tjernberg
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden.
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8
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Freitas A, Aroso M, Rocha S, Ferreira R, Vitorino R, Gomez-Lazaro M. Bioinformatic analysis of the human brain extracellular matrix proteome in neurodegenerative disorders. Eur J Neurosci 2021; 53:4016-4033. [PMID: 34013613 DOI: 10.1111/ejn.15316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022]
Abstract
Alzheimer's, Parkinson's, and Huntington's diseases are characterized by selective degeneration of specific brain areas. Although increasing number of studies report alteration of the extracellular matrix on these diseases, an exhaustive characterization at the brain's matrix level might contribute to the development of more efficient cell restoration therapies. In that regard, proteomics-based studies are a powerful approach to uncover matrix changes. However, to date, the majority of proteomics studies report no or only a few brain matrix proteins with altered expression. This study aims to reveal the changes in the brain extracellular matrix by integrating several proteomics-based studies performed with postmortem tissue. In total, 67 matrix proteins with altered expression were collected. By applying a bioinformatic approach, we were able to reveal the dysregulated biological processes. Among them are processes related to the organization of the extracellular matrix, glycosaminoglycans and proteoglycans' metabolism, blood coagulation, and response to injury and oxidative stress. In addition, a protein was found altered in all three diseases-collagen type I alpha 2-and its binding partners further identified. A ClueGO network was created, depicting the GO groups associated with these binding partners, uncovering the processes that may consequently be affected. These include cellular adhesion, cell signaling through membrane receptors, inflammatory processes, and apoptotic cell death in response to oxidative stress. Overall, we were able to associate the contribution of the modification of extracellular matrix components to essential biological processes, highlighting the investment needed on proteomics studies with specific focus on the extracellular matrix in neurodegeneration.
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Affiliation(s)
- Ana Freitas
- i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,INEB -Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.,FMUP - Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Miguel Aroso
- i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,INEB -Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Sara Rocha
- i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,INEB -Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Rita Ferreira
- QOPNA &, LAQV, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Maria Gomez-Lazaro
- i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,INEB -Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
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9
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Schedin-Weiss S, Nilsson P, Sandebring-Matton A, Axenhus M, Sekiguchi M, Saito T, Winblad B, Saido T, Tjernberg LO. Proteomics Time-Course Study of App Knock-In Mice Reveals Novel Presymptomatic Aβ42-Induced Pathways to Alzheimer's Disease Pathology. J Alzheimers Dis 2021; 75:321-335. [PMID: 32280097 PMCID: PMC7902969 DOI: 10.3233/jad-200028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background: The 42 amino acids long amyloid-β peptide, Aβ42, may initiate a cascade of events leading to the severe neurodegeneration observed in Alzheimer’s disease (AD) brain. However, the underlying molecular mechanisms remain to be established. Objective: To find early Aβ42-induced AD related mechanisms, we performed a brain proteomics time-course study on a novel App knock-in AD mouse model, AppNL-F, expressing high levels of Aβ42 without AβPP overexpression artifacts. Methods: Hippocampus and cortex were analyzed separately by using 18O-labelling mass spectrometry to reveal alterations in protein levels. Pathway analysis of proteomics data was used to identify altered biological functions. Immunohistochemistry was used to further investigate a significant key regulatory protein. Results: Around 100 proteins were differently expressed in AppNL-F mice at each time point (3, 6, 9, and 18 months of age) as compared to wild type mice. Strikingly, already at 3 months of age—long before Aβ plaque development and memory impairment—several pathways, including long-term potentiation and synaptic plasticity, were downregulated, and neuritogenesis was increased. Huntingtin (HTT) was identified as an upstream regulator, i.e., a key protein affecting the levels of several proteins. Increased levels of HTT in hippocampus of AppNL-F mice was supported by immunofluorescence microscopy. Conclusion: Notably, the proteome was significantly altered already at 3 months of age, 6 months before the development of plaques. Differentially expressed proteins varied over time, indicating that increased Aβ42 levels initiate a cascade of events that eventually manifests in amyloid depositions, inflammation, and decline in memory.
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Affiliation(s)
- Sophia Schedin-Weiss
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Per Nilsson
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Anna Sandebring-Matton
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden.,Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics Center for Alzheimer Research, Karolinska Institutet, Stockholm, Sweden
| | - Michael Axenhus
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Misaki Sekiguchi
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan.,Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, Nagoya, Japan
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Japan
| | - Lars O Tjernberg
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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10
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Sathe G, Albert M, Darrow J, Saito A, Troncoso J, Pandey A, Moghekar A. Quantitative proteomic analysis of the frontal cortex in Alzheimer's disease. J Neurochem 2021; 156:988-1002. [PMID: 32614981 PMCID: PMC7775912 DOI: 10.1111/jnc.15116] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by intracellular formation of neurofibrillary tangles and extracellular deposition of β-amyloid protein (Aβ) in the extracellular matrix. The pathogenesis of AD has not yet been fully elucidated and little is known about global alterations in the brain proteome that are related to AD. To identify and quantify such AD-related changes in the brain, we employed a tandem mass tags approach coupled to high-resolution mass spectrometry. We compared the proteomes of frontal cortex from AD patients with corresponding age-matched brain samples. Liquid chromatography-mass spectrometry/MS analysis carried out on an Orbitrap Fusion Lumos Tribrid mass spectrometer led to identification of 8,066 proteins. Of these, 432 proteins were observed to be significantly altered (>1.5 fold) in their expression in AD brains. Proteins whose abundance was previously known to be altered in AD were identified including secreted phosphoprotein 1 (SPP1), somatostatin (SST), SPARC-related modular calcium binding 1 (SMOC1), dual specificity phosphatase 26 (DUSP26), and neuronal pentraxin 2 (NPTX2). In addition, we identified several novel candidates whose association with AD has not been previously described. Of the novel molecules, we validated chromogranin A (CHGA), inner membrane mitochondrial protein (IMMT) and RAS like proto-oncogene A (RALA) in an additional set of 20 independent brain samples using targeted parallel reaction monitoring mass spectrometry assays. The differentially expressed proteins discovered in our study, once validated in larger cohorts, should help discern the pathogenesis of AD.
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Affiliation(s)
- Gajanan Sathe
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore 560029, India
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
| | - Marilyn Albert
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Jacqueline Darrow
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Atsushi Saito
- Department of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Juan Troncoso
- Department of Pathology and Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
- Current address: Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Abhay Moghekar
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205 USA
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11
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Bell SM, Burgess T, Lee J, Blackburn DJ, Allen SP, Mortiboys H. Peripheral Glycolysis in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:E8924. [PMID: 33255513 PMCID: PMC7727792 DOI: 10.3390/ijms21238924] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases are a group of nervous system conditions characterised pathologically by the abnormal deposition of protein throughout the brain and spinal cord. One common pathophysiological change seen in all neurodegenerative disease is a change to the metabolic function of nervous system and peripheral cells. Glycolysis is the conversion of glucose to pyruvate or lactate which results in the generation of ATP and has been shown to be abnormal in peripheral cells in Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral Sclerosis. Changes to the glycolytic pathway are seen early in neurodegenerative disease and highlight how in multiple neurodegenerative conditions pathology is not always confined to the nervous system. In this paper, we review the abnormalities described in glycolysis in the three most common neurodegenerative diseases. We show that in all three diseases glycolytic changes are seen in fibroblasts, and red blood cells, and that liver, kidney, muscle and white blood cells have abnormal glycolysis in certain diseases. We highlight there is potential for peripheral glycolysis to be developed into multiple types of disease biomarker, but large-scale bio sampling and deciphering how glycolysis is inherently altered in neurodegenerative disease in multiple patients' needs to be accomplished first to meet this aim.
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Affiliation(s)
- Simon M. Bell
- Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield S10 2HQ, UK; (T.B.); (J.L.); (D.J.B.); (S.P.A.); (H.M.)
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12
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Prpar Mihevc S, Zakošek Pipan M, Štrbenc M, Rogelj B, Majdič G. Nitrosative Stress in the Frontal Cortex From Dogs With Canine Cognitive Dysfunction. Front Vet Sci 2020; 7:573155. [PMID: 33330694 PMCID: PMC7717931 DOI: 10.3389/fvets.2020.573155] [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: 06/16/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022] Open
Abstract
Canine cognitive dysfunction (CCD) is an age-related disorder similar to human Alzheimer's disease (AD) that occurs in elderly dogs. Nitrosative stress has been implicated as one of the causes leading to neurodegenerative diseases, particularly AD. Its involvement in the development of CCD has not been studied so far. In the present study, immunohistochemical staining detected all three isoforms of nitric oxide synthases (nNOS, eNOS, and iNOS) and 3-nitrotyrosine (3-NT) in brains from CCD-affected dogs and non-demented control dogs in all layers of the canine frontal cortex. In CCD-affected and non-demented brains, nNOS was highly expressed in pyramidal-like neurons in the upper cortical layers. nNOS has also been observed in astrocytes in the CCD frontal cortex. The nNOS immunohistochemical staining was statistically significantly elevated in dogs with CCD in comparison to non-demented dogs. Blood vessel wall cells were positive for eNOS, which was also expressed in astrocytes and neurons. Intense 3-NT immunoreactivity was observed in the upper cortical layers, where amyloid-beta deposits spread in the last stage of CCD. Brain cells in the same area were highly immunoreactive for iNOS. This infers that neuroinflammation and nitrosative stress might exacerbate the neurodegenerative process in CCD-affected brains, ultimately leading to cognitive impairment.
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Affiliation(s)
- Sonja Prpar Mihevc
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zakošek Pipan
- Veterinary Faculty, Clinic for Reproduction and Large Animals, University of Ljubljana, Ljubljana, Slovenia
| | - Malan Štrbenc
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Biomedical Research Institute (BRIS), Ljubljana, Slovenia.,Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Majdič
- Veterinary Faculty, Institute of Preclinical Sciences, University of Ljubljana, Ljubljana, Slovenia
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13
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Hashimoto M, Yamazaki A, Ohno A, Kimura T, Winblad B, Tjernberg LO. A Fragment of S38AA is a Novel Plasma Biomarker of Alzheimer's Disease. J Alzheimers Dis 2020; 71:1163-1174. [PMID: 31524172 DOI: 10.3233/jad-190700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease without a cure. The pathological process starts decades before clinical onset, and thus clinical trials of drugs aimed at treating AD should start at a presymptomatic stage. Therefore, it is critical to diagnose AD at an early stage. Tau, phosphorylated tau, and amyloid-β peptide (Aβ) in cerebrospinal fluid (CSF), and positron emission tomography (PET) imaging of Aβ or tau accumulation are supportive biomarkers for AD diagnosis, but there is no reliable presymptomatic diagnostic marker. Since CSF sampling is invasive, and PET imaging is expensive and available only at specialized centers, a reliable blood biomarker has long been sought for. Here we describe a novel extramembrane fragment from solute carrier family 38 member 10 (SLC38A10, S38AA) that we found to be decreased in pyramidal neurons in AD cases by proteomics and immunohistochemical analysis. We detected a S38AA fragment in CSF and found the levels to correlate with severity of AD and APOE genotype. Importantly, the plasma levels of the fragment also showed a significant correlation with Mini-Mental State Examination scores in AD. Moreover, plasma from other neurodegenerative disease was analyzed and the fragment was found to be increased specifically in AD. Interestingly, the fragment is detected in mouse, rat, and monkey, and increases in amyloid precursor protein transgenic mice as the AD-like pathology progresses. We propose that the S38AA fragment in plasma could be a novel quantitative diagnostic marker for AD and potentially a marker of disease progression in AD.
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Affiliation(s)
- Masakazu Hashimoto
- Drug Research Division, Sumitomo Dainippon Pharma Co., Ltd., Konohana-ku, Osaka, Japan
| | - Akira Yamazaki
- Drug Research Division, Sumitomo Dainippon Pharma Co., Ltd., Konohana-ku, Osaka, Japan
| | - Atsushi Ohno
- Drug Research Division, Sumitomo Dainippon Pharma Co., Ltd., Konohana-ku, Osaka, Japan
| | - Toru Kimura
- Drug Research Division, Sumitomo Dainippon Pharma Co., Ltd., Konohana-ku, Osaka, Japan
| | - Bengt Winblad
- Department of Neurobiology, Division for Neurogeriatrics, Care Sciences and Society (NVS), Karolinska Institutet, BioClinicum J9:20, Solna, Sweden.,Karolinska University Hospital, Theme Aging, Huddinge/Solna, Sweden
| | - Lars O Tjernberg
- Department of Neurobiology, Division for Neurogeriatrics, Care Sciences and Society (NVS), Karolinska Institutet, BioClinicum J9:20, Solna, Sweden
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14
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Gaunitz S, Tjernberg LO, Schedin-Weiss S. The N-glycan profile in cortex and hippocampus is altered in Alzheimer disease. J Neurochem 2020; 159:292-304. [PMID: 32986846 PMCID: PMC8596851 DOI: 10.1111/jnc.15202] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/20/2020] [Accepted: 09/08/2020] [Indexed: 12/30/2022]
Abstract
Protein glycosylation is crucial for the central nervous system and brain functions, including processes that are defective in Alzheimer disease (AD) such as neurogenesis, synaptic function, and memory formation. Still, the roles of glycans in the development of AD are relatively unexplored. Glycomics studies of cerebrospinal fluid (CSF) have previously shown altered glycosylation pattern in patients with different stages of cognitive impairment, including AD, compared to healthy controls. As a consequence, we hypothesized that the glycan profile is altered in the brain of patients with AD and analyzed the asparagine‐linked (N‐linked) glycan profile in hippocampus and cortex in AD and control brain. Glycans were enzymatically liberated from brain glycoproteins and analyzed by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). Eleven glycans showed significantly different levels in hippocampus compared to cortex in both control and AD brain. Two glycans in cortex and four in hippocampus showed different levels in AD compared to control brain. All glycans that differed between controls and AD brain had similar structures with one sialic acid, at least one fucose and a confirmed or potential bisecting N‐acetylglucosamine (GlcNAc). The glycans that were altered in AD brain differed from those that were altered in AD CSF. One glycan found to be present in significantly lower levels in both hippocampus and cortex in AD compared to control contained a structurally and functionally interesting epitope that we assign as a terminal galactose decorated with fucose and sialic acid. Altogether, these studies suggest that protein glycosylation is an important component in the development of AD and warrants further studies.
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Affiliation(s)
- Stefan Gaunitz
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Solna, Sweden
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Solna, Sweden
| | - Sophia Schedin-Weiss
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Solna, Sweden
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15
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Haytural H, Mermelekas G, Emre C, Nigam SM, Carroll SL, Winblad B, Bogdanovic N, Barthet G, Granholm AC, Orre LM, Tjernberg LO, Frykman S. The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease. Mol Cell Proteomics 2020; 19:128-141. [PMID: 31699905 PMCID: PMC6944231 DOI: 10.1074/mcp.ra119.001737] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/05/2019] [Indexed: 01/13/2023] Open
Abstract
Synaptic dysfunction is an early pathogenic event in Alzheimer disease (AD) that contributes to network disturbances and cognitive decline. Some synapses are more vulnerable than others, including the synapses of the perforant path, which provides the main excitatory input to the hippocampus. To elucidate the molecular mechanisms underlying the dysfunction of these synapses, we performed an explorative proteomic study of the dentate terminal zone of the perforant path. The outer two-thirds of the molecular layer of the dentate gyrus, where the perforant path synapses are located, was microdissected from five subjects with AD and five controls. The microdissected tissues were dissolved and digested by trypsin. Peptides from each sample were labeled with different isobaric tags, pooled together and pre-fractionated into 72 fractions by high-resolution isoelectric focusing. Each fraction was then analyzed by liquid chromatography-mass spectrometry. We quantified the relative expression levels of 7322 proteins, whereof 724 showed significantly altered levels in AD. Our comprehensive data analysis using enrichment and pathway analyses strongly indicated that presynaptic signaling, such as exocytosis and synaptic vesicle cycle processes, is severely disturbed in this area in AD, whereas postsynaptic proteins remained unchanged. Among the significantly altered proteins, we selected three of the most downregulated synaptic proteins; complexin-1, complexin-2 and synaptogyrin-1, for further validation, using a new cohort consisting of six AD and eight control cases. Semi-quantitative analysis of immunohistochemical staining confirmed decreased levels of complexin-1, complexin-2 and synaptogyrin-1 in the outer two-thirds of the molecular layer of the dentate gyrus in AD. Our in-depth proteomic analysis provides extensive knowledge on the potential molecular mechanism underlying synaptic dysfunction related to AD and supports that presynaptic alterations are more important than postsynaptic changes in early stages of the disease. The specific synaptic proteins identified could potentially be targeted to halt synaptic dysfunction in AD.
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Affiliation(s)
- Hazal Haytural
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden.
| | - Georgios Mermelekas
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ceren Emre
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | | | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Bengt Winblad
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden; Karolinska University Hospital, Theme Aging, Stockholm, Sweden
| | - Nenad Bogdanovic
- Karolinska University Hospital, Theme Aging, Stockholm, Sweden; Division of Clinical geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Gaël Barthet
- Interdisciplinary Institute for Neuroscience, CNRS UMR, Bordeaux, France; University of Bordeaux, Bordeaux, France
| | - Ann-Charlotte Granholm
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden; Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado
| | - Lukas M Orre
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Susanne Frykman
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
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16
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Tau binding protein CAPON induces tau aggregation and neurodegeneration. Nat Commun 2019; 10:2394. [PMID: 31160584 PMCID: PMC6546774 DOI: 10.1038/s41467-019-10278-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
To understand the molecular processes that link Aβ amyloidosis, tauopathy and neurodegeneration, we screened for tau-interacting proteins by immunoprecipitation/LC-MS. We identified the carboxy-terminal PDZ ligand of nNOS (CAPON) as a novel tau-binding protein. CAPON is an adaptor protein of neuronal nitric oxide synthase (nNOS), and activated by the N-methyl-D-aspartate receptor. We observed accumulation of CAPON in the hippocampal pyramidal cell layer in the AppNL-G-F -knock-in (KI) brain. To investigate the effect of CAPON accumulation on Alzheimer’s disease (AD) pathogenesis, CAPON was overexpressed in the brain of AppNL-G-F mice crossbred with MAPT (human tau)-KI mice. This produced significant hippocampal atrophy and caspase3-dependent neuronal cell death in the CAPON-expressing hippocampus, suggesting that CAPON accumulation increases neurodegeneration. CAPON expression also induced significantly higher levels of phosphorylated, oligomerized and insoluble tau. In contrast, CAPON deficiency ameliorated the AD-related pathological phenotypes in tauopathy model. These findings suggest that CAPON could be a druggable AD target. To understand the molecular processes that link Aβ amyloidosis, tauopathy and neurodegeneration, the authors screened for tau-interacting proteins. They demonstrated that a novel tau binding protein CAPON accelerates tau pathology and neuronal cell death in an Alzheimer’s disease mouse model.
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17
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MacDonald ML, Favo D, Garver M, Sun Z, Arion D, Ding Y, Yates N, Sweet RA, Lewis DA. Laser capture microdissection-targeted mass spectrometry: a method for multiplexed protein quantification within individual layers of the cerebral cortex. Neuropsychopharmacology 2019; 44:743-748. [PMID: 30390066 PMCID: PMC6372704 DOI: 10.1038/s41386-018-0260-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/17/2018] [Indexed: 11/09/2022]
Abstract
The mammalian neocortex is organized into layers distinguished by the size, packing density, and connectivity of their constituent neurons. Many neuropsychiatric illnesses are complex trait disorders with etiologic factors converging on neuronal protein networks. Cortical pathology of neuropsychiatric diseases, such as schizophrenia, is often restricted to, or more pronounced in, certain cortical layers, suggesting that genetic vulnerabilities manifest with laminar specificity. Thus, the ability to investigate cortical layer-specific protein levels in human postmortem brain is highly desirable. Here, we developed and validated a laser capture microdissection-mass spectrometry (LCM-MS) approach to quantify over 200 proteins in cortical layers 3 and 5 of two cohorts of human subjects as well as a monkey model of postmortem interval. LCM-MS was readily implementable and reliably identified protein patterns that differed between cortical layers 3 and 5. Our findings suggest that LCM-MS facilitates the precise quantification of proteins within individual cortical layers from human postmortem brain tissue, providing a powerful tool in the study of neuropsychiatric disease.
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Affiliation(s)
- Matthew L MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Daley Favo
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan Garver
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sun
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dominique Arion
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathan Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
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18
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Eriksdotter M, Navarro-Oviedo M, Mitra S, Wahlberg L, Linderoth B, Tjernberg LO, Behbahani H. Cerebrospinal fluid from Alzheimer patients affects cell-mediated nerve growth factor production and cell survival in vitro. Exp Cell Res 2018; 371:175-184. [PMID: 30092220 DOI: 10.1016/j.yexcr.2018.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/06/2018] [Accepted: 08/05/2018] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease (AD) is characterized by early degeneration of cholinergic neurons and decreased levels of nerve growth factor (NGF). Thus, increasing the NGF levels by for instance encapsulated cell bio-delivery (ECB) is a potential treatment strategy. The results from our previous first-in-human studies on ECB of NGF to the basal forebrain cholinergic neurons were promising, but indicated some variability of long-term viability of the encapsulated cells and associated reduced NGF-release. Here we studied the effect of amyloid beta-peptides (Aβ), interleukin 1-beta (IL-1β), and CSF from AD, Lewy body dementia (LBD) or subjective cognitive impairment (SCI) patients on the NGF overproducing cell line NGC-0295. At physiological concentrations, neither Aβ40 nor Aβ42 had any major impact on cell viability or NGF-production. In contrast, IL-1β dose-dependently affected NGF-production over time. Exposure of NGF-producing cells to CSF from AD patients showed significantly reduced NGF-release as compared to CSF from LBD or SCI patients. By mass spectrometry we found 3 proteins involved in inflammatory pathways to have an altered expression in AD CSF compared to LBD and SCI. Cell survival and NGF-release were not affected by Aβ. NGF-release was affected by IL-1β, suggesting that inflammation has a negative effect on ECB cells.
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Affiliation(s)
- Maria Eriksdotter
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Clinical Geriatrics, Stockholm, Sweden; Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska University Hospital, Theme Aging, Stockholm, Sweden
| | - Manuel Navarro-Oviedo
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Clinical Geriatrics, Stockholm, Sweden
| | - Sumonto Mitra
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Clinical Geriatrics, Stockholm, Sweden
| | | | - Bengt Linderoth
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Clinical Neuroscience, Stockholm, Sweden
| | - Lars O Tjernberg
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Stockholm, Sweden
| | - Homira Behbahani
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Stockholm, Sweden.
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19
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Buneeva O, Kopylov A, Kapitsa I, Ivanova E, Zgoda V, Medvedev A. The Effect of Neurotoxin MPTP and Neuroprotector Isatin on the Profile of Ubiquitinated Brain Mitochondrial Proteins. Cells 2018; 7:E91. [PMID: 30065189 PMCID: PMC6115780 DOI: 10.3390/cells7080091] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/30/2022] Open
Abstract
Mitochondria are a crucial target for the actions of neurotoxins, causing symptoms of Parkinson's disease in various experimental animal models, and also neuroprotectors. There is evidence that mitochondrial dysfunction induced by the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) influences functioning of the ubiquitin-proteasomal system (UPS) responsible for selective proteolytic degradation of proteins from various intracellular compartments (including mitochondria) and neuroprotective effects of certain anti-Parkisonian agents (monoamine oxidase inhibitors) may be associated with their effects on the UPS. In this study, we have investigated the effect of the neurotoxin MPTP and neuroprotector isatin, and their combination on the profile of ubiquitinated brain mitochondrial proteins. The development of movement disorders induced by MPTP administration caused dramatic changes in the profile of ubiquitinated proteins associated with mitochondria. Pretreatment with the neuroprotector isatin decreased manifestations of MPTP-induced Parkinsonism, and had a significant impact on the profile of ubiquitinated mitochondrial proteins (including oxidative modified proteins). Administration of isatin alone to intact mice also influenced the profile of ubiquitinated mitochondrial proteins, and increased the proportion of oxidized proteins carrying the ubiquitination signature. These alterations in the ubiquitination of mitochondrial proteins observed within 2 h after administration of MPTP and isatin obviously reflect immediate short-term biological responses to these treatments.
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Affiliation(s)
- Olga Buneeva
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
| | - Arthur Kopylov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
| | - Inga Kapitsa
- Zakusov Institute of Pharmacology, 8 Baltiskaya Street, Moscow 124315, Russia.
| | - Elena Ivanova
- Zakusov Institute of Pharmacology, 8 Baltiskaya Street, Moscow 124315, Russia.
| | - Victor Zgoda
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
| | - Alexei Medvedev
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia.
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20
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Yu Y, Jans DC, Winblad B, Tjernberg LO, Schedin-Weiss S. Neuronal Aβ42 is enriched in small vesicles at the presynaptic side of synapses. Life Sci Alliance 2018; 1:e201800028. [PMID: 30456353 PMCID: PMC6238618 DOI: 10.26508/lsa.201800028] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
Super-resolution microscopy reveals that Aβ42 is mainly present at the presynaptic side of the synapse. The amyloid β-peptide (Aβ) is a physiological ubiquitously expressed peptide suggested to be involved in synaptic function, long-term potentiation, and memory function. The 42 amino acid-long variant (Aβ42) forms neurotoxic oligomers and amyloid plaques and plays a key role in the loss of synapses and other pathogenic events of Alzheimer disease. Still, the exact localization of Aβ42 in neurons and at synapses has not been reported. Here, we used super-resolution microscopy and show that Aβ42 was present in small vesicles in presynaptic compartments, but not in postsynaptic compartments, in the neurites of hippocampal neurons. Some of these vesicles appeared to lack synaptophysin, indicating that they differ from the synaptic vesicles responsible for neurotransmitter release. The Aβ42-containing vesicles existed in presynapses connected to stubby spines and mushroom spines, and were also present in immature presynapses. These vesicles were scarce in other parts of the neurites, where Aβ42 was instead present in large, around 200–600 nm, vesicular structures. Three-dimensional super-resolution microscopy confirmed that Aβ42 was present in the presynapse and absent in the postsynapse.
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Affiliation(s)
- Yang Yu
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Huddinge, Sweden
| | - Daniel C Jans
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Bengt Winblad
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Huddinge, Sweden
| | - Lars O Tjernberg
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Huddinge, Sweden
| | - Sophia Schedin-Weiss
- Center for Alzheimer Research, Division of Neurogeriatrics, Department of Neurobiology, Care Sciences, and Society, Karolinska Institutet, Huddinge, Sweden
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21
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Nilsson P, Loganathan K, Sekiguchi M, Winblad B, Iwata N, Saido TC, Tjernberg LO. Loss of neprilysin alters protein expression in the brain of Alzheimer's disease model mice. Proteomics 2015; 15:3349-55. [PMID: 26194619 DOI: 10.1002/pmic.201400211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 04/28/2015] [Accepted: 07/15/2015] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease displaying extracellular plaques formed by the neurotoxic amyloid β-peptide (Aβ), and intracellular neurofibrillary tangles consisting of protein tau. However, how these pathologies relate to the massive neuronal death that occurs in AD brains remain elusive. Neprilysin is the major Aβ-degrading enzyme and a lack thereof increases Aβ levels in the brain twofold. To identify altered protein expression levels induced by increased Aβ levels, we performed a proteomic analysis of the brain of the AD mouse model APPsw and compared it to that of APPsw mice lacking neprilysin. To this end we established an LC-MS/MS method to analyze brain homogenate, using an (18) O-labeled internal standard to accurately quantify the protein levels. To distinguish between alterations in protein levels caused by increased Aβ levels and those induced by neprilysin deficiency independently of Aβ, the brain proteome of neprilysin deficient APPsw mice was also compared to that of neprilysin deficient mice. By this approach we identified approximately 600 proteins and the levels of 300 of these were quantified. Pathway analysis showed that many of the proteins with altered expression were involved in neurological disorders, and that tau, presenilin and APP were key regulators in the identified networks. The data have been deposited to the ProteomeXchange Consortium with identifiers PXD000968 and PXD001786 (http://proteomecentral.proteomexchange.org/dataset/PXD000968 and (http://proteomecentral.proteomexchange.org/dataset/PXD001786). Interestingly, the levels of several proteins, including some not previously reported to be linked to AD, were associated with increased Aβ levels.
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Affiliation(s)
- Per Nilsson
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Saitama, Japan.,Karolinska Institutet, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Huddinge, Sweden
| | - Krishnapriya Loganathan
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Saitama, Japan.,Karolinska Institutet, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Huddinge, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Misaki Sekiguchi
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Saitama, Japan
| | - Bengt Winblad
- Karolinska Institutet, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Huddinge, Sweden
| | - Nobuhisa Iwata
- Dept of Biotechnology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Saitama, Japan
| | - Lars O Tjernberg
- Karolinska Institutet, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Huddinge, Sweden
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22
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Enrichment of single neurons and defined brain regions from human brain tissue samples for subsequent proteome analysis. J Neural Transm (Vienna) 2015; 122:993-1005. [PMID: 26123835 DOI: 10.1007/s00702-015-1414-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/11/2015] [Indexed: 12/11/2022]
Abstract
Brain function in normal aging and neurological diseases has long been a subject of interest. With current technology, it is possible to go beyond descriptive analyses to characterize brain cell populations at the molecular level. However, the brain comprises over 100 billion highly specialized cells, and it is a challenge to discriminate different cell groups for analyses. Isolating intact neurons is not feasible with traditional methods, such as tissue homogenization techniques. The advent of laser microdissection techniques promises to overcome previous limitations in the isolation of specific cells. Here, we provide a detailed protocol for isolating and analyzing neurons from postmortem human brain tissue samples. We describe a workflow for successfully freezing, sectioning and staining tissue for laser microdissection. This protocol was validated by mass spectrometric analysis. Isolated neurons can also be employed for western blotting or PCR. This protocol will enable further examinations of brain cell-specific molecular pathways and aid in elucidating distinct brain functions.
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23
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The workflow from post-mortem human brain sampling to cell microdissection: a Brain Net Europe study. J Neural Transm (Vienna) 2015; 122:975-91. [DOI: 10.1007/s00702-015-1378-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 02/04/2015] [Indexed: 11/25/2022]
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24
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Plum S, Steinbach S, Abel L, Marcus K, Helling S, May C. Proteomics in neurodegenerative diseases: Methods for obtaining a closer look at the neuronal proteome. Proteomics Clin Appl 2014; 9:848-71. [DOI: 10.1002/prca.201400030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/25/2014] [Accepted: 09/03/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Sarah Plum
- Medizinisches Proteom-Center; Funktionelle Proteomik; Ruhr-Universität Bochum; Bochum Germany
| | - Simone Steinbach
- Medizinisches Proteom-Center; Medical Proteomics/Bioanalytics; Ruhr-Universität Bochum; Bochum Germany
| | - Laura Abel
- Medizinisches Proteom-Center; Medical Proteomics/Bioanalytics; Ruhr-Universität Bochum; Bochum Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center; Funktionelle Proteomik; Ruhr-Universität Bochum; Bochum Germany
| | - Stefan Helling
- Medizinisches Proteom-Center; Funktionelle Proteomik; Ruhr-Universität Bochum; Bochum Germany
| | - Caroline May
- Medizinisches Proteom-Center; Medical Proteomics/Bioanalytics; Ruhr-Universität Bochum; Bochum Germany
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25
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Ding B, Xi Y, Gao M, Li Z, Xu C, Fan S, He W. Gene expression profiles of entorhinal cortex in Alzheimer's disease. Am J Alzheimers Dis Other Demen 2014; 29:526-32. [PMID: 24558171 PMCID: PMC10852653 DOI: 10.1177/1533317514523487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The incidence of Alzheimer's disease (AD) has been increasing in the recent years but the underlying mechanisms remain uncertain. This study aimed to analyze the differentially expressed genes (DEGs) in entorhinal cortex with AD and identify featured genes related to AD. Gene expression profile GSE5281 was downloaded from Gene Expression Omnibus, including 10 AD and 13 control samples. Differentially expressed genes were identified by Student t test including 119 upregulated and 591 downregulated DEGs. Then, we obtained 14 enrichment Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways among which 11 pathways were significantly enriched (adjusted P value < .05). The KEGG pathway network which was constructed by 14 KEGG pathways showed that 6-phosphofructokinase, muscle type, phosphoglucomutase 1, aldolase A, and adolase C had high degree. Glycometabolism pathways network which was constructed by 4 glycometabolism pathways showed that adenosine triphosphate (ATP) synthase, H+transporting, mitochondrial F1 complex ATP5B, ATP5C1, ATP5D, and ATP5G1 had high degree related to ATP metabolism. These findings suggested that these genes with high degree may be the underlying potential therapeutic targets for AD.
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Affiliation(s)
- Bingqian Ding
- Department of Neurosurgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Yan Xi
- Department of Pathology, Medical College of Henan University, Kaifeng, China
| | - Ming Gao
- Department of Neurosurgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Zhenjiang Li
- Department of Neurosurgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Chenyang Xu
- Department of Neurosurgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Shaokang Fan
- Department of Neurosurgery, Huaihe Hospital of Henan University, Kaifeng, China
| | - Weiya He
- Department of Neurosurgery, Huaihe Hospital of Henan University, Kaifeng, China
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26
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Demartini DR, Schilling LP, da Costa JC, Carlini CR. Alzheimer's and Parkinson's diseases: an environmental proteomic point of view. J Proteomics 2014; 104:24-36. [PMID: 24751585 DOI: 10.1016/j.jprot.2014.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/07/2014] [Accepted: 04/10/2014] [Indexed: 11/25/2022]
Abstract
Alzheimer's and Parkinson's diseases are severe neurodegenerative conditions triggered by complex biochemical routes. Many groups are currently pursuing the search for valuable biomarkers to either perform early diagnostic or to follow the disease's progress. Several studies have reported relevant findings regarding environmental issues and the progression of such diseases. Here the etiology and mechanisms of these diseases are briefly reviewed. Approaches that might reveal candidate biomarkers and environmental stressors associated to the diseases were analyzed under a proteomic perspective. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Diogo Ribeiro Demartini
- Center of Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, 91501-970 Porto Alegre, RS, Brazil.
| | - Lucas Porcello Schilling
- Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil.
| | - Célia Regina Carlini
- Center of Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, 91501-970 Porto Alegre, RS, Brazil; Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil
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27
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Schedin-Weiss S, Winblad B, Tjernberg LO. The role of protein glycosylation in Alzheimer disease. FEBS J 2013; 281:46-62. [PMID: 24279329 DOI: 10.1111/febs.12590] [Citation(s) in RCA: 225] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 12/18/2022]
Abstract
Glycosylation is one of the most common, and the most complex, forms of post-translational modification of proteins. This review serves to highlight the role of protein glycosylation in Alzheimer disease (AD), a topic that has not been thoroughly investigated, although glycosylation defects have been observed in AD patients. The major pathological hallmarks in AD are neurofibrillary tangles and amyloid plaques. Neurofibrillary tangles are composed of phosphorylated tau, and the plaques are composed of amyloid β-peptide (Aβ), which is generated from amyloid precursor protein (APP). Defects in glycosylation of APP, tau and other proteins have been reported in AD. Another interesting observation is that the two proteases required for the generation of amyloid β-peptide (Aβ), i.e. γ-secretase and β-secretase, also have roles in protein glycosylation. For instance, γ-secretase and β-secretase affect the extent of complex N-glycosylation and sialylation of APP, respectively. These processes may be important in AD pathogenesis, as proper intracellular sorting, processing and export of APP are affected by how it is glycosylated. Furthermore, lack of one of the key components of γ-secretase, presenilin, leads to defective glycosylation of many additional proteins that are related to AD pathogenesis and/or neuronal function, including nicastrin, reelin, butyrylcholinesterase, cholinesterase, neural cell adhesion molecule, v-ATPase, and tyrosine-related kinase B. Improved understanding of the effects of AD on protein glycosylation, and vice versa, may therefore be important for improving the diagnosis and treatment of AD patients.
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Affiliation(s)
- Sophia Schedin-Weiss
- Karolinska Institutet Alzheimer Disease Research Center (KI-ADRC), Novum, Stockholm, Sweden
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28
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Föcking M, Chen WQ, Dicker P, Dunn MJ, Lubec G, Cotter DR. Proteomic analysis of human hippocampus shows differential protein expression in the different hippocampal subfields. Proteomics 2012; 12:2477-81. [DOI: 10.1002/pmic.201200031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Melanie Föcking
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Wei-Qiang Chen
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Patrick Dicker
- Department of Epidemiology; Royal College of Surgeons in Ireland; Dublin; Ireland
| | - Michael J. Dunn
- Proteome Research Centre; UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences; Dublin; Ireland
| | - Gert Lubec
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - David R. Cotter
- Department of Psychiatry; Royal College of Surgeons in Ireland; Dublin; Ireland
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29
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Cuello AC, Allard S, Ferretti MT. Evidence for the accumulation of Abeta immunoreactive material in the human brain and in transgenic animal models. Life Sci 2012; 91:1141-7. [PMID: 22705309 DOI: 10.1016/j.lfs.2012.05.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 05/11/2012] [Accepted: 05/24/2012] [Indexed: 12/19/2022]
Abstract
In this review we highlight the evidence for an intracellular origin of Abeta (Aβ) amyloid peptides as well as the observations for a pathological accumulation of these peptides in Alzheimer's disease and Down syndrome, as well as in transgenic animal models. We deliberate on the controversy as to whether the intracellular Aβ immunoreactive material is simply an accumulation of unprocessed full length amyloid precursor protein (APP) or a mix of processed APP fragments including Aβ. Finally, we discuss the possible pathological significance of these intracellular APP fragments and the expected future research directions regarding this thought-provoking problem.
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Affiliation(s)
- A Claudio Cuello
- Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Room 1210, Montreal, Quebec, Canada.
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