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Talluri B, Addya S, Terashvili M, Medda BK, Banerjee A, Shaker R, Sengupta JN, Banerjee B. Adult zymosan re-exposure exacerbates the molecular alterations in the brainstem rostral ventromedial medulla of rats with early life zymosan-induced cystitis. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2024; 16:100160. [PMID: 39252992 PMCID: PMC11381896 DOI: 10.1016/j.ynpai.2024.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 09/11/2024]
Abstract
Recent evidence suggests that the descending modulatory pathways from the brainstem rostral ventromedial medulla (RVM) are important for bladder inflammatory pain. This study aimed to identify the long-term molecular changes in RVM neurons due to early life cystitis during neuronal development and the effect of reexposure later in adulthood. RVM tissues from two treatment protocols were used: (1) neonatal zymosan exposures with acute adult rechallenge (RC) and (2) only neonatal zymosan exposures (NRC). RNAseq analysis showed upregulation of several genes associated with synaptic plasticity (Grin1, Grip2, Notch1, Arc, and Scn2b) in the cystitis groups compared to controls in both protocols. The RC protocol exhibited a stronger treatment effect with significantly higher fold differences between the groups compared to the NRC protocol (p < 0.001, fold differences RC vs NRC). In microarrays, miR-34a-5p showed cystitis-induced downregulation in both protocols. Bioinformatics analysis identified multiple 3'UTRs complementary binding sites for miR-34a-5p on Grin2b, Notch1, Grip2, Scn2b, and Arc genes. The enhanced response in the RC protocol indicates a possible priming effect of early life cystitis on rechallenge in adulthood. These long-term molecular alterations may play a critical role in the development of chronic bladder pain conditions as seen in patients with Interstitial Cystitis/Bladder pain syndrome.
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Affiliation(s)
- Bhavana Talluri
- Gastroenterology & Hepatology Division, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sankar Addya
- Sydney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maia Terashvili
- Gastroenterology & Hepatology Division, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bidyut K Medda
- Gastroenterology & Hepatology Division, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anjishnu Banerjee
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Reza Shaker
- Gastroenterology & Hepatology Division, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jyoti N Sengupta
- Gastroenterology & Hepatology Division, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Banani Banerjee
- Gastroenterology & Hepatology Division, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
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Smukowski SN, Danyko C, Somberg J, Kaufman EJ, Course MM, Postupna N, Barker-Haliski M, Keene CD, Valdmanis PN. mRNA and circRNA mislocalization to synapses are key features of Alzheimer's disease. PLoS Genet 2024; 20:e1011359. [PMID: 39074152 PMCID: PMC11309398 DOI: 10.1371/journal.pgen.1011359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/08/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Proper transport of RNAs to synapses is essential for localized translation of proteins in response to synaptic signals and synaptic plasticity. Alzheimer's disease (AD) is a neurodegenerative disease characterized by accumulation of amyloid aggregates and hyperphosphorylated tau neurofibrillary tangles followed by widespread synapse loss. To understand whether RNA synaptic localization is impacted in AD, we performed RNA sequencing on synaptosomes and brain homogenates from AD patients and cognitively healthy controls. This resulted in the discovery of hundreds of mislocalized mRNAs in AD among frontal and temporal brain regions. Similar observations were found in an APPswe/PSEN1dE9 mouse model. Furthermore, major differences were observed among circular RNAs (circRNAs) localized to synapses in AD including two overlapping isoforms of circGSK3β, one upregulated, and one downregulated. Expression of these distinct isoforms affected tau phosphorylation in neuronal cells substantiating the importance of circRNAs in the brain and pointing to a new class of therapeutic targets.
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Affiliation(s)
- Samuel N. Smukowski
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Cassidy Danyko
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Fred Hutch Cancer Center, Basic Sciences Division, University of Washington, Seattle, Washington, United States of America
| | - Jenna Somberg
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Eli J. Kaufman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Meredith M. Course
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Nadia Postupna
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Melissa Barker-Haliski
- Department of Pharmacy, University of Washington School of Pharmacy, Seattle, Washington, United States of America
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Paul N. Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
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Ibrahim MJ, Baiju V, Sen S, Chandran PP, Ashraf GM, Haque S, Ahmad F. Utilities of Isolated Nerve Terminals in Ex Vivo Analyses of Protein Translation in (Patho)physiological Brain States: Focus on Alzheimer's Disease. Mol Neurobiol 2024; 61:91-103. [PMID: 37582987 DOI: 10.1007/s12035-023-03562-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 08/17/2023]
Abstract
Synapses are the cellular substrates of higher-order brain functions, and their dysfunction is an early and primary pathogenic mechanism across several neurological disorders. In particular, Alzheimer's disease (AD) is categorized by prodromal structural and functional synaptic deficits, prior to the advent of classical behavioral and pathological features. Recent research has shown that the development, maintenance, and plasticity of synapses depend on localized protein translation. Synaptosomes and synaptoneurosomes are biochemically isolated synaptic terminal preparations which have long been used to examine a variety of synaptic processes ex vivo in both healthy and pathological conditions. These ex vivo preparations preserve the mRNA species and the protein translational machinery. Hence, they are excellent in organello tools for the study of alterations in mRNA levels and protein translation in neuropathologies. Evaluation of synapse-specific basal and activity-driven de novo protein translation activity can be conveniently performed in synaptosomal/synaptoneurosomal preparations from both rodent and human brain tissue samples. This review gives a quick overview of the methods for isolating synaptosomes and synaptoneurosomes before discussing the studies that have utilized these preparations to study localized synapse-specific protein translation in (patho)physiological situations, with an emphasis on AD. While the review is not an exhaustive accumulation of all the studies evaluating synaptic protein translation using the synaptosomal model, the aim is to assemble the most relevant studies that have done so. The hope is to provide a suitable research platform to aid neuroscientists to utilize the synaptosomal/synaptoneurosomal models to evaluate the molecular mechanisms of synaptic dysfunction within the specific confines of mRNA localization and protein translation research.
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Affiliation(s)
- Mohammad Jasim Ibrahim
- Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India, 632014
| | - Viswanath Baiju
- Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India, 632014
| | - Shivam Sen
- Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India, 632014
| | - Pranav Prathapa Chandran
- Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India, 632014
| | - Ghulam Md Ashraf
- University of Sharjah, College of Health Sciences, and Research Institute for Medical and Health Sciences, Department of Medical Laboratory Sciences, University City, 27272, Sharjah, United Arab Emirates.
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, 45142, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Faraz Ahmad
- Department of Biotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India, 632014.
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Abghari M, Vu JTCM, Eckberg N, Aldana BI, Kohlmeier KA. Decanoic Acid Rescues Differences in AMPA-Mediated Calcium Rises in Hippocampal CA1 Astrocytes and Neurons in the 5xFAD Mouse Model of Alzheimer's Disease. Biomolecules 2023; 13:1461. [PMID: 37892143 PMCID: PMC10604953 DOI: 10.3390/biom13101461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
Alzheimer's disease (AD), a devastating neurodegenerative disease characterized by cognitive dysfunctions, is associated with high levels of amyloid beta 42 (Aβ42), which is believed to play a role in cellular damage and signaling changes in AD. Decanoic acid has been shown to be therapeutic in AD. Glutamatergic signaling within neurons and astrocytes of the CA1 region of the hippocampus is critical in cognitive processes, and previous work has indicated deficiencies in this signaling in a mouse model of AD. In this study, we investigated glutamate-mediated signaling by evaluating AMPA-mediated calcium rises in female and male CA1 neurons and astrocytes in a mouse model of AD and examined the potential of decanoic acid to normalize this signaling. In brain slices from 5xFAD mice in which there are five mutations leading to increasing levels of Aβ42, AMPA-mediated calcium transients in CA1 neurons and astrocytes were significantly lower than that seen in wildtype controls in both females and males. Interestingly, incubation of 5xFAD slices in decanoic acid restored AMPA-mediated calcium levels in neurons and astrocytes in both females and males to levels indistinguishable from those seen in wildtype, whereas similar exposure to decanoic acid did not result in changes in AMPA-mediated transients in neurons or astrocytes in either sex in the wildtype. Our data indicate that one mechanism by which decanoic acid could improve cognitive functioning is through normalizing AMPA-mediated signaling in CA1 hippocampal cells.
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Niu M, Zong C. Reply to: Methodological concerns and lack of evidence for single-synapse RNA-seq. Nat Biotechnol 2023; 41:1225-1228. [PMID: 37500916 DOI: 10.1038/s41587-023-01878-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Affiliation(s)
- Muchun Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute, Baylor College of Medicine, Houston, TX, USA.
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Gomes Moreira D, Jan A. A beginner's guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration. Sci Data 2023; 10:432. [PMID: 37414779 PMCID: PMC10325954 DOI: 10.1038/s41597-023-02338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this "beginner's guide" will benefit the research community in NDDs, and would serve as a useful educational tool.
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Affiliation(s)
- Diana Gomes Moreira
- Department of Clinical Medicine, Palle Juul-Jensens Boulevard 165, DK-8200, Aarhus N, Denmark
| | - Asad Jan
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK-8000, Aarhus C, Denmark.
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Yang S, Yi L, Xia X, Chen X, Hou X, Zhang L, Yang F, Liao J, Han Z, Fu Y. Transcriptome comparative analysis of amygdala-hippocampus in depression: A rat model induced by chronic unpredictable mild stress (CUMS). J Affect Disord 2023; 334:258-270. [PMID: 37105469 DOI: 10.1016/j.jad.2023.04.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 04/11/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Depression is a common and complex mental disease, and its pathogenesis involves several brain regions. Abnormalities in the amygdala-hippocampal neural circuits have been shown to be involved in depression. However, the underlying molecular mechanisms remain unclear. METHODS A rat model was used to determine the transcriptome changes in the amygdala-hippocampal neural network under chronic unpredictable mild stress (CUMS). Depression-related modules in this neural network were identified using weighted gene co-expression network analysis (WGCNA). Difference and enrichment analyses were used to determine differential gene expression in the two brain regions. RESULTS The modules in the amygdala and hippocampus associated with depression-like behavior contained 363 and 225 genes, respectively. Forty-two differentially expressed genes were identified in the amygdala candidate module and 37 in the hippocampus. Enrichment analysis showed that candidate genes in the amygdala were associated with neuronal myelination and candidate genes in the hippocampus were associated with synaptic transmission. Finally, based on module hub gene statistics, differential gene expression, and protein-protein interaction networks, 11 central genes were found in the amygdala candidate module, and one central gene was found in the hippocampal module. LIMITATIONS Our study was based on a rat CUMS model. Further evidence is needed to prove that our results are applicable to patients with depression. CONCLUSION This study identified critical modules and central genes involved in the amygdala-hippocampal circuit in the context of depression, and may provide further understanding of the pathogenesis of depression and help identify potential targets for antidepressant therapy.
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Affiliation(s)
- Shu Yang
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Yi
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaodi Xia
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaolu Chen
- The First Branch, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiao Hou
- Department of Clinical Medicine, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Longjie Zhang
- Department of Pharmacy, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Fang Yang
- Department of pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Jiaxin Liao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yixiao Fu
- Department of Psychiatry, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Griffiths J, Grant SGN. Synapse pathology in Alzheimer's disease. Semin Cell Dev Biol 2023; 139:13-23. [PMID: 35690535 DOI: 10.1016/j.semcdb.2022.05.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 12/31/2022]
Abstract
Synapse loss and damage are central features of Alzheimer's disease (AD) and contribute to the onset and progression of its behavioural and physiological features. Here we review the literature describing synapse pathology in AD, from what we have learned from microscopy in terms of its impacts on synapse architecture, to the mechanistic role of Aβ, tau and glial cells, mitochondrial dysfunction, and the link with AD risk genes. We consider the emerging view that synapse pathology may operate at a further level, that of synapse diversity, and discuss the prospects for leveraging new synaptome mapping methods to comprehensively understand the molecular properties of vulnerable and resilient synapses. Uncovering AD impacts on brain synapse diversity should inform therapeutic approaches targeted at preserving or replenishing lost and damaged synapses and aid the interpretation of clinical imaging approaches that aim to measure synapse damage.
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Affiliation(s)
- Jessica Griffiths
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK; Dementia Research Institute at Imperial College, Department of Brain Sciences, Imperial College London, London W12 0NN, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK.
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Beck JS, Madaj Z, Cheema CT, Kara B, Bennett DA, Schneider JA, Gordon MN, Ginsberg SD, Mufson EJ, Counts SE. Co-expression network analysis of frontal cortex during the progression of Alzheimer's disease. Cereb Cortex 2022; 32:5108-5120. [PMID: 35076713 PMCID: PMC9667180 DOI: 10.1093/cercor/bhac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/29/2023] Open
Abstract
Mechanisms of Alzheimer's disease (AD) and its putative prodromal stage, amnestic mild cognitive impairment (aMCI), involve the dysregulation of multiple candidate molecular pathways that drive selective cellular vulnerability in cognitive brain regions. However, the spatiotemporal overlap of markers for pathway dysregulation in different brain regions and cell types presents a challenge for pinpointing causal versus epiphenomenal changes characterizing disease progression. To approach this problem, we performed Weighted Gene Co-expression Network Analysis and STRING interactome analysis of gene expression patterns quantified in frontal cortex samples (Brodmann area 10) from subjects who died with a clinical diagnosis of no cognitive impairment, aMCI, or mild/moderate AD. Frontal cortex was chosen due to the relatively protracted involvement of this region in AD, which might reveal pathways associated with disease onset. A co-expressed network correlating with clinical diagnosis was functionally associated with insulin signaling, with insulin (INS) being the most highly connected gene within the network. Co-expressed networks correlating with neuropathological diagnostic criteria (e.g., NIA-Reagan Likelihood of AD) were associated with platelet-endothelium-leucocyte cell adhesion pathways and hypoxia-oxidative stress. Dysregulation of these functional pathways may represent incipient alterations impacting disease progression and the clinical presentation of aMCI and AD.
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Affiliation(s)
- John S Beck
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI 49503, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Calvin T Cheema
- Department of Mathematics and Computer Science, Kalamazoo College, Kalamazoo, MI 49006, USA
| | - Betul Kara
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI 49503, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI 48824, USA
| | - David A Bennett
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
- Rush Alzheimer’s Disease Research Center, Chicago, IL 60612, USA
| | - Julie A Schneider
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
- Rush Alzheimer’s Disease Research Center, Chicago, IL 60612, USA
| | - Marcia N Gordon
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI 49503, USA
| | - Stephen D Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Elliott J Mufson
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Scott E Counts
- Department of Translational Neuroscience, Michigan State University, Grand Rapids, MI 49503, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI 48824, USA
- Department of Family Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Hauenstein Neurosciences Center, Mercy Health Saint Mary’s Hospital, Grand Rapids, MI 49503, USA
- Michigan Alzheimer’s Disease Research Center, Ann Arbor, MI 48109, USA
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10
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Ganguly D, Thomas JA, Ali A, Kumar R. Mechanistic and therapeutic implications of EphA-4 receptor tyrosine kinase in the pathogenesis of Alzheimer's disease. Eur J Neurosci 2022; 56:5532-5546. [PMID: 34989046 DOI: 10.1111/ejn.15591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors belong to a family of tyrosine kinase receptors that plays a pivotal role in the development of the brain. Eph can be divided broadly into two groups, namely, EphA and EphB, comprising nine and five members, respectively. In recent years, the role of EphA-4 has become increasingly apparent in the onset of Alzheimer's disease (AD). Emerging evidence suggests that EphA-4 results in synaptic dysfunction, which in turn promotes the progression of AD. Moreover, pharmacological or genetic ablation of EphA-4 in the murine model of AD can alleviate the symptoms. The current review summarizes different pathways by which EphA-4 can influence pathogenesis. Since, majority of the studies had reported the protective effect of EphA-4 inhibition during AD, designing therapeutics based on decreasing its enzymatic activity might be necessary for introducing the novel interventions. Therefore, the review described peptide and nanobodies inhibitors of EphA-4 that exhibit the potential to modulate EphA-4 and could be used as lead molecules for the targeted therapy of AD.
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Affiliation(s)
- Devargya Ganguly
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Joshua Abby Thomas
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Abid Ali
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rahul Kumar
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
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11
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Paasila PJ, Aramideh JA, Sutherland GT, Graeber MB. Synapses, Microglia, and Lipids in Alzheimer's Disease. Front Neurosci 2022; 15:778822. [PMID: 35095394 PMCID: PMC8789683 DOI: 10.3389/fnins.2021.778822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease (AD) is characterised by synaptic dysfunction accompanied by the microscopically visible accumulation of pathological protein deposits and cellular dystrophy involving both neurons and glia. Late-stage AD shows pronounced loss of synapses and neurons across several differentially affected brain regions. Recent studies of advanced AD using post-mortem brain samples have demonstrated the direct involvement of microglia in synaptic changes. Variants of the Apolipoprotein E and Triggering Receptors Expressed on Myeloid Cells gene represent important determinants of microglial activity but also of lipid metabolism in cells of the central nervous system. Here we review evidence that may help to explain how abnormal lipid metabolism, microglial activation, and synaptic pathophysiology are inter-related in AD.
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Affiliation(s)
- Patrick J. Paasila
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Jason A. Aramideh
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Greg T. Sutherland
- Charles Perkins Centre, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Manuel B. Graeber
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
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12
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Sahadevan S, Pérez-Berlanga M, Polymenidou M. Identification of RNA-RBP Interactions in Subcellular Compartments by CLIP-Seq. Methods Mol Biol 2022; 2428:305-323. [PMID: 35171488 DOI: 10.1007/978-1-0716-1975-9_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) allows the identification of RNA targets bound by a specific RNA-binding protein (RBP) in in vivo and ex vivo experimental models with high specificity. Due to the little RNA yield obtained after cross-linking, immunoprecipitation, polyacrylamide gel electrophoresis, membrane transfer, and RNA extraction, CLIP-seq is usually performed from relatively large amounts of starting material, like cell lysates or tissue homogenates. However, RBP binding of its specific RNA targets depends on its subcellular localization, and a different set of RNAs may be bound by the same RBP within distinct subcellular sites. To uncover these RNA subsets, preparation of CLIP-seq libraries from specific subcellular compartments and comparison to CLIP-seq datasets from total lysates is necessary, yet there are currently no available protocols for this. Here we describe the adaptation of CLIP-seq to identify the specific RNA targets of an RBP (FUS) at a small subcompartment, that is, neuronal synapses, including subcompartment isolation, RBP-RNA complex enrichment, and upscaling steps.
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Affiliation(s)
- Sonu Sahadevan
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
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13
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Yuen SC, Lee SMY, Leung SW. Putative Factors Interfering Cell Cycle Re-Entry in Alzheimer's Disease: An Omics Study with Differential Expression Meta-Analytics and Co-Expression Profiling. J Alzheimers Dis 2021; 85:1373-1398. [PMID: 34924393 DOI: 10.3233/jad-215349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Neuronal cell cycle re-entry (CCR) is a mechanism, along with amyloid-β (Aβ) oligomers and hyperphosphorylated tau proteins, contributing to toxicity in Alzheimer's disease (AD). OBJECTIVE This study aimed to examine the putative factors in CCR based on evidence corroboration by combining meta-analysis and co-expression analysis of omic data. METHODS The differentially expressed genes (DEGs) and CCR-related modules were obtained through the differential analysis and co-expression of transcriptomic data, respectively. Differentially expressed microRNAs (DEmiRNAs) were extracted from the differential miRNA expression studies. The dysregulations of DEGs and DEmiRNAs as binary outcomes were independently analyzed by meta-analysis based on a random-effects model. The CCR-related modules were mapped to human protein-protein interaction databases to construct a network. The importance score of each node within the network was determined by the PageRank algorithm, and nodes that fit the pre-defined criteria were treated as putative CCR-related factors. RESULTS The meta-analysis identified 18,261 DEGs and 36 DEmiRNAs, including genes in the ubiquitination proteasome system, mitochondrial homeostasis, and CCR, and miRNAs associated with AD pathologies. The co-expression analysis identified 156 CCR-related modules to construct a protein-protein interaction network. Five genes, UBC, ESR1, EGFR, CUL3, and KRAS, were selected as putative CCR-related factors. Their functions suggested that the combined effects of cellular dyshomeostasis and receptors mediating Aβ toxicity from impaired ubiquitination proteasome system are involved in CCR. CONCLUSION This study identified five genes as putative factors and revealed the significance of cellular dyshomeostasis in the CCR of AD.
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Affiliation(s)
- Sze Chung Yuen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Siu-Wai Leung
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, China.,Edinburgh Bayes Centre for AI Research in Shenzhen, College of Science and Engineering, University of Edinburgh, Scotland, United Kingdom
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14
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Ponton E, Turecki G, Nagy C. Sex Differences in the Behavioral, Molecular, and Structural Effects of Ketamine Treatment in Depression. Int J Neuropsychopharmacol 2021; 25:75-84. [PMID: 34894233 PMCID: PMC8756094 DOI: 10.1093/ijnp/pyab082] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/08/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022] Open
Abstract
Major depressive disorder (MDD) is a common psychiatric illness that manifests in sex-influenced ways. Men and women may experience depression differently and also respond to various antidepressant treatments in sex-influenced ways. Ketamine, which is now being used as a rapid-acting antidepressant, is likely the same. To date, the majority of studies investigating treatment outcomes in MDD do not disaggregate the findings in males and females, and this is also true for ketamine. This review aims to highlight that gap by exploring pre-clinical data-at a behavioral, molecular, and structural level-and recent clinical trials. Sex hormones, particularly estrogen and progesterone, influence the response at all levels examined, and sex is therefore a critical factor to examine when looking at ketamine response. Taken together, the data show females are more sensitive to ketamine than males, and it might be possible to monitor the phase of the menstrual cycle to mitigate some risks associated with the use of ketamine for females with MDD. Based on the studies reviewed in this article, we suggest that ketamine should be administered adhering to sex-specific considerations.
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Affiliation(s)
- Ethan Ponton
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
- Correspondence: Corina Nagy, PhD, 6875 LaSalle Blvd, Verdun, Québec, Canada H4H 1R3 ()
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15
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Rahman MH, Rana HK, Peng S, Kibria MG, Islam MZ, Mahmud SMH, Moni MA. Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. Comput Biol Med 2021; 138:104859. [PMID: 34601390 PMCID: PMC8483812 DOI: 10.1016/j.compbiomed.2021.104859] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/21/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) still tends to propagate and increase the occurrence of COVID-19 across the globe. The clinical and epidemiological analyses indicate the link between COVID-19 and Neurological Diseases (NDs) that drive the progression and severity of NDs. Elucidating why some patients with COVID-19 influence the progression of NDs and patients with NDs who are diagnosed with COVID-19 are becoming increasingly sick, although others are not is unclear. In this research, we investigated how COVID-19 and ND interact and the impact of COVID-19 on the severity of NDs by performing transcriptomic analyses of COVID-19 and NDs samples by developing the pipeline of bioinformatics and network-based approaches. The transcriptomic study identified the contributing genes which are then filtered with cell signaling pathway, gene ontology, protein-protein interactions, transcription factor, and microRNA analysis. Identifying hub-proteins using protein-protein interactions leads to the identification of a therapeutic strategy. Additionally, the incorporation of comorbidity interactions score enhances the identification beyond simply detecting novel biological mechanisms involved in the pathophysiology of COVID-19 and its NDs comorbidities. By computing the semantic similarity between COVID-19 and each of the ND, we have found gene-based maximum semantic score between COVID-19 and Parkinson's disease, the minimum semantic score between COVID-19 and Multiple sclerosis. Similarly, we have found gene ontology-based maximum semantic score between COVID-19 and Huntington disease, minimum semantic score between COVID-19 and Epilepsy disease. Finally, we validated our findings using gold-standard databases and literature searches to determine which genes and pathways had previously been associated with COVID-19 and NDs.
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Affiliation(s)
- Md Habibur Rahman
- Dept. of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Humayan Kabir Rana
- Dept. of Computer Science and Engineering, Green University of Bangladesh, Dhaka, Bangladesh
| | - Silong Peng
- Institute of Automation, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Md Golam Kibria
- Dept. of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, Canada
| | - Md Zahidul Islam
- Department of Electronics, Graduate School of Engineering, Nagoya University, Japan
| | - S M Hasan Mahmud
- Dept. of Computer Science, American International University Bangladesh, Dhaka, Bangladesh
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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16
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Revelation of Pivotal Genes Pertinent to Alzheimer's Pathogenesis: A Methodical Evaluation of 32 GEO Datasets. J Mol Neurosci 2021; 72:303-322. [PMID: 34668150 PMCID: PMC8526053 DOI: 10.1007/s12031-021-01919-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/18/2021] [Indexed: 11/26/2022]
Abstract
Alzheimer’s disease (AD), a dreadful neurodegenerative disorder that affects cognitive and behavioral function in geriatric populations, is characterized by the presence of amyloid deposits and neurofibrillary tangles in brain regions. The International D World Alzheimer Report2018 noted a global prevalence of 50 million AD cases and forecasted a threefold rise to 139 million by 2050. Although there exist numerous genetic association studies pertinent to AD in different ethnicities, critical genetic factors and signaling pathways underlying its pathogenesis remain ambiguous. This study was aimed to analyze the genetic data retrieved from 32 Gene Expression Omnibus datasets belonging to diverse ethnic cohorts in order to identify overlapping differentially expressed genes (DEGs). Stringent selection criteria were framed to shortlist appropriate datasets based on false discovery rate (FDR) p-value and log FC, and relevant details of upregulated and downregulated DEGs were retrieved. Among the 32 datasets, only six satisfied the selection criteria. The GEO2R tool was employed to retrieve significant DEGs. Nine common DEGs, i.e., SLC5A3, BDNF, SST, SERPINA3, RTN3, RGS4, NPTX, ENC1 and CRYM were found in more than 60% of the selected datasets. These DEGs were later subjected to protein–protein interaction analysis with 18 AD-specific literature-derived genes. Among the nine common DEGs, BDNF, SST, SERPINA3, RTN3 and RGS4 exhibited significant interactions with crucial proteins including BACE1, GRIN2B, APP, APOE, COMT, PSEN1, INS, NEP and MAPT. Functional enrichment analysis revealed involvement of these genes in trans-synaptic signaling, chemical transmission, PI3K pathway signaling, receptor–ligand activity and G protein signaling. These processes are interlinked with AD pathways.
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17
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Di Paolo A, Garat J, Eastman G, Farias J, Dajas-Bailador F, Smircich P, Sotelo-Silveira JR. Functional Genomics of Axons and Synapses to Understand Neurodegenerative Diseases. Front Cell Neurosci 2021; 15:686722. [PMID: 34248504 PMCID: PMC8267896 DOI: 10.3389/fncel.2021.686722] [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] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
Functional genomics studies through transcriptomics, translatomics and proteomics have become increasingly important tools to understand the molecular basis of biological systems in the last decade. In most cases, when these approaches are applied to the nervous system, they are centered in cell bodies or somatodendritic compartments, as these are easier to isolate and, at least in vitro, contain most of the mRNA and proteins present in all neuronal compartments. However, key functional processes and many neuronal disorders are initiated by changes occurring far away from cell bodies, particularly in axons (axopathologies) and synapses (synaptopathies). Both neuronal compartments contain specific RNAs and proteins, which are known to vary depending on their anatomical distribution, developmental stage and function, and thus form the complex network of molecular pathways required for neuron connectivity. Modifications in these components due to metabolic, environmental, and/or genetic issues could trigger or exacerbate a neuronal disease. For this reason, detailed profiling and functional understanding of the precise changes in these compartments may thus yield new insights into the still intractable molecular basis of most neuronal disorders. In the case of synaptic dysfunctions or synaptopathies, they contribute to dozens of diseases in the human brain including neurodevelopmental (i.e., autism, Down syndrome, and epilepsy) as well as neurodegenerative disorders (i.e., Alzheimer's and Parkinson's diseases). Histological, biochemical, cellular, and general molecular biology techniques have been key in understanding these pathologies. Now, the growing number of omics approaches can add significant extra information at a high and wide resolution level and, used effectively, can lead to novel and insightful interpretations of the biological processes at play. This review describes current approaches that use transcriptomics, translatomics and proteomic related methods to analyze the axon and presynaptic elements, focusing on the relationship that axon and synapses have with neurodegenerative diseases.
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Affiliation(s)
- Andres Di Paolo
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Proteínas y Ácidos Nucleicos, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquin Garat
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Guillermo Eastman
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Joaquina Farias
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Polo de Desarrollo Universitario “Espacio de Biología Vegetal del Noreste”, Centro Universitario Regional Noreste, Universidad de la República (UdelaR), Tacuarembó, Uruguay
| | - Federico Dajas-Bailador
- School of Life Sciences, Medical School Building, University of Nottingham, Nottingham, United Kingdom
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
| | - José Roberto Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
- Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
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18
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Sahadevan S, Hembach KM, Tantardini E, Pérez-Berlanga M, Hruska-Plochan M, Megat S, Weber J, Schwarz P, Dupuis L, Robinson MD, De Rossi P, Polymenidou M. Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS. Nat Commun 2021; 12:3027. [PMID: 34021139 PMCID: PMC8140117 DOI: 10.1038/s41467-021-23188-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Mutations disrupting the nuclear localization of the RNA-binding protein FUS characterize a subset of amyotrophic lateral sclerosis patients (ALS-FUS). FUS regulates nuclear RNAs, but its role at the synapse is poorly understood. Using super-resolution imaging we determined that the localization of FUS within synapses occurs predominantly near the vesicle reserve pool of presynaptic sites. Using CLIP-seq on synaptoneurosomes, we identified synaptic FUS RNA targets, encoding proteins associated with synapse organization and plasticity. Significant increase of synaptic FUS during early disease in a mouse model of ALS was accompanied by alterations in density and size of GABAergic synapses. mRNAs abnormally accumulated at the synapses of 6-month-old ALS-FUS mice were enriched for FUS targets and correlated with those depicting increased short-term mRNA stability via binding primarily on multiple exonic sites. Our study indicates that synaptic FUS accumulation in early disease leads to synaptic impairment, potentially representing an initial trigger of neurodegeneration.
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Affiliation(s)
- Sonu Sahadevan
- Department of Quantitative Biomedicine, University of Zurich, Zürich, Switzerland
| | - Katharina M Hembach
- Department of Quantitative Biomedicine, University of Zurich, Zürich, Switzerland
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zürich, Switzerland
| | - Elena Tantardini
- Department of Quantitative Biomedicine, University of Zurich, Zürich, Switzerland
| | | | | | - Salim Megat
- Inserm, University of Strasbourg, Strasbourg, France
| | - Julien Weber
- Department of Quantitative Biomedicine, University of Zurich, Zürich, Switzerland
| | - Petra Schwarz
- Institute of Neuropathology, University Hospital Zurich, Zürich, Switzerland
| | - Luc Dupuis
- Inserm, University of Strasbourg, Strasbourg, France
| | - Mark D Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zürich, Switzerland
| | - Pierre De Rossi
- Department of Quantitative Biomedicine, University of Zurich, Zürich, Switzerland
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19
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Chemical Stimulation of Rodent and Human Cortical Synaptosomes: Implications in Neurodegeneration. Cells 2021; 10:cells10051174. [PMID: 34065927 PMCID: PMC8151714 DOI: 10.3390/cells10051174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/29/2021] [Accepted: 05/09/2021] [Indexed: 12/14/2022] Open
Abstract
Synaptic plasticity events, including long-term potentiation (LTP), are often regarded as correlates of brain functions of memory and cognition. One of the central players in these plasticity-related phenomena is the α-amino-3-hydroxy-5-methylisoxazole-4-propionate receptor (AMPAR). Increased levels of AMPARs on postsynaptic membranes thus constitute a biochemical measure of LTP. Isolated synaptic terminals (synaptosomes) are an excellent ex vivo tool to monitor synaptic physiology in healthy and diseased brains, particularly in human research. We herein describe three protocols for chemically-induced LTP (cLTP) in synaptosomes from both rodent and human brain tissues. Two of these chemical stimulation protocols are described for the first time in synaptosomes. A pharmacological block of synaptosomal actin dynamics confirmed the efficiency of the cLTP protocols. Furthermore, the study prototypically evaluated the deficiency of cLTP in cortical synaptosomes obtained from human cases of early-onset Alzheimer’s disease (EOAD) and frontotemporal lobar degeneration (FLTD), as well as an animal model that mimics FLTD.
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20
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Chowdhury UN, Ahmad S, Islam MB, Alyami SA, Quinn JMW, Eapen V, Moni MA. System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study. PLoS One 2021; 16:e0250660. [PMID: 33956862 PMCID: PMC8101720 DOI: 10.1371/journal.pone.0250660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/12/2021] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease (AD) is the commonest progressive neurodegenerative condition in humans, and is currently incurable. A wide spectrum of comorbidities, including other neurodegenerative diseases, are frequently associated with AD. How AD interacts with those comorbidities can be examined by analysing gene expression patterns in affected tissues using bioinformatics tools. We surveyed public data repositories for available gene expression data on tissue from AD subjects and from people affected by neurodegenerative diseases that are often found as comorbidities with AD. We then utilized large set of gene expression data, cell-related data and other public resources through an analytical process to identify functional disease links. This process incorporated gene set enrichment analysis and utilized semantic similarity to give proximity measures. We identified genes with abnormal expressions that were common to AD and its comorbidities, as well as shared gene ontology terms and molecular pathways. Our methodological pipeline was implemented in the R platform as an open-source package and available at the following link: https://github.com/unchowdhury/AD_comorbidity. The pipeline was thus able to identify factors and pathways that may constitute functional links between AD and these common comorbidities by which they affect each others development and progression. This pipeline can also be useful to identify key pathological factors and therapeutic targets for other diseases and disease interactions.
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Affiliation(s)
- Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamim Ahmad
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - M. Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Salem A. Alyami
- Department of Mathematics and Statistics, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Julian M. W. Quinn
- Healthy Ageing Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Valsamma Eapen
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mohammad Ali Moni
- Healthy Ageing Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia
- WHO Collaborating Centre on eHealth, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, Australia
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21
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Walker CK, Greathouse KM, Boros BD, Poovey EH, Clearman KR, Ramdas R, Muhammad HM, Herskowitz JH. Dendritic Spine Remodeling and Synaptic Tau Levels in PS19 Tauopathy Mice. Neuroscience 2021; 455:195-211. [PMID: 33346120 PMCID: PMC8142378 DOI: 10.1016/j.neuroscience.2020.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 12/07/2020] [Indexed: 01/13/2023]
Abstract
Synapse or dendritic spine loss is the strongest correlate of cognitive decline in Alzheimer's disease (AD), and neurofibrillary tangles (NFTs), but not amyloid-β plaques, associate more closely with transition to mild cognitive impairment. Yet, how dendritic spine architecture is affected by hyperphosphorylated tau is still an ongoing question. To address this, we combined cell and biochemical analyses of the Tau P301S mouse line (PS19). Individual pyramidal neurons in the hippocampus and medial prefrontal cortex (mPFC) were targeted for iontophoretic microinjection of fluorescent dye, followed by high-resolution confocal microscopy and 3D morphometry analysis. In the hippocampus, PS19 mice and non-transgenic (NTG) littermates displayed equivalent spine density at 6 and 9 months, but both genotypes exhibited age-related thin spine loss. PS19 mice exhibited significant increases in synaptic tau protein levels and mean dendritic spine head diameter with age. This suggests that CA1 pyramidal neurons in PS19 mice may undergo spine remodeling in response to tau accumulation and age. In the mPFC, spine density was similar among PS19 mice and NTG littermates at 6 and 9 months, but age-related reductions in synaptic tau levels were observed among PS19 mice. Collectively, these studies reveal brain region-specific changes in dendritic spine density and morphology in response to age and the presence of hyperphosphorylated tau in the PS19 mouse line.
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Affiliation(s)
- Courtney K Walker
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Kelsey M Greathouse
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Benjamin D Boros
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Emily H Poovey
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Kelsey R Clearman
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Raksha Ramdas
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Hamad M Muhammad
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Jeremy H Herskowitz
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States.
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22
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Loeffler DA. Modifiable, Non-Modifiable, and Clinical Factors Associated with Progression of Alzheimer's Disease. J Alzheimers Dis 2021; 80:1-27. [PMID: 33459643 DOI: 10.3233/jad-201182] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is an extensive literature relating to factors associated with the development of Alzheimer's disease (AD), but less is known about factors which may contribute to its progression. This review examined the literature with regard to 15 factors which were suggested by PubMed search to be positively associated with the cognitive and/or neuropathological progression of AD. The factors were grouped as potentially modifiable (vascular risk factors, comorbidities, malnutrition, educational level, inflammation, and oxidative stress), non-modifiable (age at clinical onset, family history of dementia, gender, Apolipoprotein E ɛ4, genetic variants, and altered gene regulation), and clinical (baseline cognitive level, neuropsychiatric symptoms, and extrapyramidal signs). Although conflicting results were found for the majority of factors, a positive association was found in nearly all studies which investigated the relationship of six factors to AD progression: malnutrition, genetic variants, altered gene regulation, baseline cognitive level, neuropsychiatric symptoms, and extrapyramidal signs. Whether these or other factors which have been suggested to be associated with AD progression actually influence the rate of decline of AD patients is unclear. Therapeutic approaches which include addressing of modifiable factors associated with AD progression should be considered.
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Affiliation(s)
- David A Loeffler
- Beaumont Research Institute, Department of Neurology, Beaumont Health, Royal Oak, MI, USA
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23
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Ahmad F, Liu P. Synaptosome as a tool in Alzheimer's disease research. Brain Res 2020; 1746:147009. [PMID: 32659233 DOI: 10.1016/j.brainres.2020.147009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/21/2020] [Accepted: 07/04/2020] [Indexed: 12/29/2022]
Abstract
Synapse dysfunction is an integral feature of Alzheimer's disease (AD) pathophysiology. In fact, prodromal manifestation of structural and functional deficits in synapses much prior to appearance of overt pathological hallmarks of the disease indicates that AD might be considered as a degenerative disorder of the synapses. Several research instruments and techniques have allowed us to study synaptic function and plasticity and their alterations in pathological conditions, such as AD. One such tool is the biochemically isolated preparations of detached and resealed synaptic terminals, the "synaptosomes". Because of the preservation of many of the physiological processes such as metabolic and enzymatic activities, synaptosomes have proved to be an indispensable ex vivo model system to study synapse physiology both when isolated from fresh or cryopreserved tissues, and from animal or human post-mortem tissues. This model system has been tremendously successful in the case of post-mortem tissues because of their accessibility relative to acute brain slices or cultures. The current review details the use of synaptosomes in AD research and its potential as a valuable tool in furthering our understanding of the pathogenesis and in devising and testing of therapeutic strategies for the disease.
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Affiliation(s)
- Faraz Ahmad
- Department of Anatomy, School of Biomedical Sciences, Brain Research New Zealand, University of Otago, Dunedin, New Zealand.
| | - Ping Liu
- Department of Anatomy, School of Biomedical Sciences, Brain Research New Zealand, University of Otago, Dunedin, New Zealand
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24
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Findley CA, Bartke A, Hascup KN, Hascup ER. Amyloid Beta-Related Alterations to Glutamate Signaling Dynamics During Alzheimer's Disease Progression. ASN Neuro 2020; 11:1759091419855541. [PMID: 31213067 PMCID: PMC6582288 DOI: 10.1177/1759091419855541] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Alzheimer’s disease (AD) ranks sixth on the Centers for Disease Control and Prevention Top 10 Leading Causes of Death list for 2016, and the Alzheimer’s Association attributes 60% to 80% of dementia cases as AD related. AD pathology hallmarks include accumulation of senile plaques and neurofibrillary tangles; however, evidence supports that soluble amyloid beta (Aβ), rather than insoluble plaques, may instigate synaptic failure. Soluble Aβ accumulation results in depression of long-term potentiation leading to cognitive deficits commonly characterized in AD. The mechanisms through which Aβ incites cognitive decline have been extensively explored, with a growing body of evidence pointing to modulation of the glutamatergic system. The period of glutamatergic hypoactivation observed alongside long-term potentiation depression and cognitive deficits in later disease stages may be the consequence of a preceding period of increased glutamatergic activity. This review will explore the Aβ-related changes to the tripartite glutamate synapse resulting in altered cell signaling throughout disease progression, ultimately culminating in oxidative stress, synaptic dysfunction, and neuronal loss.
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Affiliation(s)
- Caleigh A Findley
- 1 Department of Neurology, Center for Alzheimer's Disease and Related Disorders, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, IL, USA.,2 Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Andrzej Bartke
- 3 Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Kevin N Hascup
- 1 Department of Neurology, Center for Alzheimer's Disease and Related Disorders, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, IL, USA.,2 Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA.,4 Department of Molecular Biology, Microbiology & Biochemistry, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Erin R Hascup
- 1 Department of Neurology, Center for Alzheimer's Disease and Related Disorders, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, IL, USA.,2 Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
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25
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Sampaio-Baptista C, Vallès A, Khrapitchev AA, Akkermans G, Winkler AM, Foxley S, Sibson NR, Roberts M, Miller K, Diamond ME, Martens GJM, De Weerd P, Johansen-Berg H. White matter structure and myelin-related gene expression alterations with experience in adult rats. Prog Neurobiol 2020; 187:101770. [PMID: 32001310 PMCID: PMC7086231 DOI: 10.1016/j.pneurobio.2020.101770] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/19/2019] [Accepted: 01/24/2020] [Indexed: 11/30/2022]
Abstract
White matter (WM) plasticity during adulthood is a recently described phenomenon by which experience can shape brain structure. It has been observed in humans using diffusion tensor imaging (DTI) and myelination has been suggested as a possible mechanism. Here, we set out to identify molecular and cellular changes associated with WM plasticity measured by DTI. We combined DTI, immunohistochemistry and mRNA expression analysis and examined the effects of somatosensory experience in adult rats. First, we observed experience-induced DTI differences in WM and in grey matter structure. C-Fos mRNA expression, a marker of cortical activity, in the barrel cortex correlated with the MRI WM metrics, indicating that molecular correlates of cortical activity relate to macroscale measures of WM structure. Analysis of myelin-related genes revealed higher myelin basic protein (MBP) mRNA expression. Higher MBP protein expression was also found via immunohistochemistry in WM. Finally, unbiased RNA sequencing analysis identified 134 differentially expressed genes encoding proteins involved in functions related to cell proliferation and differentiation, regulation of myelination and neuronal activity modulation. In conclusion, macroscale measures of WM plasticity are supported by both molecular and cellular evidence and confirm that myelination is one of the underlying mechanisms.
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Affiliation(s)
- Cassandra Sampaio-Baptista
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.
| | - Astrid Vallès
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands; Department of Neurocognition, Faculty of Psychology and Neurosciences, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Alexandre A Khrapitchev
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Guus Akkermans
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Anderson M Winkler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sean Foxley
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Nicola R Sibson
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | - Mark Roberts
- Department of Neurocognition, Faculty of Psychology and Neurosciences, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Karla Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Mathew E Diamond
- Tactile Perception and Learning Lab, International School for Advanced Studies (SISSA), 34136 Trieste, Italy
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Peter De Weerd
- Department of Neurocognition, Faculty of Psychology and Neurosciences, Maastricht University, 6200 MD Maastricht, The Netherlands; Department of Cognitive Neuroscience, Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, The Netherlands; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Heidi Johansen-Berg
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
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26
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Yuen SC, Zhu H, Leung SW. A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. Front Neurosci 2020; 14:209. [PMID: 32231518 PMCID: PMC7083177 DOI: 10.3389/fnins.2020.00209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
Potential pathogenic factors, other than well-known APP, APOE4, and PSEN, can be further identified from transcriptomics studies of differentially expressed genes (DEGs) that are specific for Alzheimer’s disease (AD), but findings are often inconsistent or even contradictory. Evidence corroboration by combining meta-analysis and bioinformatics methods may help to resolve existing inconsistencies and contradictions. This study aimed to demonstrate a systematic workflow for evidence synthesis of transcriptomic studies using both meta-analysis and bioinformatics methods to identify potential pathogenic factors. Transcriptomic data were assessed from GEO and ArrayExpress after systematic searches. The DEGs and their dysregulation states from both DNA microarray and RNA sequencing datasets were analyzed and corroborated by meta-analysis. Statistically significant DEGs were used for enrichment analysis based on KEGG and protein–protein interaction network (PPIN) analysis based on STRING. AD-specific modules were further determined by the DIAMOnD algorithm, which identifies significant connectivity patterns between specific disease-associated proteins and non-specific proteins. Within AD-specific modules, the nodes of highest degrees (>95th percentile) were considered as potential pathogenic factors. After systematic searches of 225 datasets, extensive meta-analyses among 25 datasets (21 DNA microarray datasets and 4 RNA sequencing datasets) identified 9,298 DEGs. The dysregulated genes and pathways in AD were associated with impaired amyloid-β (Aβ) clearance. From the AD-specific module, Fyn, and EGFR were the most statistically significant and biologically relevant. This meta-analytical study suggested that the reduced Aβ clearance in AD pathogenesis was associated with the genes encoding Fyn and EGFR, which were key receptors in Aβ downstream signaling.
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Affiliation(s)
- Sze Chung Yuen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hongmei Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Siu-Wai Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.,School of Informatics, College of Science and Engineering, University of Edinburgh, Edinburgh, United Kingdom
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27
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Wu PC, Fann MJ, Tran TT, Chen SC, Devina T, Cheng IHJ, Lien CC, Kao LS, Wang SJ, Fuh JL, Tzeng TT, Huang CY, Shiao YJ, Wong YH. Assessing the therapeutic potential of Graptopetalum paraguayense on Alzheimer's disease using patient iPSC-derived neurons. Sci Rep 2019; 9:19301. [PMID: 31848379 PMCID: PMC6917798 DOI: 10.1038/s41598-019-55614-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/13/2019] [Indexed: 12/26/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common type of dementia and also one of the leading causes of death worldwide. However, the underlying mechanisms remain unclear, and currently there is no drug treatment that can prevent or cure AD. Here, we have applied the advantages of using induced pluripotent stem cell (iPSC)-derived neurons (iNs) from AD patients, which are able to offer human-specific drug responsiveness, in order to evaluate therapeutic candidates for AD. Using approach involving an inducible neurogenin-2 transgene, we have established a robust and reproducible protocol for differentiating human iPSCs into glutamatergic neurons. The AD-iN cultures that result have mature phenotypic and physiological properties, together with AD-like biochemical features that include extracellular β-amyloid (Aβ) accumulation and Tau protein phosphorylation. By screening using a gene set enrichment analysis (GSEA) approach, Graptopetalum paraguayense (GP) has been identified as a potential therapeutic agent for AD from among a range of Chinese herbal medicines. We found that administration of a GP extract caused a significantly reduction in the AD-associated phenotypes of the iNs, including decreased levels of extracellular Aβ40 and Aβ42, as well as reduced Tau protein phosphorylation at positions Ser214 and Ser396. Additionally, the effect of GP was more prominent in AD-iNs compared to non-diseased controls. These findings provide valuable information that suggests moving extracts of GP toward drug development, either for treating AD or as a health supplement to prevent AD. Furthermore, our human iN-based platform promises to be a useful strategy when it is used for AD drug discovery.
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Affiliation(s)
- Pei-Chun Wu
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Ming-Ji Fann
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Tu Thanh Tran
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Shu-Cian Chen
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Tania Devina
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan (ROC)
| | - Irene Han-Juo Cheng
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).,Institute of Brain Science, National Yang Ming University, Taipei, 11221, Taiwan (ROC)
| | - Cheng-Chang Lien
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).,Institute of Neuroscience, National Yang Ming University, Taipei, 11221, Taiwan (ROC)
| | - Lung-Sen Kao
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Shuu-Jiun Wang
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).,Division of General Neurology, Neurological Institute, Taipei Veterans Hospital, Taipei, 11217, Taiwan (ROC)
| | - Jong-Ling Fuh
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).,Division of General Neurology, Neurological Institute, Taipei Veterans Hospital, Taipei, 11217, Taiwan (ROC)
| | - Tsai-Teng Tzeng
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Chi-Ying Huang
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, 11221, Taiwan (ROC)
| | - Young-Ji Shiao
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, 11221, Taiwan (ROC). .,National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, 11221, Taiwan (ROC).
| | - Yu-Hui Wong
- Brain Research Center, National Yang-Ming University, Taipei, 11221, Taiwan (ROC).
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28
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Zhang Y, Yu F, Bao S, Sun J. Systematic Characterization of Circular RNA-Associated CeRNA Network Identified Novel circRNA Biomarkers in Alzheimer's Disease. Front Bioeng Biotechnol 2019; 7:222. [PMID: 31572720 PMCID: PMC6749152 DOI: 10.3389/fbioe.2019.00222] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD), a degenerative disease of the central nervous system, is the most common form of dementia in old age. The complexity and behavior of circular RNA (circRNA)-associated competing endogenous RNA (ceRNA) network remained poorly characterized in AD. The aim of this study was to elucidate the regulatory networks of dysregulated circRNAs from ceRNA view and identify potential risk circRNAs involved in AD pathogenesis. Consistent differentially expressed genes (CDEGs) were obtained using meta-analysis for multiple microarrays, and differentially expressed miRNAs (DEmiRs) were identified using empirical Bayes method. The circRNA-associated ceRNA network (cirCeNET) was constructed based on “ceRNA hypothesis” using an integrated system biology method. A total of 1,872 CDEGs and 48 DEmiRs were screened across different datasets. By mapping CDEGs and DEmiRs into the cirCeNET, an AD-related circRNA-associated ceRNA network (ADcirCeNET) was constructed, including 3,907 edges and 1,407 nodes (276 circRNAs, 14 miRNAs and 1,117 mRNAs). By prioritizing AD risk circRNA-associated ceRNAs, we found that the circRNA KIAA1586 occurred most frequently in the AD risk circRNA-associated ceRNAs and function as a ceRNA that operates by competitively binding three known AD-risk miRNAs. In silico functional analysis suggested that circRNA KIAA1586-related ceRNA network was significantly enriched in known AD-associated biological processes. Our study provided a global view and systematic dissection of circRNA-associated ceRNA network. The identified circRNA KIAA1586 may be a key risk factor involved in AD pathogenesis.
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Affiliation(s)
- Yan Zhang
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Fulong Yu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Siqi Bao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jie Sun
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
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29
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Godini R, Pocock R, Fallahi H. Caenorhabditis elegans hub genes that respond to amyloid beta are homologs of genes involved in human Alzheimer's disease. PLoS One 2019; 14:e0219486. [PMID: 31291334 PMCID: PMC6619800 DOI: 10.1371/journal.pone.0219486] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022] Open
Abstract
The prominent characteristic of Alzheimer’s disease (AD) is the accumulation of amyloid beta (Abeta) proteins in the form of plaques that cause molecular and cellular alterations in the brain. Due to the paucity of brain samples of early-stage Abeta aggregation, animal models have been developed to study early events in AD. Caenorhabditis elegans is a genetically tractable animal model for AD. Here, we used transcriptomic data, network-based protein-protein interactions and weighted gene co-expression network analysis (WGCNA), to detect modules and their gene ontology in response to Abeta aggregation in C. elegans. Additionally, hub genes and their orthologues in human and mouse were identified to study their relation to AD. We also found several transcription factors (TFs) responding to Abeta accumulation. Our results show that Abeta expression in C. elegans relates to general processes such as molting cycle, locomotion, and larval development plus AD-associated processes, including protein phosphorylation, and G-protein coupled receptor-regulated pathways. We reveal that many hub genes and TFs including ttbk-2, daf-16, and unc-49 have human and mouse orthologues that are directly or potentially associated with AD and neural development. In conclusion, using systems biology we identified important genes and biological processes in C. elegans that respond to Abeta aggregation, which could be used as potential diagnostic or therapeutic targets. In addition, because of evolutionary relationship to AD in human, we suggest that C. elegans is a useful model for studying early molecular events in AD.
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Affiliation(s)
- Rasoul Godini
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
- * E-mail:
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30
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Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry. eNeuro 2019; 6:ENEURO.0009-19.2019. [PMID: 31118205 PMCID: PMC6565374 DOI: 10.1523/eneuro.0009-19.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2019] [Accepted: 04/27/2019] [Indexed: 11/21/2022] Open
Abstract
Flow cytometry and fluorescence-activated sorting are powerful techniques that hold great promise for studying heterogeneous populations of submicron particles such as synaptosomes, but many technical challenges arise in these experiments. To date, most flow cytometry studies of synaptosomes have relied on particle detection using forward scatter (FSC) measurements and size estimation with polystyrene (PS) bead standards. However, these practices have serious limitations, and special care must be taken to overcome the poor sensitivity of conventional flow cytometers in the analysis of submicron particles. Technical artifacts can confound these experiments, especially the detection of multiple particles as a single event. Here, we compared analysis of P2 crude synaptosomal preparations from murine forebrain on multiple flow cytometers using both FSC-triggered and fluorescence-triggered detection. We implemented multicolor fluorescent dye-based assays to quantify coincident particle detection and aggregation, and we assessed the false colocalization of antigens in immunostaining analyses. Our results demonstrate that fluorescence triggering and proper dilution can control for coincident particle detection, but not particle aggregation. We confirmed previous studies showing that FSC-based size estimation with PS beads underestimates biological particle size, and we identified pervasive aggregation in the FSC range analyzed in most synaptosome flow cytometry studies. We found that analyzing P2 samples in sucrose/EDTA/tris (SET) buffer reduces aggregation compared to PBS, but does not completely eliminate the presence of aggregates, especially in immunostaining experiments. Our study highlights challenges and pitfalls in synaptosome flow cytometry and provides a methodological framework for future studies.
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31
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Genetic association of the cytochrome c oxidase-related genes with Alzheimer's disease in Han Chinese. Neuropsychopharmacology 2018; 43:2264-2276. [PMID: 30054583 PMCID: PMC6135758 DOI: 10.1038/s41386-018-0144-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 02/05/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. Mitochondrial dysfunction has been widely reported in AD due to its important role in cellular metabolism and energy production. Complex IV (cytochrome c oxidase, COX) of mitochondrial electron transport chain, is particularly vulnerable in AD. Defects of COX in AD have been well documented, but there is little evidence to support the genetic association of the COX-related genes with AD. In this study, we investigated the genetic association between 17 nuclear-encoded COX-related genes and AD in 1572 Han Chinese. The whole exons of these genes were also screened in 107 unrelated AD patients with a high probability of hereditarily transmitted AD. Variants in COX6B1, NDUFA4, SURF1, and COX10 were identified to be associated with AD. An integrative analysis with data of eQTL, expression and pathology revealed that most of the COX-related genes were significantly downregulated in AD patients and mouse models, and the AD-associated variants in COX6B1, SURF1, and COX10 were linked to altered mRNA levels in brain tissues. Furthermore, mRNA levels of Ndufa4, Cox5a, Cox10, Cox6b2, Cox7a2, and Lrpprc were significantly correlated with Aβ plaque burden in hippocampus of AD mice. Convergent functional genomics analysis revealed strong supportive evidence for the roles of COX6B1, COX10, NDUFA4, and SURF1 in AD. As the result of our comprehensive analysis of the COX-related genes at the genetic, expression, and pathology levels, we have been able to provide a systematic view for understanding the relationships of the COX-related genes in the pathology of AD.
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32
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O'Brien MA, Weston RM, Sheth NU, Bradley S, Bigbee J, Pandey A, Williams RW, Wolstenholme JT, Miles MF. Ethanol-Induced Behavioral Sensitization Alters the Synaptic Transcriptome and Exon Utilization in DBA/2J Mice. Front Genet 2018; 9:402. [PMID: 30319688 PMCID: PMC6166094 DOI: 10.3389/fgene.2018.00402] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/03/2018] [Indexed: 11/15/2022] Open
Abstract
Alcoholism is a complex behavioral disorder characterized by loss of control in limiting intake, and progressive compulsion to seek and consume ethanol. Prior studies have suggested that the characteristic behaviors associated with escalation of drug use are caused, at least in part, by ethanol-evoked changes in gene expression affecting synaptic plasticity. Implicit in this hypothesis is a dependence on new protein synthesis and remodeling at the synapse. It is well established that mRNA can be transported to distal dendritic processes, where it can undergo localized translation. It is unknown whether such modulation of the synaptic transcriptome might contribute to ethanol-induced synaptic plasticity. Using ethanol-induced behavioral sensitization as a model of neuroplasticity, we investigated whether repeated exposure to ethanol altered the synaptic transcriptome, contributing to mechanisms underlying subsequent increases in ethanol-evoked locomotor activity. RNAseq profiling of DBA/2J mice subjected to acute ethanol or ethanol-induced behavioral sensitization was performed on frontal pole synaptoneurosomes to enrich for synaptic mRNA. Genomic profiling showed distinct functional classes of mRNA enriched in the synaptic vs. cytosolic fractions, consistent with their role in synaptic function. Ethanol sensitization regulated more than twice the number of synaptic localized genes compared to acute ethanol exposure. Synaptic biological processes selectively perturbed by ethanol sensitization included protein folding and modification as well as and mitochondrial respiratory function, suggesting repeated ethanol exposure alters synaptic energy production and the processing of newly translated proteins. Additionally, marked differential exon usage followed ethanol sensitization in both synaptic and non-synaptic cellular fractions, with little to no perturbation following acute ethanol exposure. Altered synaptic exon usage following ethanol sensitization strongly affected genes related to RNA processing and stability, translational regulation, and synaptic function. These genes were also enriched for targets of the FMRP RNA-binding protein and contained consensus sequence motifs related to other known RNA binding proteins, suggesting that ethanol sensitization altered selective mRNA trafficking mechanisms. This study provides a foundation for investigating the role of ethanol in modifying the synaptic transcriptome and inducing changes in synaptic plasticity.
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Affiliation(s)
- Megan A O'Brien
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Rory M Weston
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States
| | - Nihar U Sheth
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Steven Bradley
- VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - John Bigbee
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA, United States
| | - Ashutosh Pandey
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jennifer T Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States.,VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Michael F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, United States.,VCU Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States.,Department of Neurology, Virginia Commonwealth University, Richmond, VA, United States
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33
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Cellular Receptors of Amyloid β Oligomers (AβOs) in Alzheimer's Disease. Int J Mol Sci 2018; 19:ijms19071884. [PMID: 29954063 PMCID: PMC6073792 DOI: 10.3390/ijms19071884] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/19/2018] [Accepted: 06/22/2018] [Indexed: 12/15/2022] Open
Abstract
It is estimated that Alzheimer’s disease (AD) affects tens of millions of people, comprising not only suffering patients, but also their relatives and caregivers. AD is one of age-related neurodegenerative diseases (NDs) characterized by progressive synaptic damage and neuronal loss, which result in gradual cognitive impairment leading to dementia. The cause of AD remains still unresolved, despite being studied for more than a century. The hallmark pathological features of this disease are senile plaques within patients’ brain composed of amyloid beta (Aβ) and neurofibrillary tangles (NFTs) of Tau protein. However, the roles of Aβ and Tau in AD pathology are being questioned and other causes of AD are postulated. One of the most interesting theories proposed is the causative role of amyloid β oligomers (AβOs) aggregation in the pathogenesis of AD. Moreover, binding of AβOs to cell membranes is probably mediated by certain proteins on the neuronal cell surface acting as AβO receptors. The aim of our paper is to describe alternative hypotheses of AD etiology, including genetic alterations and the role of misfolded proteins, especially Aβ oligomers, in Alzheimer’s disease. Furthermore, in this review we present various putative cellular AβO receptors related to toxic activity of oligomers.
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34
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Ovsepian SV, Blazquez-Llorca L, Freitag SV, Rodrigues EF, Herms J. Ambient Glutamate Promotes Paroxysmal Hyperactivity in Cortical Pyramidal Neurons at Amyloid Plaques via Presynaptic mGluR1 Receptors. Cereb Cortex 2018; 27:4733-4749. [PMID: 27600841 DOI: 10.1093/cercor/bhw267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/03/2016] [Indexed: 02/06/2023] Open
Abstract
Synaptic dysfunctions and altered neuronal activity play major role in the pathophysiology of Alzheimer's disease (AD), with underlying mechanisms largely unknown. We report that in the prefrontal cortex of amyloid precursor protein-presenilin 1 and APP23 AD mice, baseline activity of pyramidal cells is disrupted by episodes of paroxysmal hyperactivity. Induced by spontaneous EPSC bursts, these incidents are prevalent in neurons proximal to amyloid plaques and involve enhanced activity of glutamate with metabotropic effects. Abolition of EPSC bursts by tetrodotoxin and SERCA ATPase blockers thapsigargin or cyclopiasonic acid suggests their presynaptic origin and sensitized store-released calcium. Accordingly, the rate of EPSC bursts activated by single axon stimulation is enhanced. Aggravation of the hyperactivity by blockers of excitatory amino acid transporter (±)-HIP-A and DL-TBOA together with histochemical and ultrastructural evidence for enrichment of plaque-related dystrophies with synaptic vesicles and SNARE protein SNAP-25 infer the later as hot-spots for ectopic release of glutamate. Inhibition of EPSC bursts by I/II mGluR1 blocker MCPG or selective mGluR1 antagonist LY367385 implicate metabotropic glutamatergic effects in generation of paroxysmal bursts. These findings demonstrate for the first time that at amyloid plaques, enhanced activity of nonsynaptic glutamate can promote irregular EPSC bursts with hyperactivity of pyramidal cells via mGluR1 receptors.
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Affiliation(s)
- Saak Victor Ovsepian
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Straße 17, 81377 Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig Maximilian University, Feodor-Lynen-Straße 23, 81377 Munich, Germany
| | - Lidia Blazquez-Llorca
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Straße 17, 81377 Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig Maximilian University, Feodor-Lynen-Straße 23, 81377 Munich, Germany
| | - Susana Valero Freitag
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Straße 17, 81377Munich, Germany
| | - Eva Ferreira Rodrigues
- Center for Neuropathology and Prion Research, Ludwig Maximilian University, Feodor-Lynen-Straße 23, 81377 Munich, Germany.,Munich Cluster of Systems Neurology (SyNergy), Ludwig Maximilian University, Feodor-Lynen-Straße 17, 81377 Munich, Germany
| | - Jochen Herms
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Straße 17, 81377 Munich, Germany.,Center for Neuropathology and Prion Research, Ludwig Maximilian University, Feodor-Lynen-Straße 23, 81377 Munich, Germany.,Munich Cluster of Systems Neurology (SyNergy), Ludwig Maximilian University, Feodor-Lynen-Straße 17, 81377 Munich, Germany
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35
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Neonatal maternal deprivation impairs localized de novo activity-induced protein translation at the synapse in the rat hippocampus. Biosci Rep 2018; 38:BSR20180118. [PMID: 29700212 PMCID: PMC5997792 DOI: 10.1042/bsr20180118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 11/17/2022] Open
Abstract
Neonatal neuropsychiatric stress induces alterations in neurodevelopment that can lead to irreversible damage to neuronal physiology, and social, behavioral, and cognitive skills. In addition, this culminates to an elevated vulnerability to stress and anxiety later in life. Developmental deficits in hippocampal synaptic function and plasticity are among the primary contributors of detrimental alterations in brain function induced by early-life stress. However, the underlying molecular mechanisms are not completely understood. Localized protein translation, occurring at the synapse and triggered by neuronal activity, is critical for synapse function, maintenance, and plasticity. We used a rodent model of chronic maternal deprivation to characterize the effects of early-life neuropsychiatric stress on localized de novo protein translation at synaptic connections between neurons. Synaptoneurosomal preparations isolated biochemically from the hippocampi of rat pups that were subjected to maternal deprivation were deficient in depolarization-induced activity-dependent protein translation when compared with littermate controls. Conversely, basal unstimulated protein translation was not affected. Moreover, deficits in activity-driven synaptic protein translation were significantly correlated with a reduction in phosphorylated cell survival protein kinase protein B or Akt (p473 Ser and p308 Thr), but not phosphorylated extracellular signal-regulated kinase.
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Aguayo FI, Pacheco AA, García-Rojo GJ, Pizarro-Bauerle JA, Doberti AV, Tejos M, García-Pérez MA, Rojas PS, Fiedler JL. Matrix Metalloproteinase 9 Displays a Particular Time Response to Acute Stress: Variation in Its Levels and Activity Distribution in Rat Hippocampus. ACS Chem Neurosci 2018; 9:945-956. [PMID: 29361213 DOI: 10.1021/acschemneuro.7b00387] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A single stress exposure facilitates memory formation through neuroplastic processes that reshape excitatory synapses in the hippocampus, probably requiring changes in extracellular matrix components. We tested the hypothesis that matrix metalloproteinase 9 (MMP-9), an enzyme that degrades components of extracellular matrix and synaptic proteins such as β-dystroglycan (β-DG43), changes their activity and distribution in rat hippocampus during the acute stress response. After 2.5 h of restraint stress, we found (i) increased MMP-9 levels and potential activity in whole hippocampal extracts, accompanied by β-DG43 cleavage, and (ii) a significant enhancement of MMP-9 immunoreactivity in dendritic fields such as stratum radiatum and the molecular layer of hippocampus. After 24 h of stress, we found that (i) MMP-9 net activity rises at somatic field, i.e., stratum pyramidale and granule cell layers, and also at synaptic field, mainly stratum radiatum and the molecular layer of hippocampus, and (ii) hippocampal synaptoneurosome fractions are enriched with MMP-9, without variation of its potential enzymatic activity, in accordance with the constant level of cleaved β-DG43. These findings indicate that stress triggers a peculiar timing response in the MMP-9 levels, net activity, and subcellular distribution in the hippocampus, suggesting its involvement in the processing of substrates during the stress response.
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Affiliation(s)
- Felipe I. Aguayo
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Aníbal A. Pacheco
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Gonzalo J. García-Rojo
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Javier A. Pizarro-Bauerle
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Ana V. Doberti
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Macarena Tejos
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - María A. García-Pérez
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Paulina S. Rojas
- Escuela de Quı́mica y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Jenny L. Fiedler
- Laboratorio de Neuroplasticidad y Neurogenética, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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Moradifard S, Hoseinbeyki M, Ganji SM, Minuchehr Z. Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach. Sci Rep 2018; 8:4767. [PMID: 29555910 PMCID: PMC5859169 DOI: 10.1038/s41598-018-20959-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Understanding the molecular mechanisms underlying Alzheimer’s disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways. A total of 179 differentially expressed miRNAs (DEmiRs) and 1404 differentially expressed genes (DEGs) were obtained from a comprehensive meta-analysis. Also, regions specific genes with their molecular function in AD have been demonstrated. We then focused on miRNAs which regulated most genes in AD, alongside we analyzed their pathways. The miRNA-30a-5p and miRNA-335 elicited a major function in AD after analyzing the regulatory network, we showed they were the most regulatory miRNAs in the AD. In conclusion, we demonstrated the most important genes, miRNAs, miRNA-mRNA interactions and their related pathways in AD using Bioinformatics methods. Accordingly, our defined genes and miRNAs could be used for future molecular studies in the context of AD.
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Affiliation(s)
- Shirin Moradifard
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moslem Hoseinbeyki
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Zarrin Minuchehr
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Izadi F, Soheilifar MH. Exploring Potential Biomarkers Underlying Pathogenesis of Alzheimer's Disease by Differential Co-expression Analysis. Avicenna J Med Biotechnol 2018; 10:233-241. [PMID: 30555656 PMCID: PMC6252023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Alzheimer's Disease (AD) is the most common form of dementia in the elderly. Due to the facts that biological causes of AD are complex in addition to increasing rates of AD worldwide, a deeper understanding of AD etiology is required for AD treatment and diagnosis. METHODS To identify molecular pathological alterations in AD brains, GSE36980 series containing microarray data samples from temporal cortex, frontal cortex and hippocampus were downloaded from Gene Expression Omnibus (GEO) database and valid gene symbols were subjected to building a gene co-expression network by a bioinformatics tool known as differential regulation from differential co-expression (DCGL) software package. Then, a network-driven integrative analysis was performed to find significant genes and underlying biological terms. RESULTS A total of 17088 unique genes were parsed into three independent differential co-expression networks. As a result, a small number of differentially co-regulated genes mostly in frontal and hippocampus lobs were detected as potential biomarkers related to AD brains. Ultimately differentially co-regulated genes were enriched in biological terms including response to lipid and fatty acid and pathways mainly signaling pathway such as G-protein signaling pathway and glutamate receptor groups II and III. By conducting co-expression analysis, our study identified multiple genes that may play an important role in the pathogenesis of AD. CONCLUSION The study aimed to provide a systematic understanding of the potential relationships among these genes and it is hoped that it could aid in AD biomarker discovery.
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Affiliation(s)
- Fereshteh Izadi
- Department of Genetics, Evolution and Environment, Darwin Building, University College London (UCL), London, UK,Corresponding author: Fereshteh Izadi, PhD, Department of Genetics, Evolution and Environment, Darwin Building, University College London (UCL), Gower Street, London WC1E 6BT, UK, Tel: +44 7846280861, E-mail:
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Ahmad F, Salahuddin M, Alsamman K, AlMulla AA, Salama KF. Developmental lead (Pb)-induced deficits in hippocampal protein translation at the synapses are ameliorated by ascorbate supplementation. Neuropsychiatr Dis Treat 2018; 14:3289-3298. [PMID: 30568451 PMCID: PMC6276627 DOI: 10.2147/ndt.s174083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Lead (Pb) is a persistent environmental neurotoxin and its exposure even in minute quantities has been known to induce neuronal defects. The immature brain is singularly sensitive to Pb neurotoxicity, and its exposure during development has permanent detrimental effects on the brain developmental trajectory and neuronal signaling and plasticity, culminating into compromises in the cognitive and behavioral attributes which persists even later in adulthood. Several molecular pathways have been implicated in the Pb-mediated disruption of neuronal signaling, including elevated oxidative stress, alterations in neurotransmitter biology, and mitochondrial dysfunction. Nevertheless, the neuronal targets and biochemical pathways underlying these Pb-mediated alterations in synaptic development and function have not been completely deduced. In this respect, recent studies have shown that synaptic signaling and its maintenance and plasticity are critically dependent on localized de novo protein translation at the synaptic terminals. MATERIALS AND METHODS The present study hence aimed to assess the alterations in the synapse-specific translation induced by developmental Pb exposure. To this end, in vitro protein translation rate was analyzed in the hippocampal synaptoneurosomal fractions of rat pups pre- and postnatally exposed to Pb using a puromycin incorporation assay. Moreover, we evaluated the therapeutic effects of ascorbic acid supplementation against Pb-induced deficits in synapse-localized protein translation. RESULTS We observed a significant loss in the rates of de novo protein translation in synaptoneurosomes of Pb-exposed pups compared to age-matched control pups. Interestingly, ascorbate supplementation lead to an appreciable recovery in Pb-induced translational deficits. Moreover, the deficit in activity-dependent synaptic protein translation was found to correlate significantly with the increase in the blood Pb levels. CONCLUSION Dysregulation of synapse-localized de novo protein translation is a potentially critical determinant of Pb-induced synaptic dysfunction and the consequent deficits in behavioral, social, and psychological attributes of the organisms. In addition, our study establishes ascorbate supplementation as a key ameliorative agent against Pb-induced neurotoxicity.
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Affiliation(s)
- Faraz Ahmad
- School of Life Science, BS Abdur Rahman Crescent Institute of Science & Technology, Vandulur, Chennai 600048, India,
| | - Mohammad Salahuddin
- Animal House Department, Institute for Research and Medical Consultations, Imam Abdurrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Khaldoon Alsamman
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdurrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Abdulaziz A AlMulla
- Department of Environmental Health, College of Public Health, Imam Abdurrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Khaled F Salama
- Department of Environmental Health, College of Public Health, Imam Abdurrahman Bin Faisal University, Dammam 31441, Saudi Arabia
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Ahmad F, Singh K, Das D, Gowaikar R, Shaw E, Ramachandran A, Rupanagudi KV, Kommaddi RP, Bennett DA, Ravindranath V. Reactive Oxygen Species-Mediated Loss of Synaptic Akt1 Signaling Leads to Deficient Activity-Dependent Protein Translation Early in Alzheimer's Disease. Antioxid Redox Signal 2017; 27:1269-1280. [PMID: 28264587 PMCID: PMC5655421 DOI: 10.1089/ars.2016.6860] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
AIMS Synaptic deficits are known to underlie the cognitive dysfunction seen in Alzheimer's disease (AD). Generation of reactive oxygen species (ROS) by β-amyloid has also been implicated in AD pathogenesis. However, it is unclear whether ROS contributes to synaptic dysfunction seen in AD pathogenesis and, therefore, we examined whether altered redox signaling could contribute to synaptic deficits in AD. RESULTS Activity dependent but not basal translation was impaired in synaptoneurosomes from 1-month old presymptomatic APPSwe/PS1ΔE9 (APP/PS1) mice, and this deficit was sustained till middle age (MA, 9-10 months). ROS generation leads to oxidative modification of Akt1 in the synapse and consequent reduction in Akt1-mechanistic target of rapamycin (mTOR) signaling, leading to deficiency in activity-dependent protein translation. Moreover, we found a similar loss of activity-dependent protein translation in synaptoneurosomes from postmortem AD brains. INNOVATION Loss of activity-dependent protein translation occurs presymptomatically early in the pathogenesis of AD. This is caused by ROS-mediated loss of pAkt1, leading to reduced synaptic Akt1-mTOR signaling and is rescued by overexpression of Akt1. ROS-mediated damage is restricted to the synaptosomes, indicating selectivity. CONCLUSIONS We demonstrate that ROS-mediated oxidative modification of Akt1 contributes to synaptic dysfunction in AD, seen as loss of activity-dependent protein translation that is essential for synaptic plasticity and maintenance. Therapeutic strategies promoting Akt1-mTOR signaling at synapses may provide novel target(s) for disease-modifying therapy in AD. Antioxid. Redox Signal. 27, 1269-1280.
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Affiliation(s)
- Faraz Ahmad
- 1 Centre for Neuroscience, Indian Institute of Science , Bangalore, India
| | - Kunal Singh
- 1 Centre for Neuroscience, Indian Institute of Science , Bangalore, India
| | - Debajyoti Das
- 1 Centre for Neuroscience, Indian Institute of Science , Bangalore, India
| | - Ruturaj Gowaikar
- 1 Centre for Neuroscience, Indian Institute of Science , Bangalore, India
| | - Eisha Shaw
- 1 Centre for Neuroscience, Indian Institute of Science , Bangalore, India
| | | | | | | | - David A Bennett
- 2 Rush Alzheimer's Disease Center, Rush University Medical Center , Chicago, Illinois
| | - Vijayalakshmi Ravindranath
- 1 Centre for Neuroscience, Indian Institute of Science , Bangalore, India .,3 Centre for Brain Research , Bangalore, India
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Xu M, Zhang D, Luo R, Wu Y, Zhou H, Kong L, Bi R, Yao Y. A systematic integrated analysis of brain expression profiles reveals
YAP1
and other prioritized hub genes as important upstream regulators in Alzheimer's disease. Alzheimers Dement 2017; 14:215-229. [DOI: 10.1016/j.jalz.2017.08.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Deng‐Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Rongcan Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Hejiang Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Li‐Li Kong
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Institute of Health Science Anhui University Hefei Anhui China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Yong‐Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences Shanghai China
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Chen BJ, Ueberham U, Mills JD, Kirazov L, Kirazov E, Knobloch M, Bochmann J, Jendrek R, Takenaka K, Bliim N, Arendt T, Janitz M. RNA sequencing reveals pronounced changes in the noncoding transcriptome of aging synaptosomes. Neurobiol Aging 2017; 56:67-77. [PMID: 28499146 DOI: 10.1016/j.neurobiolaging.2017.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/31/2017] [Accepted: 04/08/2017] [Indexed: 12/12/2022]
Abstract
Normal aging is associated with impairments in cognitive functions. These alterations are caused by diminutive changes in the biology of synapses, and ineffective neurotransmission, rather than loss of neurons. Hitherto, only a few studies, exploring molecular mechanisms of healthy brain aging in higher vertebrates, utilized synaptosomal fractions to survey local changes in aging-related transcriptome dynamics. Here we present, for the first time, a comparative analysis of the synaptosomes transcriptome in the aging mouse brain using RNA sequencing. Our results show changes in the expression of genes contributing to biological pathways related to neurite guidance, synaptosomal physiology, and RNA splicing. More intriguingly, we also discovered alterations in the expression of thousands of novel, unannotated lincRNAs during aging. Further, detailed characterization of the cleavage and polyadenylation factor I subunit 1 (Clp1) mRNA and protein expression indicates its increased expression in neuronal processes of hippocampal stratum radiatum in aging mice. Together, our study uncovers a new layer of transcriptional regulation which is targeted by aging within the local environment of interconnecting neuronal cells.
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Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Uwe Ueberham
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - James D Mills
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ludmil Kirazov
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany; Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Evgeni Kirazov
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany; Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Mara Knobloch
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Jana Bochmann
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Renate Jendrek
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicola Bliim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas Arendt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Venkatachari NJ, Jain S, Walker L, Bivalkar-Mehla S, Chattopadhyay A, Bar-Joseph Z, Rinaldo C, Ragin A, Seaberg E, Levine A, Becker J, Martin E, Sacktor N, Ayyavoo V. Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men. AIDS 2017; 31:623-633. [PMID: 28005686 PMCID: PMC5389669 DOI: 10.1097/qad.0000000000001379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVE HIV-1 viral proteins and host inflammatory factors have a direct role in neuronal toxicity in vitro; however, the contribution of these factors in vivo in HIV-1-associated neurocognitive disorder (HAND) is not fully understood. We applied novel Systems Biology approaches to identify specific cellular and viral factors and their related pathways that are associated with different stages of HAND. DESIGN A cross-sectional study of individuals enrolled in the Multicenter AIDS Cohort Study including HIV-1-seronegative (N = 36) and HIV-1-seropositive individuals without neurocognitive symptoms (N = 16) or with mild neurocognitive disorder (MND) (N = 8) or HIV-associated dementia (HAD) (N = 16). METHODS A systematic evaluation of global transcriptome of peripheral blood mononuclear cells (PBMCs) obtained from HIV-1-seronegative individuals and from HIV-1-positive men without neurocognitive symptoms, or MND or HAD was performed. RESULTS MND and HAD were associated with specific changes in mRNA transcripts and microRNAs in PBMCs. Comparison of upstream regulators and TimePath analyses identified specific cellular factors associated with MND and HAD, whereas HIV-1 viral proteins played a greater role in HAD. In addition, expression of specific microRNAs - miR-let-7a, miR-124, miR-15a and others - were found to correlate with mRNA gene expression and may have a potential protective role in asymptomatic HIV-1-seropositive individuals by regulating cellular signal transduction pathways downstream of chemokines and cytokines. CONCLUSION These results identify signature transcriptome changes in PBMCs associated with stages of HAND and shed light on the potential contribution of host cellular factors and viral proteins in HAND development.
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Affiliation(s)
- Narasimhan J. Venkatachari
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Siddhartha Jain
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15217, USA
| | - Leah Walker
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Shalmali Bivalkar-Mehla
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ansuman Chattopadhyay
- Molecular Biology Information Service, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA
| | - Ziv Bar-Joseph
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15217, USA
| | - Charles Rinaldo
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ann Ragin
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Suite 1600, 737 N. Michigan Ave, Chicago, IL 60611, USA
| | - Eric Seaberg
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21209, USA
| | - Andrew Levine
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, CA 90095
| | - James Becker
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Eileen Martin
- Department of Psychiatry, Rush University Medical Center, 1645 W Jackson Blvd, Chicago, IL, 60612, USA
| | - Ned Sacktor
- Department of Neurology, Johns Hopkins Bayview Medical Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21209, USA
| | - Velpandi Ayyavoo
- Department of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
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Li GD, Bi R, Zhang DF, Xu M, Luo R, Wang D, Fang Y, Li T, Zhang C, Yao YG. Female-specific effect of the BDNF gene on Alzheimer's disease. Neurobiol Aging 2017; 53:192.e11-192.e19. [PMID: 28202203 DOI: 10.1016/j.neurobiolaging.2016.12.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/21/2016] [Accepted: 12/24/2016] [Indexed: 02/05/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease influenced by genetic and environmental factors. Brain-derived neurotrophic factor (BDNF) plays an important role in the progression of AD, but the genetic association between BDNF and AD remains controversial. In this study, we aimed to explore the potential association between genetic variants in BDNF and AD in Han Chinese and to investigate whether the association is affected by gender. A 3-stage study was conducted to evaluate the genetic association between BDNF and AD. Data mining of the reported expression data, brain-imaging data, and biomarker data in AD patients was also performed to further validate the results. We found a female-specific genetic association of rs6265 with AD and a gender-related messenger RNA expression of BDNF in brain tissues of AD patients. In addition, we observed a clear female-specific risk trend for the effect of rs6265 on AD endophenotypes. Our results clarified the available controversies regarding the role of rs6265 in AD and indicated that BDNF may be a female-specific risk gene for AD.
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Affiliation(s)
- Guo-Dong Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Rongcan Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | | | - Yiru Fang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Li
- The Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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Functional Maturation of Human Stem Cell-Derived Neurons in Long-Term Cultures. PLoS One 2017; 12:e0169506. [PMID: 28052116 PMCID: PMC5215418 DOI: 10.1371/journal.pone.0169506] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022] Open
Abstract
Differentiated neurons can be rapidly acquired, within days, by inducing stem cells to express neurogenic transcription factors. We developed a protocol to maintain long-term cultures of human neurons, called iNGNs, which are obtained by inducing Neurogenin-1 and Neurogenin-2 expression in induced pluripotent stem cells. We followed the functional development of iNGNs over months and they showed many hallmark properties for neuronal maturation, including robust electrical and synaptic activity. Using iNGNs expressing a variant of channelrhodopsin-2, called CatCh, we could control iNGN activity with blue light stimulation. In combination with optogenetic tools, iNGNs offer opportunities for studies that require precise spatial and temporal resolution. iNGNs developed spontaneous network activity, and these networks had excitatory glutamatergic synapses, which we characterized with single-cell synaptic recordings. AMPA glutamatergic receptor activity was especially dominant in postsynaptic recordings, whereas NMDA glutamatergic receptor activity was absent from postsynaptic recordings but present in extrasynaptic recordings. Our results on long-term cultures of iNGNs could help in future studies elucidating mechanisms of human synaptogenesis and neurotransmission, along with the ability to scale-up the size of the cultures.
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46
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Kroes RA, Nilsson CL. Towards the Molecular Foundations of Glutamatergic-targeted Antidepressants. Curr Neuropharmacol 2017; 15:35-46. [PMID: 26955966 PMCID: PMC5327457 DOI: 10.2174/1570159x14666160309114740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 05/08/2015] [Accepted: 01/30/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Depression affects over 120 million individuals of all ages and is the leading cause of disability worldwide. The lack of objective diagnostic criteria, together with the heterogeneity of the depressive disorder itself, makes it challenging to develop effective therapies. The accumulation of preclinical data over the past 20 years derived from a multitude of models using many divergent approaches, has fueled the resurgence of interest in targeting glutamatergic neurotransmission for the treatment of major depression. OBJECTIVE The emergence of mechanistic studies are advancing our understanding of the molecular underpinnings of depression. While clearly far from complete and conclusive, they offer the potential to lead to the rational design of more specific therapeutic strategies and the development of safer and more effective rapid acting, long lasting antidepressants. METHODS The development of comprehensive omics-based approaches to the dysregulation of synaptic transmission and plasticity that underlies the core pathophysiology of MDD are reviewed to illustrate the fundamental elements. RESULTS This review frames the rationale for the conceptualization of depression as a "pathway disease". As such, it culminates in the call for the development of novel state-of-the-art "-omics approaches" and neurosystems biological techniques necessary to advance our understanding of spatiotemporal interactions associated with targeting glutamatergic-triggered signaling in the CNS. CONCLUSION These technologies will enable the development of novel psychiatric medications specifically targeted to impact specific, critical intracellular networks in a more focused manner and have the potential to offer new dimensions in the area of translational neuropsychiatry.
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Affiliation(s)
- Roger A. Kroes
- Naurex, Inc., 1801 Maple Street, Evanston, Illinois 60201, United States
| | - Carol L. Nilsson
- Department of Pharmacology & Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555-1074, United States
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Freyburger M, Pierre A, Paquette G, Bélanger-Nelson E, Bedont J, Gaudreault PO, Drolet G, Laforest S, Blackshaw S, Cermakian N, Doucet G, Mongrain V. EphA4 is Involved in Sleep Regulation but Not in the Electrophysiological Response to Sleep Deprivation. Sleep 2016; 39:613-24. [PMID: 26612390 DOI: 10.5665/sleep.5538] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/15/2015] [Indexed: 01/10/2023] Open
Abstract
STUDY OBJECTIVES Optimal sleep is ensured by the interaction of circadian and homeostatic processes. Although synaptic plasticity seems to contribute to both processes, the specific players involved are not well understood. The EphA4 tyrosine kinase receptor is a cell adhesion protein regulating synaptic plasticity. We investigated the role of EphA4 in sleep regulation using electrocorticography in mice lacking EphA4 and gene expression measurements. METHODS EphA4 knockout (KO) mice, Clock(Δ19/Δ19) mutant mice and littermates, C57BL/6J and CD-1 mice, and Sprague-Dawley rats were studied under a 12 h light: 12 h dark cycle, under undisturbed conditions or 6 h sleep deprivation (SLD), and submitted to a 48 h electrophysiological recording and/or brain sampling at different time of day. RESULTS EphA4 KO mice showed less rapid eye movement sleep (REMS), enhanced duration of individual bouts of wakefulness and nonrapid eye movement sleep (NREMS) during the light period, and a blunted daily rhythm of NREMS sigma activity. The NREMS delta activity response to SLD was unchanged in EphA4 KO mice. However, SLD increased EphA4 expression in the thalamic/hypothalamic region in C57BL/6J mice. We further show the presence of E-boxes in the promoter region of EphA4, a lower expression of EphA4 in Clock mutant mice, a rhythmic expression of EphA4 ligands in several brain areas, expression of EphA4 in the suprachiasmatic nuclei of the hypothalamus (SCN), and finally an unchanged number of cells expressing Vip, Grp and Avp in the SCN of EphA4 KO mice. CONCLUSIONS Our results suggest that EphA4 is involved in circadian sleep regulation.
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Affiliation(s)
- Marlène Freyburger
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
| | - Audrey Pierre
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada
| | - Gabrielle Paquette
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada
| | - Erika Bélanger-Nelson
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada
| | - Joseph Bedont
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Pierre-Olivier Gaudreault
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Psychology, Université de Montréal, Montreal, QC, Canada
| | - Guy Drolet
- Centre de Recherche du CHU de Québec, Université Laval, Québec, QC, Canada
| | - Sylvie Laforest
- Centre de Recherche du CHU de Québec, Université Laval, Québec, QC, Canada
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nicolas Cermakian
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Guy Doucet
- Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
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48
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Farris SP, Pietrzykowski AZ, Miles MF, O'Brien MA, Sanna PP, Zakhari S, Mayfield RD, Harris RA. Applying the new genomics to alcohol dependence. Alcohol 2015; 49:825-36. [PMID: 25896098 PMCID: PMC4586299 DOI: 10.1016/j.alcohol.2015.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 12/15/2022]
Abstract
This review summarizes the proceedings of a symposium presented at the "Alcoholism and Stress: A Framework for Future Treatment Strategies" conference held in Volterra, Italy on May 6-9, 2014. The overall goal of the symposium titled "Applying the New Genomics to Alcohol Dependence", chaired by Dr. Adron Harris, was to highlight recent genomic discoveries and applications for profiling alcohol use disorder (AUD). Dr. Sean Farris discussed the gene expression networks related to lifetime consumption of alcohol within human prefrontal cortex. Dr. Andrzej Pietrzykowski presented the effects of alcohol on microRNAs in humans and animal models. Alcohol-induced alterations in the synaptic transcriptome were discussed by Dr. Michael Miles. Dr. Pietro Sanna examined methods to probe the gene regulatory networks that drive excessive alcohol drinking, and Dr. Samir Zakhari served as a panel discussant and summarized the proceedings. Collectively, the presentations emphasized the power of integrating multiple levels of genetics and transcriptomics with convergent biological processes and phenotypic behaviors to determine causal factors of AUD. The combined use of diverse data types demonstrates how unique approaches and applications can help categorize genetic complexities into relevant biological networks using a systems-level model of disease.
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Affiliation(s)
- Sean P Farris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, Austin, TX 78712, USA
| | - Andrzej Z Pietrzykowski
- Department of Animal Sciences, Rutgers University, New Brunswick, NJ, USA; Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Michael F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Megan A O'Brien
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Pietro P Sanna
- Molecular and Cellular Neuroscience Department, The Scripps Research Institute, La Jolla, CA, USA
| | - Samir Zakhari
- Office of Science, Distilled Spirits Council of the United States, Washington, DC, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, Austin, TX 78712, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, Austin, TX 78712, USA.
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49
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Weinberg RB, Mufson EJ, Counts SE. Evidence for a neuroprotective microRNA pathway in amnestic mild cognitive impairment. Front Neurosci 2015; 9:430. [PMID: 26594146 PMCID: PMC4633499 DOI: 10.3389/fnins.2015.00430] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) that regulate mRNA stability have been linked to amyloid production, tau phosphorylation, and inflammation in Alzheimer's disease (AD). However, whether cerebral miRNA networks are dysregulated during the earliest stages of AD remains underexplored. We performed miRNA expression analysis using frontal cortex tissue harvested from subjects who died with a clinical diagnosis of no cognitive impairment (NCI), amnestic mild cognitive impairment (aMCI, a putative prodromal AD stage), or mild AD. Analysis revealed that the miRNA clusters miR-212/132 and miR-23a/23b were down-regulated in the frontal cortex of aMCI subjects. Both miR-212/132 and miR23a/b are predicted to destabilize the message for sirtuin 1 (sirt1); hence, down-regulation of either miR-212/132 or miR-23a/b in frontal cortex should promote sirt1 mRNA expression in this region. qPCR studies revealed that frontal cortex levels of sirt1 were increased in aMCI. Given the ability of frontal cortex to respond to the onset of dementia by neuronal reorganization, these data suggest that miRNA-mediated up-regulation of the sirt1 pathway represents a compensatory response to the onset of the disease. By contrast, qPCR analysis of inferior temporal cortex, an area affected early in the progression of AD, showed no changes in miR-212/132, miR-23a/b, or sirt1 transcripts in the same aMCI subjects. In vitro mechanistic studies showed that coordinated down-regulation of miR-212 and miR-23a increased sirt1 protein expression and provided neuroprotection from β-amyloid toxicity in human neuronal cells. Taken together, these data suggest a novel miRNA-mediated neuroprotective pathway activated during the progression of AD that may be amenable to therapeutic manipulation.
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Affiliation(s)
- Rebecca B. Weinberg
- Department of Translational Science and Molecular Medicine, Michigan State UniversityGrand Rapids, MI, USA
| | - Elliott J. Mufson
- Department of Neurobiology, Barrow Neurological InstitutePhoenix, AZ, USA
| | - Scott E. Counts
- Department of Translational Science and Molecular Medicine, Michigan State UniversityGrand Rapids, MI, USA
- Department of Family Medicine, Michigan State UniversityGrand Rapids, MI, USA
- Hauenstein Neuroscience Center, Mercy Health Saint Mary's HospitalGrand Rapids, MI, USA
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50
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Talwar P, Sinha J, Grover S, Rawat C, Kushwaha S, Agarwal R, Taneja V, Kukreti R. Dissecting Complex and Multifactorial Nature of Alzheimer's Disease Pathogenesis: a Clinical, Genomic, and Systems Biology Perspective. Mol Neurobiol 2015; 53:4833-64. [PMID: 26351077 DOI: 10.1007/s12035-015-9390-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/11/2015] [Indexed: 01/14/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by loss of memory and other cognitive functions. AD can be classified into familial AD (FAD) and sporadic AD (SAD) based on heritability and into early onset AD (EOAD) and late onset AD (LOAD) based on age of onset. LOAD cases are more prevalent with genetically complex architecture. In spite of significant research focused on understanding the etiological mechanisms, search for diagnostic biomarker(s) and disease-modifying therapy is still on. In this article, we aim to comprehensively review AD literature on established etiological mechanisms including role of beta-amyloid and apolipoprotein E (APOE) along with promising newer etiological factors such as epigenetic modifications that have been associated with AD suggesting its multifactorial nature. As genomic studies have recently played a significant role in elucidating AD pathophysiology, a systematic review of findings from genome-wide linkage (GWL), genome-wide association (GWA), genome-wide expression (GWE), and epigenome-wide association studies (EWAS) was conducted. The availability of multi-dimensional genomic data has further coincided with the advent of computational and network biology approaches in recent years. Our review highlights the importance of integrative approaches involving genomics and systems biology perspective in elucidating AD pathophysiology. The promising newer approaches may provide reliable means of early and more specific diagnosis and help identify therapeutic interventions for LOAD.
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Affiliation(s)
- Puneet Talwar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India.,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Juhi Sinha
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Sandeep Grover
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India.,Department of Paediatrics, Division of Pneumonology-Immunology, Charité University Medical Centre, Berlin, Germany
| | - Chitra Rawat
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India.,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India
| | - Suman Kushwaha
- Institute of Human Behaviour and Allied Sciences (IHBAS), Delhi, India
| | - Rachna Agarwal
- Institute of Human Behaviour and Allied Sciences (IHBAS), Delhi, India
| | - Vibha Taneja
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
| | - Ritushree Kukreti
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) Campus, New Delhi, India. .,Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110 007, India.
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