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Zheng M, Ye H, Yang X, Shen L, Dang X, Liu X, Gong Y, Wu Q, Wang L, Ge X, Fang X, Hou B, Zhang P, Tang R, Zheng K, Huang XF, Yu Y. Probiotic Clostridium butyricum ameliorates cognitive impairment in obesity via the microbiota-gut-brain axis. Brain Behav Immun 2024; 115:565-587. [PMID: 37981012 DOI: 10.1016/j.bbi.2023.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
Obesity is a risk factor for cognitive dysfunction and neurodegenerative disease, including Alzheimer's disease (AD). The gut microbiota-brain axis is altered in obesity and linked to cognitive impairment and neurodegenerative disorders. Here, we targeted obesity-induced cognitive impairment by testing the impact of the probiotic Clostridium butyricum, which has previously shown beneficial effects on gut homeostasis and brain function. Firstly, we characterized and analyzed the gut microbial profiles of participants with obesity and the correlation between gut microbiota and cognitive scores. Then, using an obese mouse model induced by a Western-style diet (high-fat and fiber-deficient diet), the effects of Clostridium butyricum on the microbiota-gut-brain axis and hippocampal cognitive function were evaluated. Finally, fecal microbiota transplantation was performed to assess the functional link between Clostridium butyricum remodeling gut microbiota and hippocampal synaptic protein and cognitive behaviors. Our results showed that participants with obesity had gut microbiota dysbiosis characterized by an increase in phylum Proteobacteria and a decrease in Clostridium butyricum, which were closely associated with cognitive decline. In diet-induced obese mice, oral Clostridium butyricum supplementation significantly alleviated cognitive impairment, attenuated the deficit of hippocampal neurite outgrowth and synaptic ultrastructure, improved hippocampal transcriptome related to synapses and dendrites; a comparison of the effects of Clostridium butyricum in mice against human AD datasets revealed that many of the genes changes in AD were reversed by Clostridium butyricum; concurrently, Clostridium butyricum also prevented gut microbiota dysbiosis, colonic barrier impairment and inflammation, and attenuated endotoxemia. Importantly, fecal microbiota transplantation from donor-obese mice with Clostridium butyricum supplementation facilitated cognitive variables and colonic integrity compared with from donor obese mice, highlighting that Clostridium butyricum's impact on cognitive function is largely due to its ability to remodel gut microbiota. Our findings provide the first insights into the neuroprotective effects of Clostridium butyricum on obesity-associated cognitive impairments and neurodegeneration via the gut microbiota-gut-brain axis.
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Affiliation(s)
- Mingxuan Zheng
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Huaiyu Ye
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xiaoying Yang
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Lijun Shen
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xuemei Dang
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xiaoli Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Yuying Gong
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Qingyuan Wu
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Li Wang
- Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang 110033, China
| | - Xing Ge
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xiaoli Fang
- Department of Neurology, Affiliated Hospital of Xuzhou Medical University, Jiangsu 221004, China
| | - Benchi Hou
- Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang 110033, China
| | - Peng Zhang
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Renxian Tang
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Kuiyang Zheng
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China; National Experimental Demonstration Center for Basic Medicine Education, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xu-Feng Huang
- Illawarra Health and Medical Research Institute (IHMRI) and School of Medicine, University of Wollongong, NSW 2522, Australia
| | - Yinghua Yu
- Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China.
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Luckett ES, Zielonka M, Kordjani A, Schaeverbeke J, Adamczuk K, De Meyer S, Van Laere K, Dupont P, Cleynen I, Vandenberghe R. Longitudinal APOE4- and amyloid-dependent changes in the blood transcriptome in cognitively intact older adults. Alzheimers Res Ther 2023; 15:121. [PMID: 37438770 PMCID: PMC10337180 DOI: 10.1186/s13195-023-01242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/06/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND Gene expression is dysregulated in Alzheimer's disease (AD) patients, both in peripheral blood and post mortem brain. We investigated peripheral whole-blood gene (co)expression to determine molecular changes prior to symptom onset. METHODS RNA was extracted and sequenced for 65 cognitively healthy F-PACK participants (65 (56-80) years, 34 APOE4 non-carriers, 31 APOE4 carriers), at baseline and follow-up (interval: 5.0 (3.4-8.6) years). Participants received amyloid PET at both time points and amyloid rate of change derived. Accumulators were defined with rate of change ≥ 2.19 Centiloids. We performed differential gene expression and weighted gene co-expression network analysis to identify differentially expressed genes and networks of co-expressed genes, respectively, with respect to traits of interest (APOE4 status, amyloid accumulation (binary/continuous)), and amyloid positivity status, followed by Gene Ontology annotation. RESULTS There were 166 significant differentially expressed genes at follow-up compared to baseline in APOE4 carriers only, whereas 12 significant differentially expressed genes were found only in APOE4 non-carriers, over time. Among the significant genes in APOE4 carriers, several had strong evidence for a pathogenic role in AD based on direct association scores generated from the DISQOVER platform: NGRN, IGF2, GMPR, CLDN5, SMIM24. Top enrichment terms showed upregulated mitochondrial and metabolic pathways, and an exacerbated upregulation of ribosomal pathways in APOE4 carriers compared to non-carriers. Similarly, there were 33 unique significant differentially expressed genes at follow-up compared to baseline in individuals classified as amyloid negative at baseline and positive at follow-up or amyloid positive at both time points and 32 unique significant differentially expressed genes over time in individuals amyloid negative at both time points. Among the significant genes in the first group, the top five with the highest direct association scores were as follows: RPL17-C18orf32, HSP90AA1, MBP, SIRPB1, and GRINA. Top enrichment terms included upregulated metabolism and focal adhesion pathways. Baseline and follow-up gene co-expression networks were separately built. Seventeen baseline co-expression modules were derived, with one significantly negatively associated with amyloid accumulator status (r2 = - 0.25, p = 0.046). This was enriched for proteasomal protein catabolic process and myeloid cell development. Thirty-two follow-up modules were derived, with two significantly associated with APOE4 status: one downregulated (r2 = - 0.27, p = 0.035) and one upregulated (r2 = 0.26, p = 0.039) module. Top enrichment processes for the downregulated module included proteasomal protein catabolic process and myeloid cell homeostasis. Top enrichment processes for the upregulated module included cytoplasmic translation and rRNA processing. CONCLUSIONS We show that there are longitudinal gene expression changes that implicate a disrupted immune system, protein removal, and metabolism in cognitively intact individuals who carry APOE4 or who accumulate in cortical amyloid. This provides insight into the pathophysiology of AD, whilst providing novel targets for drug and therapeutic development.
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Affiliation(s)
- Emma S Luckett
- Laboratory for Cognitive Neurology, Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium
- Alzheimer Research Centre KU Leuven, Leuven Brain Institute, Leuven, 3000, Belgium
- Laboratory for Complex Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Magdalena Zielonka
- Alzheimer Research Centre KU Leuven, Leuven Brain Institute, Leuven, 3000, Belgium
- Laboratory for the Research of Neurodegenerative Diseases, VIB-KU Leuven, KU Leuven, Leuven, 3000, Belgium
| | - Amine Kordjani
- Laboratory for Complex Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Jolien Schaeverbeke
- Laboratory for Cognitive Neurology, Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium
- Alzheimer Research Centre KU Leuven, Leuven Brain Institute, Leuven, 3000, Belgium
- Laboratory of Neuropathology, Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium
| | | | - Steffi De Meyer
- Laboratory for Cognitive Neurology, Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium
- Alzheimer Research Centre KU Leuven, Leuven Brain Institute, Leuven, 3000, Belgium
- Laboratory of Molecular Neurobiomarker Research, KU Leuven, Leuven, 3000, Belgium
| | - Koen Van Laere
- Division of Nuclear Medicine, UZ Leuven, Leuven, 3000, Belgium
- Nuclear Medicine and Molecular Imaging, Department of Imaging and Pathology, KU Leuven, Leuven, 3000, Belgium
| | - Patrick Dupont
- Laboratory for Cognitive Neurology, Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium
- Alzheimer Research Centre KU Leuven, Leuven Brain Institute, Leuven, 3000, Belgium
| | - Isabelle Cleynen
- Laboratory for Complex Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Leuven Brain Institute, KU Leuven, Leuven, 3000, Belgium.
- Alzheimer Research Centre KU Leuven, Leuven Brain Institute, Leuven, 3000, Belgium.
- Neurology Department, University Hospitals Leuven, Herestraat 49, Leuven, 3000, Belgium.
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Killick R, Elliott C, Ribe E, Broadstock M, Ballard C, Aarsland D, Williams G. Neurodegenerative Disease Associated Pathways in the Brains of Triple Transgenic Alzheimer's Model Mice Are Reversed Following Two Weeks of Peripheral Administration of Fasudil. Int J Mol Sci 2023; 24:11219. [PMID: 37446396 PMCID: PMC10342807 DOI: 10.3390/ijms241311219] [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: 06/06/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The pan Rho-associated coiled-coil-containing protein kinase (ROCK) inhibitor fasudil acts as a vasodilator and has been used as a medication for post-cerebral stroke for the past 29 years in Japan and China. More recently, based on the involvement of ROCK inhibition in synaptic function, neuronal survival, and processes associated with neuroinflammation, it has been suggested that the drug may be repurposed for neurodegenerative diseases. Indeed, fasudil has demonstrated preclinical efficacy in many neurodegenerative disease models. To facilitate an understanding of the wider biological processes at play due to ROCK inhibition in the context of neurodegeneration, we performed a global gene expression analysis on the brains of Alzheimer's disease model mice treated with fasudil via peripheral IP injection. We then performed a comparative analysis of the fasudil-driven transcriptional profile with profiles generated from a meta-analysis of multiple neurodegenerative diseases. Our results show that fasudil tends to drive gene expression in a reverse sense to that seen in brains with post-mortem neurodegenerative disease. The results are most striking in terms of pathway enrichment analysis, where pathways perturbed in Alzheimer's and Parkinson's diseases are overwhelmingly driven in the opposite direction by fasudil treatment. Thus, our results bolster the repurposing potential of fasudil by demonstrating an anti-neurodegenerative phenotype in a disease context and highlight the potential of in vivo transcriptional profiling of drug activity.
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Affiliation(s)
- Richard Killick
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
- College of Medicine and Health, University of Exeter, Exeter EX1 2UL, UK;
| | - Christina Elliott
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Elena Ribe
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
| | - Martin Broadstock
- Wolfson CARD, King’s College London, London Bridge, London SE1 1UL, UK;
| | - Clive Ballard
- College of Medicine and Health, University of Exeter, Exeter EX1 2UL, UK;
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
| | - Gareth Williams
- Wolfson CARD, King’s College London, London Bridge, London SE1 1UL, UK;
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Transcriptional Profiling of Hippocampus Identifies Network Alterations in Alzheimer’s Disease. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12105035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease characterized by rapid brain cell degeneration affecting different areas of the brain. Hippocampus is one of the earliest involved brain regions in the disease. Modern technologies based on high-throughput data have identified transcriptional profiling of several neurological diseases, including AD, for a better comprehension of genetic mechanisms of the disease. In this study, we investigated differentially expressed genes (DEGs) from six Gene Expression Omnibus (GEO) datasets of hippocampus of AD patients. The identified DEGs were submitted to Weighted correlation network analysis (WGCNA) and ClueGo to explore genes with a higher degree centrality and to comprehend their biological role. Subsequently, MCODE was used to identify subnetworks of interconnected DEGs. Our study found 40 down-regulated genes and 36 up-regulated genes as consensus DEGs. Analysis of the co-expression network revealed ACOT7, ATP8A2, CDC42, GAD1, GOT1, INA, NCALD, and WWTR1 to be genes with a higher degree centrality. ClueGO revealed the pathways that were mainly enriched, such as clathrin coat assembly, synaptic vesicle endocytosis, and DNA damage response signal transduction by p53 class mediator. In addition, we found a subnetwork of 12 interconnected genes (AMPH, CA10, CALY, NEFL, SNAP25, SNAP91, SNCB, STMN2, SV2B, SYN2, SYT1, and SYT13). Only CA10 and CALY are targets of known drugs while the others could be potential novel drug targets.
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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: 0] [Impact Index Per Article: 0] [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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Wang XL, Li L. Cell type-specific potential pathogenic genes and functional pathways in Alzheimer's Disease. BMC Neurol 2021; 21:381. [PMID: 34600516 PMCID: PMC8487122 DOI: 10.1186/s12883-021-02407-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/28/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a pervasive age-related and highly heritable neurodegenerative disorder but has no effective therapy. The complex cellular microenvironment in the AD brain impedes our understanding of pathogenesis. Thus, a comprehensive investigation of cell type-specific responses in AD is crucial to provide precise molecular and cellular targets for therapeutic development. METHODS Here, we integrated analyzed 4,441 differentially expressed genes (DEGs) that were identified from 263,370 single-cells in cortex samples by single-nucleus RNA sequencing (snRNA-seq) between 42 AD-pathology subjects and 39 normal controls within 3 studies. DEGs were analyzed in microglia, astrocytes, oligodendrocytes, excitatory neurons, inhibitory neurons, and endothelial cells, respectively. In each cell type, we identified both common DEGs which were observed in all 3 studies, and overlapping DEGs which have been seen in at least 2 studies. Firstly, we showed the common DEGs expression and explained the biological functions by comparing with existing literature or multil-omics signaling pathways knowledgebase. We then determined the significant modules and hub genes, and explored the biological processes using the overlapping DEGs. Finally, we identified the common and distinct dysregulated pathways using overall DEGs and overlapping DEGs in a cell type-specific manner. RESULTS Up-regulated LINGO1 has been seen in both oligodendrocytes and excitatory neurons across 3 studies. Interestingly, genes enriched in the mitochondrial module were up-regulated across all cell types, which indicates mitochondrial dysfunction in the AD brain. The estrogen signaling pathway seems to be the most common pathway that is disrupted in AD. CONCLUSION Together, these analyses provide detailed information of cell type-specific and overall transcriptional changes and pathways underlying the human AD-pathology. These findings may provide important insights for drug development to tackle this disease.
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Affiliation(s)
- Xiao-Lan Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Université de Strasbourg, Strasbourg, France
| | - Lianjian Li
- Department of Surgery, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061 China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430076 China
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Kikuchi M, Sekiya M, Hara N, Miyashita A, Kuwano R, Ikeuchi T, Iijima KM, Nakaya A. Disruption of a RAC1-centred network is associated with Alzheimer's disease pathology and causes age-dependent neurodegeneration. Hum Mol Genet 2021; 29:817-833. [PMID: 31942999 PMCID: PMC7191305 DOI: 10.1093/hmg/ddz320] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/28/2019] [Accepted: 12/27/2019] [Indexed: 12/21/2022] Open
Abstract
The molecular biological mechanisms of Alzheimer’s disease (AD) involve disease-associated crosstalk through many genes and include a loss of normal as well as a gain of abnormal interactions among genes. A protein domain network (PDN) is a collection of physical bindings that occur between protein domains, and the states of the PDNs in patients with AD are likely to be perturbed compared to those in normal healthy individuals. To identify PDN changes that cause neurodegeneration, we analysed the PDNs that occur among genes co-expressed in each of three brain regions at each stage of AD. Our analysis revealed that the PDNs collapsed with the progression of AD stage and identified five hub genes, including Rac1, as key players in PDN collapse. Using publicly available as well as our own gene expression data, we confirmed that the mRNA expression level of the RAC1 gene was downregulated in the entorhinal cortex (EC) of AD brains. To test the causality of these changes in neurodegeneration, we utilized Drosophila as a genetic model and found that modest knockdown of Rac1 in neurons was sufficient to cause age-dependent behavioural deficits and neurodegeneration. Finally, we identified a microRNA, hsa-miR-101-3p, as a potential regulator of RAC1 in AD brains. As the Braak neurofibrillary tangle (NFT) stage progressed, the expression levels of hsa-miR-101-3p were increased specifically in the EC. Furthermore, overexpression of hsa-miR-101-3p in the human neuronal cell line SH-SY5Y caused RAC1 downregulation. These results highlight the utility of our integrated network approach for identifying causal changes leading to neurodegeneration in AD.
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Affiliation(s)
- Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Michiko Sekiya
- Department of Alzheimer's Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan.,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Aichi 467-8603, Japan
| | - Norikazu Hara
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Ryozo Kuwano
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan.,Asahigawaso Medical-Welfare Center, Asahigawaso Research Institute, Okayama 703-8207, Japan
| | - Takeshi Ikeuchi
- Department of Molecular Genetics, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Koichi M Iijima
- Department of Alzheimer's Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan.,Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Aichi 467-8603, Japan
| | - Akihiro Nakaya
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
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Chacko S, Ladiges W. Therapeutic Targeting of Histone Deacetylation to Prevent Alzheimer's Disease. EMEDICAL RESEARCH 2021; 3:100020. [PMID: 35984647 PMCID: PMC9385167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Efforts to find disease-modifying treatments for Alzheimer's disease (AD) have been largely unsuccessful. The relative lack of progress and the age-related incidence of AD suggest that modulation of aging per se may be a useful alternative treatment approach. Therapeutics aimed at preventing or reversing aging should be effective in preventing or reversing dementia and the pathology associated with progressive AD. Epigenetic dysregulation of neuronal gene expression occurs with age, propagating deficits in cellular homeostasis. Regulators of epigenetic processes, such as histone deacetylases (HDACs), are well documented and may represent promising therapeutic targets. HDAC activity becomes dysregulated with age and in AD. An intriguing concept is that HDAC inhibition effectively forestalls AD pathology measured more broadly, addressing the notion that rectifying homeostatic gene expression may be the critical step in ameliorating AD pathogenesis at the earliest stage of disease initiation. HDAC inhibitors target several pathways associated with aging and AD neuropathology including loss of synaptic function, mitochondrial dysfunction, increased oxidative stress, and decreased autophagy activity. Since transcriptional levels of numerous genes are shown to decrease with increasing age, a recovery of their transcriptional activity through HDAC inhibition could prevent or delay age-associated declines in neurological function and provide pathways for treating AD.
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Affiliation(s)
- Sophia Chacko
- Department of Comparative Medicine, School of Medicine, University of Washington, USA
| | - Warren Ladiges
- Department of Comparative Medicine, School of Medicine, University of Washington, USA,Corresponding author: Warren Ladiges, Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, USA,
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Rocha NKR, Themoteo R, Brentani H, Forlenza OV, De Paula VDJR. Neuronal-Glial Interaction in a Triple-Transgenic Mouse Model of Alzheimer's Disease: Gene Ontology and Lithium Pathways. Front Neurosci 2020; 14:579984. [PMID: 33335468 PMCID: PMC7737403 DOI: 10.3389/fnins.2020.579984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
Neuronal-glial interactions are critical for brain homeostasis, and disruption of this process may lead to excessive glial activation and inadequate pro-inflammatory responses. Abnormalities in neuronal-glial interactions have been reported in the pathophysiology of Alzheimer’s disease (AD), where lithium has been shown to exert neuroprotective effects, including the up-regulation of cytoprotective proteins. In the present study, we characterize by Gene Ontology (GO) the signaling pathways related to neuronal-glial interactions in response to lithium in a triple-transgenic mouse model of AD (3×-TgAD). Mice were treated for 8 months with lithium carbonate (Li) supplemented to chow, using two dose ranges to yield subtherapeutic working concentrations (Li1, 1.0 g/kg; and Li2, 2.0 g/kg of chow), or with standard chow (Li0). The hippocampi were removed and analyzed by proteomics. A neuronal-glial interaction network was created by a systematic literature search, and the selected genes were submitted to STRING, a functional network to analyze protein interactions. Proteomics data and neuronal-glial interactomes were compared by GO using ClueGo (Cytoscape plugin) with p ≤ 0.05. The proportional effects of neuron-glia interactions were determined on three GO domains: (i) biological process; (ii) cellular component; and (iii) molecular function. The gene ontology of this enriched network of genes was further stratified according to lithium treatments, with statistically significant effects observed in the Li2 group (as compared to controls) for the GO domains biological process and cellular component. In the former, there was an even distribution of the interactions occurring at the following functions: “positive regulation of protein localization to membrane,” “regulation of protein localization to cell periphery,” “oligodendrocyte differentiation,” and “regulation of protein localization to plasma membrane.” In cellular component, interactions were also balanced for “myelin sheath” and “rough endoplasmic reticulum.” We conclude that neuronal-glial interactions are implicated in the neuroprotective response mediated by lithium in the hippocampus of AD-transgenic mice. The effect of lithium on homeostatic pathways mediated by the interaction between neurons and glial cells are implicated in membrane permeability, protein synthesis and DNA repair, which may be relevant for the survival of nerve cells amidst AD pathology.
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Affiliation(s)
- Nicole Kemberly R Rocha
- Laboratório de Psicobiologia (LIM23), Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael Themoteo
- Laboratorio de Neurociencias (LIM27), Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Helena Brentani
- Laboratório de Psicobiologia (LIM23), Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Orestes V Forlenza
- Laboratorio de Neurociencias (LIM27), Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Vanessa De Jesus Rodrigues De Paula
- Laboratório de Psicobiologia (LIM23), Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Laboratorio de Neurociencias (LIM27), Departamento e Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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10
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Devanarayan P, Devanarayan V, Llano DA. Identification of a Simple and Novel Cut-Point Based Cerebrospinal Fluid and MRI Signature for Predicting Alzheimer's Disease Progression that Reinforces the 2018 NIA-AA Research Framework. J Alzheimers Dis 2020; 68:537-550. [PMID: 30775985 DOI: 10.3233/jad-180905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 2018 NIA-AA research framework proposes a classification system with Amyloid-β deposition, pathologic Tau, and Neurodegeneration (ATN) for diagnosis and staging of Alzheimer's disease (AD). Data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database can be utilized to identify diagnostic signatures for predicting AD progression, and to determine the utility of this NIA-AA research framework. Profiles of 320 peptides from baseline cerebrospinal fluid (CSF) samples of 287 normal, mild cognitive impairment (MCI), and AD subjects followed over a 3-10-year period were measured via multiple reaction monitoring mass spectrometry. CSF Aβ42, total-Tau (tTau), phosphorylated-Tau (pTau-181), and hippocampal volume were also measured. From these candidate markers, optimal signatures with decision thresholds to separate AD and normal subjects were first identified via unbiased regression and tree-based algorithms. The best performing signature determined via cross-validation was then tested in an independent group of MCI subjects to predict future progression. This multivariate analysis yielded a simple diagnostic signature comprising CSF pTau-181 to Aβ42 ratio, MRI hippocampal volume, and low CSF levels of a novel PTPRN peptide, with a decision threshold on each marker. When applied to a separate MCI group at baseline, subjects meeting these signature criteria experience 4.3-fold faster progression to AD compared to a 2.2-fold faster progression using only conventional markers. This novel 4-marker signature represents an advance over the current diagnostics based on widely used markers, and is easier to use in practice than recently published complex signatures. This signature also reinforces the ATN construct from the 2018 NIA-AA research framework.
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Affiliation(s)
| | - Viswanath Devanarayan
- Charles River Laboratories, Horsham, PA, USA.,Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, IL, USA
| | - Daniel A Llano
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Carle Neuroscience Institute, Urbana, IL, USA
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11
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Williams G, Gatt A, Clarke E, Corcoran J, Doherty P, Chambers D, Ballard C. Drug repurposing for Alzheimer's disease based on transcriptional profiling of human iPSC-derived cortical neurons. Transl Psychiatry 2019; 9:220. [PMID: 31492831 PMCID: PMC6731247 DOI: 10.1038/s41398-019-0555-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/21/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Alzheimer's disease is a complex disorder encompassing multiple pathological features with associated genetic and molecular culprits. However, target-based therapeutic strategies have so far proved ineffective. The aim of this study is to develop a methodology harnessing the transcriptional changes associated with Alzheimer's disease to develop a high content quantitative disease phenotype that can be used to repurpose existing drugs. Firstly, the Alzheimer's disease gene expression landscape covering severe disease stage, early pathology progression, cognitive decline and animal models of the disease has been defined and used to select a set of 153 drugs tending to oppose disease-associated changes in the context of immortalised human cancer cell lines. The selected compounds have then been assayed in the more biologically relevant setting of iPSC-derived cortical neuron cultures. It is shown that 51 of the drugs drive expression changes consistently opposite to those seen in Alzheimer's disease. It is hoped that the iPSC profiles will serve as a useful resource for drug repositioning within the context of neurodegenerative disease and potentially aid in generating novel multi-targeted therapeutic strategies.
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Affiliation(s)
- Gareth Williams
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London, SE1 1UL, UK.
| | - Ariana Gatt
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London, SE1 1UL, UK
| | - Earl Clarke
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London, SE1 1UL, UK
| | - Jonathan Corcoran
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London, SE1 1UL, UK
| | - Patrick Doherty
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London, SE1 1UL, UK
| | - David Chambers
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London, SE1 1UL, UK
| | - Clive Ballard
- College of Medicine and Health, University of Exeter, Exeter, EX1 2LU, UK
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12
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Nygaard M, Larsen MJ, Thomassen M, McGue M, Christensen K, Tan Q, Christiansen L. Global expression profiling of cognitive level and decline in middle-aged monozygotic twins. Neurobiol Aging 2019; 84:141-147. [PMID: 31585296 DOI: 10.1016/j.neurobiolaging.2019.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/18/2019] [Accepted: 08/18/2019] [Indexed: 11/18/2022]
Abstract
Only few studies have investigated the genomewide transcriptome of normative cognitive aging. We therefore aimed at investigating blood gene expression patterns associated with cognitive aging using a population-based sample of 235 middle-aged monozygotic twin pairs with longitudinal data on cognitive function. This unique setup enabled examination of gene expression differences associated with individual and intrapair differences in cognitive level and change while controlling for underlying genetic variation and shared early environment. Overall, increased expression of several gene sets was found to strongly correlate with a lower cognitive level and cognitive decline. The most significantly correlated gene sets were related to protein metabolism, translation, RNA metabolism, infectious disease, and the immune system, which are all processes previously linked to transcription signatures of pathological and normal brain aging, and aging in blood. The results of our study thus suggest that gene expression patterns of cognitive level and decline in our sample mirror those seen in cognitively impaired individuals, which could point toward a more generic response to cognitive aging and aging in general.
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Affiliation(s)
- Marianne Nygaard
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark.
| | - Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark; Department of Clinical Research, Human Genetics, University of Southern Denmark, Odense C, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark; Department of Clinical Research, Human Genetics, University of Southern Denmark, Odense C, Denmark
| | - Matt McGue
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Kaare Christensen
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Qihua Tan
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Lene Christiansen
- The Danish Twin Registry and The Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense C, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen OE, Denmark
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13
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Lachen-Montes M, González-Morales A, Palomino M, Ausin K, Gómez-Ochoa M, Zelaya MV, Ferrer I, Pérez-Mediavilla A, Fernández-Irigoyen J, Santamaría E. Early-Onset Molecular Derangements in the Olfactory Bulb of Tg2576 Mice: Novel Insights Into the Stress-Responsive Olfactory Kinase Dynamics in Alzheimer's Disease. Front Aging Neurosci 2019; 11:141. [PMID: 31244650 PMCID: PMC6579864 DOI: 10.3389/fnagi.2019.00141] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/23/2019] [Indexed: 11/13/2022] Open
Abstract
The olfactory bulb (OB) is the first processing station in the olfactory pathway. Despite smell impairment, which is considered an early event in Alzheimer’s disease (AD), little is known about the initial molecular disturbances that accompany the AD development at olfactory level. We have interrogated the time-dependent OB molecular landscape in Tg2576 AD mice prior to the appearance of neuropathological amyloid plaques (2-, and 6-month-old), using combinatorial omics analysis. The metabolic modulation induced by overproduction of human mutated amyloid precursor protein (APP) clearly differs between both time points. Besides the progressive perturbation of the APP interactome, functional network analysis unveiled an inverse regulation of downstream extracellular signal-regulated kinase (ERK1/2), and p38 mitogen-activated protein kinase (MAPK) routes in 2-month-old Tg2576 mice with respect to wild-type (WT) mice. In contrast, Akt and MAPK kinase 4 (SEK1)/ stress-activated protein kinase (SAPK) axis were parallel activated in the OB of 6-months-old-Tg2576 mice. Furthermore, a survival kinome profiling performed during the aging process (2-, 6-, and 18-month-old) revealed that olfactory APP overexpression leads to changes in the activation dynamics of protein kinase A (PKA), and SEK1/MKK4-SAPK/JNK between 6 and 18 months of age, when memory deficits appear and AD pathology is well established in transgenic mice. Interestingly, both olfactory pathways were differentially activated in a stage-dependent manner in human sporadic AD subjects with different neuropathological grading. Taken together, our data reflect the early impact of mutated APP on the OB molecular homeostasis, highlighting the progressive modulation of specific signaling pathways during the olfactory amyloidogenic pathology.
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Affiliation(s)
- Mercedes Lachen-Montes
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Andrea González-Morales
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Maialen Palomino
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Karina Ausin
- Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Marta Gómez-Ochoa
- Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - María Victoria Zelaya
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Isidro Ferrer
- Institut de Neuropatologia, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Alberto Pérez-Mediavilla
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,Proteored-ISCIII Proteomics Unit, NavarraBiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
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14
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The exploration of novel Alzheimer's therapeutic agents from the pool of FDA approved medicines using drug repositioning, enzyme inhibition and kinetic mechanism approaches. Biomed Pharmacother 2018; 109:2513-2526. [PMID: 30551512 DOI: 10.1016/j.biopha.2018.11.115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/19/2018] [Accepted: 11/25/2018] [Indexed: 12/11/2022] Open
Abstract
Novel drug development is onerous, time consuming and overpriced process with particularly low success and relatively high enfeebling rates. To overcome this burden, drug repositioning approach is being used to predict the possible therapeutic effects of FDA approved drugs in different diseases. Herein, we designed a computational and enzyme inhibitory mechanistic approach to fetch the promising drugs from the pool of FDA approved drugs against AD. The binding interaction patterns and conformations of screened drugs within active region of AChE were confirmed through molecular docking profiles. The possible associations of selected drugs with AD genes were predicted by pharmacogenomics analysis and confirmed through data mining. The stability behaviour of docked complexes (Drugs-AChE) were checked by MD simulations. The possible therapeutic potential of repositioned drugs against AChE were checked by in vitro analysis. Taken together, Cinitapride displayed a comparable results with standard and can be used as possible therapeutic agent in the treatment of AD.
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15
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Zolochevska O, Taglialatela G. Non-Demented Individuals with Alzheimer's Disease Neuropathology: Resistance to Cognitive Decline May Reveal New Treatment Strategies. Curr Pharm Des 2017; 22:4063-8. [PMID: 27189599 DOI: 10.2174/1381612822666160518142110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/17/2016] [Indexed: 11/22/2022]
Abstract
Alzheimer's disease (AD) is a terminal neurodegenerative disorder that is characterized by accumulation of amyloid plaques and neurofibrillary tangles in the central nervous system. However, certain individuals remain cognitively intact despite manifestation of substantial plaques and tangles consistent with what would be normally associated with fully symptomatic AD. Mechanisms that allow these subjects to escape dementia remain unresolved and understanding such protective biological processes could reveal novel targets for the development of effective treatments for AD. In this review article we discuss potential compensatory mechanisms that allow these individuals to remain cognitively intact despite the typical AD neuropathology.
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Affiliation(s)
- Olga Zolochevska
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, USA.
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16
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Palomino-Alonso M, Lachén-Montes M, González-Morales A, Ausín K, Pérez-Mediavilla A, Fernández-Irigoyen J, Santamaría E. Network-Driven Proteogenomics Unveils an Aging-Related Imbalance in the Olfactory IκBα-NFκB p65 Complex Functionality in Tg2576 Alzheimer's Disease Mouse Model. Int J Mol Sci 2017; 18:ijms18112260. [PMID: 29077059 PMCID: PMC5713230 DOI: 10.3390/ijms18112260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 01/12/2023] Open
Abstract
Olfaction is often deregulated in Alzheimer’s disease (AD) patients, and is also impaired in transgenic Tg2576 AD mice, which overexpress the Swedish mutated form of human amyloid precursor protein (APP). However, little is known about the molecular mechanisms that accompany the neurodegeneration of olfactory structures in aged Tg2576 mice. For that, we have applied proteome- and transcriptome-wide approaches to probe molecular disturbances in the olfactory bulb (OB) dissected from aged Tg2576 mice (18 months of age) as compared to those of age matched wild-type (WT) littermates. Some over-represented biological functions were directly relevant to neuronal homeostasis and processes of learning, cognition, and behavior. In addition to the modulation of CAMP responsive element binding protein 1 (CREB1) and APP interactomes, an imbalance in the functionality of the IκBα-NFκB p65 complex was observed during the aging process in the OB of Tg2576 mice. At two months of age, the phosphorylated isoforms of olfactory IκBα and NFκB p65 were inversely regulated in transgenic mice. However, both phosphorylated proteins were increased at 6 months of age, while a specific drop in IκBα levels was detected in 18-month-old Tg2576 mice, suggesting a transient activation of NFκB in the OB of Tg2576 mice. Taken together, our data provide a metabolic map of olfactory alterations in aged Tg2576 mice, reflecting the progressive effect of APP overproduction and β-amyloid (Aβ) accumulation on the OB homeostasis in aged stages.
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Affiliation(s)
- Maialen Palomino-Alonso
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarra Institute for Health Research, 31008 Pamplona, Spain.
| | - Andrea González-Morales
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarra Institute for Health Research, 31008 Pamplona, Spain.
| | - Karina Ausín
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarra Institute for Health Research, 31008 Pamplona, Spain.
| | - Alberto Pérez-Mediavilla
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarra Institute for Health Research, 31008 Pamplona, Spain.
- Neurobiology of Alzheimer's Disease, Neurosciences Division, Center for Applied Medical Research (CIMA), Department of Biochemistry, University of Navarra, 31008 Pamplona, Spain.
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarra Institute for Health Research, 31008 Pamplona, Spain.
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, 31008 Pamplona, Spain.
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Navarra Institute for Health Research, 31008 Pamplona, Spain.
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17
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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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18
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Lachen-Montes M, Zelaya MV, Segura V, Fernández-Irigoyen J, Santamaría E. Progressive modulation of the human olfactory bulb transcriptome during Alzheimer´s disease evolution: novel insights into the olfactory signaling across proteinopathies. Oncotarget 2017; 8:69663-69679. [PMID: 29050232 PMCID: PMC5642507 DOI: 10.18632/oncotarget.18193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/07/2017] [Indexed: 01/01/2023] Open
Abstract
Alzheimer´s disease (AD) is characterized by progressive dementia, initially presenting olfactory dysfunction. Despite the olfactory bulb (OB) is the first central structure of the olfactory pathway, we lack a complete molecular characterization of the transcriptional events that occurs in this olfactory area during AD progression. To address this gap in knowledge, we have assessed the genome-wide expression in postmortem OBs from subjects with varying degree of AD pathology. A stage-dependent deregulation of specific pathways was observed, revealing transmembrane transport, and neuroinflammation as part of the functional modules that are disrupted across AD grading. Potential drivers of neurodegeneration predicted by network-driven transcriptomics were monitored across different types of dementia, including progressive supranuclear palsy (PSP), mixed dementia, and frontotemporal lobar degeneration (FTLD). Epidermal growth factor receptor (EGFR) expression was significantly increased in the OB of AD and mixed dementia subjects. Moreover, a significant increment in the activation of signal transducer and activator of transcription 3 (STAT3) was exclusively detected in advanced AD stages, whereas total STAT3 levels were specifically overexpressed in mixed dementia. Furthermore, transcription factors deregulated in the OB of mixed dementia subjects such as cAMP Responsive Element Binding Protein 1 (CREB1) and AP-1 Transcription Factor Subunit (c-Jun) were not differentially modulated at olfactory level across AD grading. On the other hand, olfactory expression of this signal transducer panel was unchanged in PSP and FTLD subjects. Taken together, this study unveils cross-disease similarities and differences for specific signal transducers, providing mechanistic clues to the intriguing divergence of AD pathology across proteinopathies.
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Affiliation(s)
- Mercedes Lachen-Montes
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María Victoria Zelaya
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Pathological Anatomy Department, Navarra Hospital Complex, Pamplona, Spain
| | - Víctor Segura
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Bioinformatics Unit, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, Pamplona, Spain.,IDISNA, Navarra Institute for Health Research, Pamplona, Spain.,Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Departamento de Salud, Universidad Pública de Navarra, Pamplona, Spain
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19
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Age and Alzheimer's disease gene expression profiles reversed by the glutamate modulator riluzole. Mol Psychiatry 2017; 22:296-305. [PMID: 27021815 PMCID: PMC5042881 DOI: 10.1038/mp.2016.33] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/27/2016] [Accepted: 02/12/2016] [Indexed: 01/21/2023]
Abstract
Alzheimer's disease (AD) and age-related cognitive decline represent a growing health burden and involve the hippocampus, a vulnerable brain region implicated in learning and memory. To understand the molecular effects of aging on the hippocampus, this study characterized the gene expression changes associated with aging in rodents using RNA-sequencing (RNA-seq). The glutamate modulator, riluzole, which was recently shown to improve memory performance in aged rats, prevented many of the hippocampal age-related gene expression changes. A comparison of the effects of riluzole in rats against human AD data sets revealed that many of the gene changes in AD are reversed by riluzole. Expression changes identified by RNA-Seq were validated by qRT-PCR open arrays. Riluzole is known to increase the glutamate transporter EAAT2's ability to scavenge excess glutamate, regulating synaptic transmission. RNA-seq and immunohistochemistry confirmed an increase in EAAT2 expression in hippocampus, identifying a possible mechanism underlying the improved memory function after riluzole treatment.
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20
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Mendes-Silva AP, Pereira KS, Tolentino-Araujo GT, Nicolau EDS, Silva-Ferreira CM, Teixeira AL, Diniz BS. Shared Biologic Pathways Between Alzheimer Disease and Major Depression: A Systematic Review of MicroRNA Expression Studies. Am J Geriatr Psychiatry 2016; 24:903-12. [PMID: 27591915 DOI: 10.1016/j.jagp.2016.07.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/12/2016] [Accepted: 07/01/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The clinical-epidemiological relationship between major depressive disorder (MDD) and Alzheimer disease (AD) suggests that they may share common neurobiologic abnormalities. METHODS The authors conducted a systematic review and identified microRNAs abnormally expressed in both AD and MDD. The pattern of microRNA regulation in each disorder and the genes regulated by each microRNA and the biologic processes and pathways regulated by these genes were identified. RESULTS Seventy-four microRNAs were abnormally expressed in AD and 30 in MDD; 7 were common for both disorders (hsa-let-7f-5p, hsa-miR-664a-3p, hsa-miR-361-5p, hsa-let-7g-5p, hsa-let-7d-5p, hsa-miR-191-5p, hsa-miR-26b-5p). These microRNAs interact with 45 validated genes, and the main biologic pathways and processes regulated by them were proteostasis control, maintenance of genomic integrity, regulation of transcriptional activity, immune-inflammatory control, and neurotrophic support. CONCLUSION The current results suggest that the maintenance of genomic integrity, proteostasis control, immune-inflammatory regulation, and neurotrophic support are key neurobiologic links between these conditions. A comprehensive hypothetical model for the interaction between MDD, aging, and the development of AD is provided.
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Affiliation(s)
- Ana Paula Mendes-Silva
- Graduate Program in Molecular Medicine, Federal University of Minas Gerais School of Medicine, Belo Horizonte, MG, Brazil
| | - Kelly Silva Pereira
- Graduate Program in Molecular Medicine, Federal University of Minas Gerais School of Medicine, Belo Horizonte, MG, Brazil
| | | | - Eduardo de Souza Nicolau
- Graduate Program in Molecular Medicine, Federal University of Minas Gerais School of Medicine, Belo Horizonte, MG, Brazil
| | - Camila Moreira Silva-Ferreira
- Graduate Program in Molecular Medicine, Federal University of Minas Gerais School of Medicine, Belo Horizonte, MG, Brazil
| | - Antonio Lucio Teixeira
- Department of Psychiatry and Behavioral Sciences, University of Texas Medical Science Center at Houston, Houston, TX
| | - Breno S Diniz
- Graduate Program in Molecular Medicine, Federal University of Minas Gerais School of Medicine, Belo Horizonte, MG, Brazil; Department of Psychiatry and Behavioral Sciences, University of Texas Medical Science Center at Houston, Houston, TX.
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21
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Differential DNA Methylation of MicroRNA Genes in Temporal Cortex from Alzheimer's Disease Individuals. Neural Plast 2016; 2016:2584940. [PMID: 27213057 PMCID: PMC4861808 DOI: 10.1155/2016/2584940] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/20/2016] [Indexed: 11/17/2022] Open
Abstract
This study investigated for the first time the genomewide DNA methylation changes of noncoding RNA genes in the temporal cortex samples from individuals with Alzheimer's disease (AD). The methylome of 10 AD individuals and 10 age-matched controls were obtained using Illumina 450 K methylation array. A total of 2,095 among the 15,258 interrogated noncoding RNA CpG sites presented differential methylation, 161 of which were associated with miRNA genes. In particular, 10 miRNA CpG sites that were found to be hypermethylated in AD compared to control brains represent transcripts that have been previously associated with the disease. This miRNA set is predicted to target 33 coding genes from the neuregulin receptor complex (ErbB) signaling pathway, which is required for the neurons myelination process. For 6 of these miRNA genes (MIR9-1, MIR9-3, MIR181C, MIR124-1, MIR146B, and MIR451), the hypermethylation pattern is in agreement with previous results from literature that shows downregulation of miR-9, miR-181c, miR-124, miR-146b, and miR-451 in the AD brain. Our data implicate dysregulation of miRNA methylation as contributor to the pathogenesis of AD.
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22
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Naughton BJ, Duncan FJ, Murrey DA, Meadows AS, Newsom DE, Stoicea N, White P, Scharre DW, Mccarty DM, Fu H. Blood genome-wide transcriptional profiles reflect broad molecular impairments and strong blood-brain links in Alzheimer's disease. J Alzheimers Dis 2016; 43:93-108. [PMID: 25079797 DOI: 10.3233/jad-140606] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To date, little is known regarding the etiology and disease mechanisms of Alzheimer's disease (AD). There is a general urgency for novel approaches to advance AD research. In this study, we analyzed blood RNA from female patients with advanced AD and matched healthy controls using genome-wide gene expression microarrays. Our data showed significant alterations in 3,944 genes (≥2-fold, FDR ≤1%) in AD whole blood, including 2,932 genes that are involved in broad biological functions. Importantly, we observed abnormal transcripts of numerous tissue-specific genes in AD blood involving virtually all tissues, especially the brain. Of altered genes, 157 are known to be essential in neurological functions, such as neuronal plasticity, synaptic transmission and neurogenesis. More importantly, 205 dysregulated genes in AD blood have been linked to neurological disease, including AD/dementia and Parkinson's disease, and 43 are known to be the causative genes of 42 inherited mental retardation and neurodegenerative diseases. The detected transcriptional abnormalities also support robust inflammation, profound extracellular matrix impairments, broad metabolic dysfunction, aberrant oxidative stress, DNA damage, and cell death. While the mechanisms are currently unclear, this study demonstrates strong blood-brain correlations in AD. The blood transcriptional profiles reflect the complex neuropathological status in AD, including neuropathological changes and broad somatic impairments. The majority of genes altered in AD blood have not previously been linked to AD. We believe that blood genome-wide transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tauopathy for AD research.
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Affiliation(s)
- Bartholomew J Naughton
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - F Jason Duncan
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Darren A Murrey
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Aaron S Meadows
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - David E Newsom
- Biomedical Genomics Core, Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Nicoleta Stoicea
- Division of Cognitive Neurology, Forest Hills Center for Alzheimer's Disease, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA Department of Neurology, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
| | - Peter White
- Biomedical Genomics Core, Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
| | - Douglas W Scharre
- Division of Cognitive Neurology, Forest Hills Center for Alzheimer's Disease, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA Department of Neurology, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
| | - Douglas M Mccarty
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
| | - Haiyan Fu
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
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23
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Saura CA, Parra-Damas A, Enriquez-Barreto L. Gene expression parallels synaptic excitability and plasticity changes in Alzheimer's disease. Front Cell Neurosci 2015; 9:318. [PMID: 26379494 PMCID: PMC4548151 DOI: 10.3389/fncel.2015.00318] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/03/2015] [Indexed: 11/14/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by abnormal accumulation of β-amyloid and tau and synapse dysfunction in memory-related neural circuits. Pathological and functional changes in the medial temporal lobe, a region essential for explicit memory encoding, contribute to cognitive decline in AD. Surprisingly, functional imaging studies show increased activity of the hippocampus and associated cortical regions during memory tasks in presymptomatic and early AD stages, whereas brain activity declines as the disease progresses. These findings suggest an emerging scenario where early pathogenic events might increase neuronal excitability leading to enhanced brain activity before clinical manifestations of the disease, a stage that is followed by decreased brain activity as neurodegeneration progresses. The mechanisms linking pathology with synaptic excitability and plasticity changes leading to memory loss in AD remain largely unclear. Recent studies suggest that increased brain activity parallels enhanced expression of genes involved in synaptic transmission and plasticity in preclinical stages, whereas expression of synaptic and activity-dependent genes are reduced by the onset of pathological and cognitive symptoms. Here, we review recent evidences indicating a relationship between transcriptional deregulation of synaptic genes and neuronal activity and memory loss in AD and mouse models. These findings provide the basis for potential clinical applications of memory-related transcriptional programs and their regulatory mechanisms as novel biomarkers and therapeutic targets to restore brain function in AD and other cognitive disorders.
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Affiliation(s)
- Carlos A. Saura
- Institut de Neurociències, Departament de Bioquímica i Biologia Molecular, Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Universitat Autònoma de BarcelonaBarcelona, Spain
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24
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Simpson JE, Ince PG, Minett T, Matthews FE, Heath PR, Shaw PJ, Goodall E, Garwood CJ, Ratcliffe LE, Brayne C, Rattray M, Wharton SB. Neuronal DNA damage response-associated dysregulation of signalling pathways and cholesterol metabolism at the earliest stages of Alzheimer-type pathology. Neuropathol Appl Neurobiol 2015; 42:167-79. [PMID: 26095650 PMCID: PMC5102584 DOI: 10.1111/nan.12252] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/02/2015] [Indexed: 12/21/2022]
Abstract
Aims Oxidative damage and an associated DNA damage response (DDR) are evident in mild cognitive impairment and early Alzheimer's disease, suggesting that neuronal dysfunction resulting from oxidative DNA damage may account for some of the cognitive impairment not fully explained by Alzheimer‐type pathology. Methods Frontal cortex (Braak stage 0–II) was obtained from the Medical Research Council's Cognitive Function and Ageing Study cohort. Neurones were isolated from eight cases (four high and four low DDR) by laser capture microdissection and changes in the transcriptome identified by microarray analysis. Results Two thousand three hundred seventy‐eight genes were significantly differentially expressed (1690 up‐regulated, 688 down‐regulated, P < 0.001) in cases with a high neuronal DDR. Functional grouping identified dysregulation of cholesterol biosynthesis, insulin and Wnt signalling, and up‐regulation of glycogen synthase kinase 3β. Candidate genes were validated by quantitative real‐time polymerase chain reaction. Cerebrospinal fluid levels of 24(S)‐hydroxycholesterol associated with neuronal DDR across all Braak stages (rs = 0.30, P = 0.03). Conclusions A persistent neuronal DDR may result in increased cholesterol biosynthesis, impaired insulin and Wnt signalling, and increased GSK3β, thereby contributing to neuronal dysfunction independent of Alzheimer‐type pathology in the ageing brain.
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Affiliation(s)
- Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Paul G Ince
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Thais Minett
- Institute of Public Health, University of Cambridge, Cambridge, UK.,Department of Radiology, University of Cambridge, Cambridge, UK
| | - Fiona E Matthews
- MRC Biostatistics Unit, Institute of Public Health, Cambridge, UK.,Institute of Health and Society, University of Newcastle, Newcastle, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Emily Goodall
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura E Ratcliffe
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Carol Brayne
- Institute of Public Health, University of Cambridge, Cambridge, UK
| | - Magnus Rattray
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK.,Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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25
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Innate immune response is differentially dysregulated between bipolar disease and schizophrenia. Schizophr Res 2015; 161:215-21. [PMID: 25487697 DOI: 10.1016/j.schres.2014.10.055] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 01/04/2023]
Abstract
Schizophrenia (SZ) and bipolar disorder (BD) are severe psychiatric conditions with a neurodevelopmental component. Genetic findings indicate the existence of an overlap in genetic susceptibility across the disorders. Also, image studies provide evidence for a shared neurobiological basis, contributing to a dimensional diagnostic approach. This study aimed to identify the molecular mechanisms that differentiate SZ and BD patients from health controls but also that distinguish both from health individuals. Comparison of gene expression profiling in post-mortem brains of both disorders and health controls (30 cases), followed by a further comparison between 29 BD and 29 SZ revealed 28 differentially expressed genes. These genes were used in co-expression analysesthat revealed the pairs CCR1/SERPINA1, CCR5/HCST, C1QA/CD68, CCR5/S100A11 and SERPINA1/TLR1 as presenting the most significant difference in co-expression between SZ and BD. Next, a protein-protein interaction (PPI) network using the 28 differentially expressed genes as seeds revealed CASP4, TYROBP, CCR1, SERPINA1, CCR5 and C1QA as having a central role in the diseases manifestation. Both co-expression and network topological analyses pointed to genes related to microglia functions. Based on this data, we suggest that differences between SZ and BP are due to genes involved with response to stimulus, defense response, immune system process and response to stress biological processes, all having a role in the communication of environmental factors to the cells and associated to microglia.
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26
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Bastos EP, Brentani H, Pasini FS, Silva ART, Torres CH, Puga RD, Olivieri EHR, Piovezani AR, Pereira CADB, Machado-Lima A, Carraro DM, Brentani MM. MicroRNAs discriminate familial from sporadic non-BRCA1/2 breast carcinoma arising in patients ≤35 years. PLoS One 2014; 9:e101656. [PMID: 25006670 PMCID: PMC4090167 DOI: 10.1371/journal.pone.0101656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/10/2014] [Indexed: 12/16/2022] Open
Abstract
The influence of genetic factors may contribute to the poor prognosis of breast cancer (BC) at a very young age. However BRCA1/2 mutations could not explain the majority of cases arising in these patients. MicroRNAs (miRs) have been implicated in biological processes associated with BC. Therefore, we investigated differences in miRs expression between tumors from young patients (≤35 years) with sporadic or familial history and non-carriers of BRCA1/2 mutations. Thirty-six young Brazilian patients were divided into 2 groups: sporadic (NF-BC) or familial breast cancer (F-BC). Most of the samples were classified as luminal A and B and the frequency of subtypes did not differ between familial or sporadic cases. Using real time qPCR and discriminant function analysis, we identified 9 miRs whose expression levels rather than miR identity can discriminate between both patient groups. Candidate predicted targets were determined by combining results from miRWalk algorithms with mRNA expression profiles (n = 91 differently expressed genes). MiR/mRNA integrated analysis identified 91 candidate genes showing positive or negative correlation to at least 1 of the 9 miRs. Co-expression analysis of these genes with 9 miRs indicated that 49 differentially co-expressed miR-gene interactions changes in F-BC tumors as compared to those of NF-BC tumors. Out of 49, 17 (34.6%) of predicted miR-gene interactions showed an inverse correlation suggesting that miRs act as post-transcriptional regulators, whereas 14 (28.6%) miR-gene pairs tended to be co-expressed in the same direction indicating that the effects exerted by these miRs pointed to a complex level of target regulation. The remaining 18 pairs were not predicted by our criteria suggesting involvement of other regulators. MiR-mRNA co-expression analysis allowed us to identify changes in the miR-mRNA regulation that were able to distinguish tumors from familial and sporadic young BC patients non-carriers of BRCA mutations.
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MESH Headings
- Adult
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/diagnosis
- Breast Neoplasms/metabolism
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Female
- Genes, BRCA1
- Genes, BRCA2
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Transcriptome
- Young Adult
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Affiliation(s)
- Elen Pereira Bastos
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of São Paulo, Medical School, São Paulo, Brazil
| | - Helena Brentani
- Laboratory of Clinical Pathology – Laboratory of Medical Investigation 23 (LIM 23), Institute and Department of Psychiatry, University of São Paulo, Medical School, São Paulo, Brazil
| | - Fatima Solange Pasini
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of São Paulo, Medical School, São Paulo, Brazil
| | - Aderbal Ruy T. Silva
- Laboratory of Clinical Pathology – Laboratory of Medical Investigation 23 (LIM 23), Institute and Department of Psychiatry, University of São Paulo, Medical School, São Paulo, Brazil
| | - Cesar Henrique Torres
- Laboratory of Clinical Pathology – Laboratory of Medical Investigation 23 (LIM 23), Institute and Department of Psychiatry, University of São Paulo, Medical School, São Paulo, Brazil
| | - Renato David Puga
- Clinical Research Center - Hospital Israelita Albert Einstein- HIAE, São Paulo, Brazil.
| | | | | | | | - Ariane Machado-Lima
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Dirce Maria Carraro
- Laboratory of Genomics and Molecular Biology, Research Center (CIPE), A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Maria Mitzi Brentani
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of São Paulo, Medical School, São Paulo, Brazil
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27
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Silva ART, Santos ACF, Farfel JM, Grinberg LT, Ferretti REL, Campos AHJFM, Cunha IW, Begnami MD, Rocha RM, Carraro DM, de Bragança Pereira CA, Jacob-Filho W, Brentani H. Repair of oxidative DNA damage, cell-cycle regulation and neuronal death may influence the clinical manifestation of Alzheimer's disease. PLoS One 2014; 9:e99897. [PMID: 24936870 PMCID: PMC4061071 DOI: 10.1371/journal.pone.0099897] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/20/2014] [Indexed: 12/26/2022] Open
Abstract
Alzheimer’s disease (AD) is characterized by progressive cognitive decline associated with a featured neuropathology (neuritic plaques and neurofibrillary tangles). Several studies have implicated oxidative damage to DNA, DNA repair, and altered cell-cycle regulation in addition to cell death in AD post-mitotic neurons. However, there is a lack of studies that systematically assess those biological processes in patients with AD neuropathology but with no evidence of cognitive impairment. We evaluated markers of oxidative DNA damage (8-OHdG, H2AX), DNA repair (p53, BRCA1, PTEN), and cell-cycle (Cdk1, Cdk4, Cdk5, Cyclin B1, Cyclin D1, p27Kip1, phospho-Rb and E2F1) through immunohistochemistry and cell death through TUNEL in autopsy hippocampal tissue samples arrayed in a tissue microarray (TMA) composed of three groups: I) “clinical-pathological AD” (CP-AD) - subjects with neuropathological AD (Braak≥IV and CERAD = B or C) and clinical dementia (CDR≥2, IQCODE>3.8); II) “pathological AD” (P-AD) - subjects with neuropathological AD (Braak≥IV and CERAD = B or C) and without cognitive impairment (CDR 0, IQCODE<3.2); and III) “normal aging” (N) - subjects without neuropathological AD (Braak≤II and CERAD 0 or A) and with normal cognitive function (CDR 0, IQCODE<3.2). Our results show that high levels of oxidative DNA damage are present in all groups. However, significant reductions in DNA repair and cell-cycle inhibition markers and increases in cell-cycle progression and cell death markers in subjects with CP-AD were detected when compared to both P-AD and N groups, whereas there were no significant differences in the studied markers between P-AD individuals and N subjects. This study indicates that, even in the setting of pathological AD, healthy cognition may be associated with a preserved repair to DNA damage, cell-cycle regulation, and cell death in post-mitotic neurons.
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Affiliation(s)
- Aderbal R. T. Silva
- Laboratory of Clinical Pathology - Laboratory of Medical Investigations 23 (LIM 23), Department and Institute of Psychiatry, University of São Paulo, Medical School, São Paulo, Brazil
| | - Ana Cecília Feio Santos
- Laboratory of Clinical Pathology - Laboratory of Medical Investigations 23 (LIM 23), Department and Institute of Psychiatry, University of São Paulo, Medical School, São Paulo, Brazil
| | - Jose M. Farfel
- Brazilian Brain Bank of the Aging Brain Study Group - Laboratory of Medical Investigations 22 (LIM 22), University of São Paulo, Medical School, São Paulo, Brazil
- Division of Geriatrics, University of São Paulo, Medical School, São Paulo, Brazil
| | - Lea T. Grinberg
- Brazilian Brain Bank of the Aging Brain Study Group - Laboratory of Medical Investigations 22 (LIM 22), University of São Paulo, Medical School, São Paulo, Brazil
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Renata E. L. Ferretti
- Brazilian Brain Bank of the Aging Brain Study Group - Laboratory of Medical Investigations 22 (LIM 22), University of São Paulo, Medical School, São Paulo, Brazil
- Division of Geriatrics, University of São Paulo, Medical School, São Paulo, Brazil
| | | | | | | | - Rafael M. Rocha
- Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Dirce M. Carraro
- Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Wilson Jacob-Filho
- Brazilian Brain Bank of the Aging Brain Study Group - Laboratory of Medical Investigations 22 (LIM 22), University of São Paulo, Medical School, São Paulo, Brazil
- Division of Geriatrics, University of São Paulo, Medical School, São Paulo, Brazil
| | - Helena Brentani
- Laboratory of Clinical Pathology - Laboratory of Medical Investigations 23 (LIM 23), Department and Institute of Psychiatry, University of São Paulo, Medical School, São Paulo, Brazil
- * E-mail:
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28
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Humphries C, Kohli MA. Rare Variants and Transcriptomics in Alzheimer disease. CURRENT GENETIC MEDICINE REPORTS 2014; 2:75-84. [PMID: 25045597 DOI: 10.1007/s40142-014-0035-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alzheimer disease (AD) is the most common dementia in the elderly, still without effective treatment. Early-onset AD (EOAD) is caused by mutations in the genes APP, PSEN1 and PSEN2. Genome-wide association studies have identified >20 late-onset AD (LOAD) susceptibility genes with common variants of small risk, with the exception of APOE. We review rare susceptibility variants in LOAD with larger effects that have been recently identified in the EOAD gene APP and the newly discovered AD genes TREM2 and PLD3. Human genetic studies now consistently support the amyloid hypothesis of AD for both EOAD and LOAD. Moreover, they identified biological processes that overlap with human transcriptomics studies in AD across different tissues, such as inflammation, cytoskeletal organization, synaptic functions, etc. Transcriptomic profiles of pre-symptomatic AD-associated variant carriers already reflect specific molecular mechanisms reminiscent to those of AD patients. This might provide an avenue for personalized medicine.
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Affiliation(s)
- Crystal Humphries
- Department of Human Genetics, John T. Macdonald Foundation, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue (BRB-531), Miami, FL 33136, USA ; John P. Hussman Institute for Human Genomics (HIHG), University of Miami, Miller School of Medicine, 1501 NW 10th Avenue (BRB-531), Miami, FL 33136, USA
| | - Martin A Kohli
- John P. Hussman Institute for Human Genomics (HIHG), University of Miami, Miller School of Medicine, 1501 NW 10th Avenue (BRB-531), Miami, FL 33136, USA
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29
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Chen F, Guan Q, Nie ZY, Jin LJ. Gene expression profile and functional analysis of Alzheimer's disease. Am J Alzheimers Dis Other Demen 2013; 28:693-701. [PMID: 24005853 PMCID: PMC10852742 DOI: 10.1177/1533317513500838] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is a complex neurodegenerative disorder with largely unknown genetic mechanisms. Identifying altered neuronal gene expression in brain regions differentially affected by AD may provide the diagnostic or therapeutic targets of AD. METHODS The gene expression profile of AD was analyzed with bioinformatics. Function analysis was performed with Database for Annotation, Visualization and Integrated Discovery (DAVID), and TransFind was used to predict the possible transcriptional regulators in AD. Finally, connectivity map (cMap) database was used to explore small molecules targeted for AD. RESULTS The AD gene signatures associated with 6 different brain regions were identified. Functional analysis revealed that biological processes involved with metabolism, protein ubiquitination, and vasculature development were found dysregulated, and synaptic signaling pathways were found perturbated in AD. The WT1 was identified as an important transcriptional regulator in AD, and cMap database predicted that small molecules, such as histone deacetylase (HDAC) inhibitor, may be candidate drugs in the treatment of AD. CONCLUSION According to our in silico analysis, Wilms' tumor suppressor may play regulatory roles in AD development and progress. The HDAC inhibitor could possibly be used to treat AD.
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Affiliation(s)
- Fei Chen
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiang Guan
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhi-Yu Nie
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ling-Jing Jin
- Department of Neurology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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30
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Kochunov P, Charlesworth J, Winkler A, Hong LE, Nichols TE, Curran JE, Sprooten E, Jahanshad N, Thompson PM, Johnson MP, Kent JW, Landman BA, Mitchell B, Cole SA, Dyer TD, Moses EK, Goring HHH, Almasy L, Duggirala R, Olvera RL, Glahn DC, Blangero J. Transcriptomics of cortical gray matter thickness decline during normal aging. Neuroimage 2013; 82:273-83. [PMID: 23707588 DOI: 10.1016/j.neuroimage.2013.05.066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/23/2013] [Accepted: 05/14/2013] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION We performed a whole-transcriptome correlation analysis, followed by the pathway enrichment and testing of innate immune response pathway analyses to evaluate the hypothesis that transcriptional activity can predict cortical gray matter thickness (GMT) variability during normal cerebral aging. METHODS Transcriptome and GMT data were available for 379 individuals (age range=28-85) community-dwelling members of large extended Mexican American families. Collection of transcriptome data preceded that of neuroimaging data by 17 years. Genome-wide gene transcriptome data consisted of 20,413 heritable lymphocytes-based transcripts. GMT measurements were performed from high-resolution (isotropic 800 μm) T1-weighted MRI. Transcriptome-wide and pathway enrichment analysis was used to classify genes correlated with GMT. Transcripts for sixty genes from seven innate immune pathways were tested as specific predictors of GMT variability. RESULTS Transcripts for eight genes (IGFBP3, LRRN3, CRIP2, SCD, IDS, TCF4, GATA3, and HN1) passed the transcriptome-wide significance threshold. Four orthogonal factors extracted from this set predicted 31.9% of the variability in the whole-brain and between 23.4 and 35% of regional GMT measurements. Pathway enrichment analysis identified six functional categories including cellular proliferation, aggregation, differentiation, viral infection, and metabolism. The integrin signaling pathway was significantly (p<10(-6)) enriched with GMT. Finally, three innate immune pathways (complement signaling, toll-receptors and scavenger and immunoglobulins) were significantly associated with GMT. CONCLUSION Expression activity for the genes that regulate cellular proliferation, adhesion, differentiation and inflammation can explain a significant proportion of individual variability in cortical GMT. Our findings suggest that normal cerebral aging is the product of a progressive decline in regenerative capacity and increased neuroinflammation.
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Affiliation(s)
- P Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, USA.
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