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      Acupuncture Therapy on Dementia: Explained with an Integrated Analysis on Therapeutic Targets and Associated Mechanisms

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          Abstract

          Background:

          Dementia, mainly Alzheimer’s disease (AD) and vascular dementia (VaD), remains a global health challenge. Previous studies have demonstrated the benefits of acupuncture therapy (AT) in improving dementia. Nevertheless, the therapeutic targets and integrated biological mechanisms involved remain ambiguous.

          Objective:

          To identify therapeutic targets and biological mechanisms of AT in treating dementia by integrated analysis strategy.

          Methods:

          By the identification of differentially expressed genes (DEGs) of AD, VaD, and molecular targets of AT active components, the acupuncture therapeutic targets associated with the biological response to AD and VaD were extracted. Therapeutic targets-based functional enrichment analysis was conducted, and multiple networks were constructed. AT-therapeutic crucial targets were captured by weighted gene co-expression network analysis (WGCNA). The interactions between crucial targets with AT active components were verified by molecular docking.

          Results:

          Our results demonstrated that 132 and 76 acupuncture therapeutic targets were associated with AD and VaD. AT-therapeutic crucial targets including 58 for AD and 24 for VaD were captured by WGCNA, with 11 in shared, including NMU, GRP, TAC1, ADRA1D, and SST. In addition, 35 and 14 signaling pathways were significantly enriched by functional enrichment analysis, with 6 mutual pathways including neuroactive ligand-receptor interaction, GABAergic synapse, calcium signaling pathway, cAMP signaling pathway, chemokine signaling pathway, and inflammatory mediator regulation of TRP channels.

          Conclusion:

          The improvement of AD and VaD by AT was associated with modulation of synaptic function, immunity, inflammation, and apoptosis. Our study clarified the therapeutic targets of AT on dementia, providing valuable clues for complementing and combining pharmacotherapy.

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          Most cited references61

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          clusterProfiler: an R package for comparing biological themes among gene clusters.

          Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.
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            WGCNA: an R package for weighted correlation network analysis

            Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at .
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              AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

              AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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                Author and article information

                Journal
                J Alzheimers Dis
                J Alzheimers Dis
                JAD
                Journal of Alzheimer's Disease
                IOS Press (Nieuwe Hemweg 6B, 1013 BG Amsterdam, The Netherlands )
                1387-2877
                1875-8908
                06 February 2023
                25 July 2023
                2023
                : 94
                : Suppl 1 , Novel Molecular Pathways and Therapeutic Challenges in Neurodegenerative Diseases
                : S141-S158
                Affiliations
                [a ] School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine , Tianjin, China
                [b ] School of Basic Medical Sciences, Tianjin Medical University , Tianjin, China
                [c ] Department of Computer Science, RWTH Aachen University , Aachen, Germany
                [d ] School of Biomedical Engineering, Tianjin Medical University , Tianjin, China
                [e ] Aging Research Center, Department of Neurobiology, Health Care Sciences and Society Karolinska Institutet and Stockholm University , Stockholm, Sweden
                [f ] School of Integrative Medicine, Public Health Science and Engineering College, Tianjin University of Traditional Chinese Medicine , Tianjin, China
                [g ] School of Public Health, Tianjin Medical University , Tianjin, China
                Author notes
                [* ]Correspondence to: Yaogang Wang, PhD, Professor, School of Public Health, Tianjin Medical University, Qixiangtai Road 22, 300070, Tianjin, China. Tel.: +86 2259596228; Fax: +86 2259596228; Email: YaogangWANG@ 123456tmu.edu.cn .
                Article
                JAD221018
                10.3233/JAD-221018
                10473135
                36776063
                5c6843ea-96ef-44f8-b812-5139a60f39f7
                © 2023 – The authors. Published by IOS Press

                This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial (CC BY-NC 4.0) License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 11 January 2023
                Categories
                Research Article

                acupuncture,alzheimer’s disease,dementia,vascular dementia

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