scholarly journals The function of SIRT3 explored through the substrate interaction network

2020 ◽  
Author(s):  
Jarmila Nahálková
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Interaction Network ◽  
Literature Mining ◽  
Biological Functions ◽  
Alcoholic Fatty Liver ◽  
Pathway Enrichment ◽  
Substrate Interaction ◽  
Lysine Deacetylase ◽  
Brown Adipose

AbstractSIRT3 is the mitochondrial protein lysine deacetylase with a prominent role in the maintenance of mitochondrial integrity vulnerable in the range of diseases. The present study examines the SIRT3 substrate interaction network for the identification of its biological functions in the cellular anti-aging mechanisms. The pathway enrichment, the protein function prediction, and the protein node prioritization analysis were performed based on 407 SIRT3 substrates, which were collected by the data mining. The substrates are interlinked by 1230 direct protein-protein interactions included in the GeneMania database. The analysis of the SIRT3 substrate interaction network highlighted Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), and non-alcoholic fatty liver disease (NAFLD) as the most associated with SIRT3 lysine deacetylase activity. The most important biological functions of SIRT3 substrates are within the respiratory electron transport chain, tricarboxylic acid cycle and fatty acid, triacylglycerol, and ketone body metabolism. In brown adipose tissue, SIRT3 activity contributes to the adaptive thermogenesis by the increase of energy production of the organisms. SIRT3 exhibits several modes of neuroprotective actions in the brain and liver including prevention of the mitochondrial damages due to the respiratory electron transfer chain failure, the quenching of ROS, the inhibition of the mitochondrial membrane potential loss, and the regulation of mitophagy. Related to its role in Alzheimer’s disease, SIRT3 activation performs as a repressor of BACE1 through SIRT3-LKB1-AMPK-CREB-PGC-1α-PPARG-BACE1 (SIRT3-BACE1) pathway, which was created based on the literature mining and by employing Wikipathways application. The pathway enrichment analysis of the extended interaction network of the SIRT3-BACE1 pathway nodes displayed the functional relation to the circadian clock, which also deteriorates during the progress of AD and it is the causative of AD, PD, and HD. The use of SIRT3 activators in combination with the stimulating effect of regular exercise is further discussed as an attractive option for the improvement of cognitive decline during aging and the progressive stages of neurodegeneration.

Identifying Alzheimer’s Disease-related miRNA Based on Semi-clustering

2019 ◽  
Vol 19 (4) ◽  
pp. 216-223 ◽  
Author(s):  
Tianyi Zhao ◽  
Donghua Wang ◽  
Yang Hu ◽  
Ningyi Zhang ◽  
Tianyi Zang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
Feature Vector ◽  
Mirna Gene ◽  
Interaction Network ◽  
Gene Interaction ◽  
Proteinprotein Interaction ◽  
Synaptic Structures

Background: More and more scholars are trying to use it as a specific biomarker for Alzheimer’s Disease (AD) and mild cognitive impairment (MCI). Multiple studies have indicated that miRNAs are associated with poor axonal growth and loss of synaptic structures, both of which are early events in AD. The overall loss of miRNA may be associated with aging, increasing the incidence of AD, and may also be involved in the disease through some specific molecular mechanisms. Objective: Identifying Alzheimer’s disease-related miRNA can help us find new drug targets, early diagnosis. Materials and Methods: We used genes as a bridge to connect AD and miRNAs. Firstly, proteinprotein interaction network is used to find more AD-related genes by known AD-related genes. Then, each miRNA’s correlation with these genes is obtained by miRNA-gene interaction. Finally, each miRNA could get a feature vector representing its correlation with AD. Unlike other studies, we do not generate negative samples randomly with using classification method to identify AD-related miRNAs. Here we use a semi-clustering method ‘one-class SVM’. AD-related miRNAs are considered as outliers and our aim is to identify the miRNAs that are similar to known AD-related miRNAs (outliers). Results and Conclusion: We identified 257 novel AD-related miRNAs and compare our method with SVM which is applied by generating negative samples. The AUC of our method is much higher than SVM and we did case studies to prove that our results are reliable.

scholarly journals Association and Gene–-Gene Interactions Study of Late-Onset Alzheimer’s Disease in the Russian Population

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1647
Author(s):  
Anna Bocharova ◽  
Kseniya Vagaitseva ◽  
Andrey Marusin ◽  
Natalia Zhukova ◽  
Irina Zhukova ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Neurodegenerative Disorder ◽  
Factor Model ◽  
Late Onset ◽  
Interaction Network ◽  
Russian Population ◽  
Protein Protein Interaction ◽  
Protective Haplotype ◽  
Single Snps

Alzheimer’s disease (AD) is a neurodegenerative disorder, and represents the most common cause of dementia. In this study, we performed several different analyses to detect loci involved in development of the late onset AD in the Russian population. DNA samples from 472 unrelated subjects were genotyped for 63 SNPs using iPLEX Assay and real-time PCR. We identified five genetic loci that were significantly associated with LOAD risk for the Russian population (TOMM40 rs2075650, APOE rs429358 and rs769449, NECTIN rs6857, APOE ε4). The results of the analysis based on comparison of the haplotype frequencies showed two risk haplotypes and one protective haplotype. The GMDR analysis demonstrated three significant models as a result: a one-factor, a two-factor and a three-factor model. A protein–protein interaction network with three subnetworks was formed for the 24 proteins. Eight proteins with a large number of interactions are identified: APOE, SORL1, APOC1, CD33, CLU, TOMM40, CNTNAP2 and CACNA1C. The present study confirms the importance of the APOE-TOMM40 locus as the main risk locus of development and progress of LOAD in the Russian population. Association analysis and bioinformatics approaches detected interactions both at the association level of single SNPs and at the level of genes and proteins.

scholarly journals Systems Pharmacological Approach to Investigate the Mechanism of Acori Tatarinowii Rhizoma for Alzheimer’s Disease

2018 ◽  
Vol 2018 ◽  
pp. 1-20 ◽  
Author(s):  
Zhenyan Song ◽  
Fang Yin ◽  
Biao Xiang ◽  
Bin Lan ◽  
Shaowu Cheng
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Biological Processes ◽  
Pathway Enrichment ◽  
Study Results ◽  
Target Network ◽  
Anti Inflammatory

In traditional Chinese medicine (TCM), Acori Tatarinowii Rhizoma (ATR) is widely used to treat memory and cognition dysfunction. This study aimed to confirm evidence regarding the potential therapeutic effect of ATR on Alzheimer’s disease (AD) using a system network level based in silico approach. Study results showed that the compounds in ATR are highly connected to AD-related signaling pathways, biological processes, and organs. These findings were confirmed by compound-target network, target-organ location network, gene ontology analysis, and KEGG pathway enrichment analysis. Most compounds in ATR have been reported to have antifibrillar amyloid plaques, anti-tau phosphorylation, and anti-inflammatory effects. Our results indicated that compounds in ATR interact with multiple targets in a synergetic way. Furthermore, the mRNA expressions of genes targeted by ATR are elevated significantly in heart, brain, and liver. Our results suggest that the anti-inflammatory and immune system enhancing effects of ATR might contribute to its major therapeutic effects on Alzheimer’s disease.

A domain level interaction network of amyloid precursor protein and Aβ of Alzheimer's disease

PROTEOMICS ◽  
2010 ◽  
Vol 10 (12) ◽  
pp. 2377-2395 ◽  
Author(s):  
Victoria M. Perreau ◽  
Sandra Orchard ◽  
Paul A. Adlard ◽  
Shayne A. Bellingham ◽  
Roberto Cappai ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Amyloid Precursor Protein ◽  
Interaction Network ◽  
Precursor Protein ◽  
Domain Level

scholarly journals Food Quality Induces a Miscible Disease with Relevance to Alzheimer’s Disease and Neurological Diseases

2016 ◽  
Vol 5 (6) ◽  
pp. 45 ◽  
Author(s):  
Ian J. Martins
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Cerebrospinal Fluid ◽  
Developing World ◽  
Neurological Diseases ◽  
Sirtuin 1 ◽  
Oncotic Pressure ◽  
Alcoholic Fatty Liver ◽  
Bacterial Lipopolysaccharides ◽  
Type 3

Food and nutrition guidelines for the handling and processing of fresh fruit, bread, and vegetables are essential and fresh produce may require cold preservation procedures to prevent minimal bacterial and fungi contamination of food. Bacterial lipopolysaccharides (LPS) corrupt lipoprotein and amyloid beta (Aβ) metabolism in diabetes, Alzheimer’s disease (AD) and various neurological diseases. In the developing world the increased plasma LPS levels induce non-alcoholic fatty liver diseases and interfere with albumin and Aβ interactions with spontaneous Aβ oligomer formation in the cerebrospinal fluid and brain that leads to neuron apoptosis by inactivation of Starling’s equation that is responsible for the maintenance of hydrostatic and oncotic pressure with relevance to fluid balance. In the developing world increased levels of LPS, mycotoxin and xenobiotics lead to irreversible neurological diseases by inhibition of Starling’s equation for maintenance of oncotic/osmotic pressure that lead to neuron senescence or apoptosis. In the developed world nutrigenomic diets are required that prevent Sirtuin 1 gene repression and maintain neuron survival that links the brain and peripheral hepatic monomer Aβ metabolism. The maintenance of blood-cerebrospinal fluid capillary transport of albumin and monomer Aβ is relevant to stabilization of neurons not only in Alzheimer’s disease but also in Type 3 diabetes and various neurological diseases. Healthy diets reverse the inhibition of brain to peripheral Aβ transport that is sensitive to Starling’s equation for regulation of central nervous system hydrostatic and oncotic pressure with the prevention of diabetes, various neurological diseases and Alzheimer’s disease.

scholarly journals Reducing the Search Space in Literature-Based Discovery by Exploring Outlier Documents: a Case Study in Finding Links Between Gut Microbiome and Alzheimer’s Disease

2017 ◽  
Vol 3 (3) ◽  
pp. 58 ◽  
Author(s):  
Bojan Cestnik ◽  
Elsa Fabbretti ◽  
Donatella Gubiani ◽  
Tanja Urbančič ◽  
Nada Lavrač
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Gut Microbiome ◽  
Domain Knowledge ◽  
Search Space ◽  
Easy Access ◽  
Literature Mining ◽  
Cross Domain ◽  
Scientific Papers ◽  
Literature Based Discovery

Literature-based discovery tools have been often used to overcome the problem of fragmentation of science and to assist researchers in their process of cross-domain knowledge discovery. In this paper we propose a methodology for cross-domain literature-based discovery that focuses on outlier documents to reduce the search space of potential cross-domain links and to improve search efficiency. In a previous study, literature mining tools OntoGen for document clustering and CrossBee for cross-domain bridging term exploration were combined to search for hidden relations in scientific papers from two different domains of interest, where the utility of the approach was demonstrated in a study involving PubMed papers about Alzheimer’s disease and gut microbiome. This paper extends the approach by proposing a methodology, implemented as a repeatable workflow in a web-based text mining platform TextFlows, which enables easy access and execution of the methodology for the interested researcher.

scholarly journals Drug Repurposing for Alzheimer’s Disease based on Protein-Protein Interaction Network

2021 ◽  
Author(s):  
Negar Sadat Soleimani Zakeri ◽  
Saeid Pashazadeh ◽  
Habib MotieGhader
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Protein Interactions ◽  
Neurodegenerative Disorder ◽  
Gentian Violet ◽  
Interaction Network ◽  
New Drugs ◽  
Bipartite Network ◽  
Medical Studies ◽  
Gene Complexes

Abstract Background: Alzheimer's disease (AD) is known as a critical neurodegenerative disorder. It worsens as symptoms concerning dementia grow severe over the years. Due to the globalization of Alzheimer’s disease, its prevention and treatment is vital. This study proposes a method to extract substantial gene complexes and accomplish an enrichment analysis to introduce the most significant biological procedures. The next step is extracting the drugs related to AD and introduce some new drugs which may be useful for this disease. Results: To this end, protein-protein interactions (PPI) network was utilized to extract five meaningful gene complexes functionally interconnected. The next step was to construct a five bipartite network representing the genes of each group and their target miRNAs. Finally, a complete network including all the genes related to each gene complex group and genes’ target drug was illustrated. medical studies and publications were analyzed thoroughly to introduce AD-related drugs. Conclusions: This analysis proves the accuracy of the proposed method in this study. Then, new drugs were introduced that can be experimentally examined as future work. RALOXIFENE, GENTIAN VIOLET are two new drugs, which have not been introduced as AD-related drugs in previous scientific and medical studies, recommended by the method of this study. These two drugs.

scholarly journals Identification of Key Genes Related with Alzheimer’s Disease Treatment Through Bioinformatics Analysis

2018 ◽  
Vol 9 (1) ◽  
pp. 78
Author(s):  
Liqun Wang ◽  
Hongjia Qian ◽  
Liqun Wang
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Protein Interaction ◽  
Expression Profiles ◽  
Amyloid Β ◽  
Interaction Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Tg2576 Mice

T0901317, a live X receptor agonist, can reduce amyloid β generation in vitro and in a mouse Alzheimer’s disease (AD) model. To investigate the global molecular effects of T0901317 in mouse hippocampus, we downloaded public GSE31624 generated from the hippocampus of wild-type mice, Tg2576 mice and T0901317-treated Tg2576 mice. Differentially-expressed genes (DEGs) were identified on LIMMA of R software. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment were analyzed through DAVID. Protein- protein interaction and hub genes were obtained based on STRING and Cytoscape. Nine downregulated and 68 upregulated DEGs in T0901317-treated Tg2576 were identified in comparison with untreated Tg2576 mice. Annotation analyses showed these DEGs correlated with transport (BP), membrane (CC) and binding (MF) terms and the dopaminergic synapse pathway. Protein-protein interaction network was built to find out some hub genes by maximal clique centrality. Discs large homolog 4 (Dlg4), the most outstanding gene, was associated with cognition improvement in aged AD mice. T0901317 may impact the development by regulating the Dlg4 expression. In conclusion, we investigated effects of T0901317 therapy on gene expression profiles in the hippocampus of Tg2576 mice and found Dlg4 may serve as putative therapeutics target for AD treatment.

scholarly journals Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer’s Disease

2020 ◽  
Vol 21 (6) ◽  
pp. 2071 ◽  
Author(s):  
Jia Xu ◽  
Fang Wang ◽  
Jiejie Guo ◽  
Chunshuang Xu ◽  
Yanzi Cao ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Brain Plasticity ◽  
Topological Analysis ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Neuroprotective Effects ◽  
Main Compound ◽  
Protein Protein Interaction ◽  
Alpinia Oxyphylla

Alpinia oxyphylla Miq. (i.e., A. oxyphylla), a traditional Chinese medicine, can exert neuroprotective effects in ameliorating mild cognitive impairment and improving the pathological hallmarks of Alzheimer’s disease (AD). Here, 50 active compounds and 164 putative targets were collected and identified with 251 clinically tested AD-associated target proteins using network pharmacology approaches. Based on the Gene Ontology/Kyoto Encyclopedia of Genes and Genomes pathway enrichments, the compound-target-pathway-disease/protein–protein interaction network constructions, and the network topological analysis, we concluded that A. oxyphylla may have neuroprotective effects by regulating neurotransmitter function, as well as brain plasticity in neuronal networks. Moreover, closely-related AD proteins, including the amyloid-beta precursor protein, the estrogen receptor 1, acetylcholinesterase, and nitric oxide synthase 2, were selected as the bottleneck nodes of network for further verification by molecular docking. Our analytical results demonstrated that terpene, as the main compound of A. oxyphylla extract, exerts neuroprotective effects, providing new insights into the development of a natural therapy for the prevention and treatment of AD.

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