Hippocampal Proteomics Profiling Along with Protein-Protein Interaction Analysis Elucidates Alzheimer's Disease Pathways and Genes

2019 ◽  
Author(s):  
Mohammad Azizur Rahman ◽  
Noorlidah Abdullah ◽  
Norhaniza Aminudin
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Protein Interaction ◽  
Interaction Analysis ◽  
Protein Protein Interaction ◽  
Disease Pathways

Putative Factors Interfering Cell Cycle Re-Entry in Alzheimer’s Disease: An Omics Study with Differential Expression Meta-Analytics and Co-Expression Profiling

2021 ◽  
pp. 1-26
Author(s):  
Sze Chung Yuen ◽  
Simon Ming-Yuen Lee ◽  
Siu-wai Leung
Keyword(s):  
Alzheimer’S Disease ◽  
Cell Cycle ◽  
Alzheimer's Disease ◽  
Expression Analysis ◽  
Protein Interaction ◽  
Meta Analysis ◽  
Differentially Expressed ◽  
Tau Proteins ◽  
Related Factors ◽  
Protein Protein Interaction

Background: Neuronal cell cycle re-entry (CCR) is a mechanism, along with amyloid-β (Aβ) oligomers and hyperphosphorylated tau proteins, contributing to toxicity in Alzheimer’s disease (AD). Objective: This study aimed to examine the putative factors in CCR based on evidence corroboration by combining meta-analysis and co-expression analysis of omic data. Methods: The differentially expressed genes (DEGs) and CCR-related modules were obtained through the differential analysis and co-expression of transcriptomic data, respectively. Differentially expressed microRNAs (DEmiRNAs) were extracted from the differential miRNA expression studies. The dysregulations of DEGs and DEmiRNAs as binary outcomes were independently analyzed by meta-analysis based on a random-effects model. The CCR-related modules were mapped to human protein-protein interaction databases to construct a network. The importance score of each node within the network was determined by the PageRank algorithm, and nodes that fit the pre-defined criteria were treated as putative CCR-related factors. Results: The meta-analysis identified 18,261 DEGs and 36 DEmiRNAs, including genes in the ubiquitination proteasome system, mitochondrial homeostasis, and CCR, and miRNAs associated with AD pathologies. The co-expression analysis identified 156 CCR-related modules to construct a protein-protein interaction network. Five genes, UBC, ESR1, EGFR, CUL3, and KRAS, were selected as putative CCR-related factors. Their functions suggested that the combined effects of cellular dyshomeostasis and receptors mediating Aβ toxicity from impaired ubiquitination proteasome system are involved in CCR. Conclusion: This study identified five genes as putative factors and revealed the significance of cellular dyshomeostasis in the CCR of AD.

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 MicroRNA-Target Interaction Regulatory Network in Alzheimer’s Disease

2021 ◽  
Vol 11 (12) ◽  
pp. 1275
Author(s):  
Aleksander Turk ◽  
Tanja Kunej ◽  
Borut Peterlin
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Neurodegenerative Disorder ◽  
Interaction Analysis ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Microrna Target ◽  
Target Interaction ◽  
Pathway Enrichment ◽  
Protein Protein Interaction

Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia; however, early diagnosis of the disease is challenging. Research suggests that biomarkers found in blood, such as microRNAs (miRNA), may be promising for AD diagnostics. Experimental data on miRNA–target interactions (MTI) associated with AD are scattered across databases and publications, thus making the identification of promising miRNA biomarkers for AD difficult. In response to this, a list of experimentally validated AD-associated MTIs was obtained from miRTarBase. Cytoscape was used to create a visual MTI network. STRING software was used for protein–protein interaction analysis and mirPath was used for pathway enrichment analysis. Several targets regulated by multiple miRNAs were identified, including: BACE1, APP, NCSTN, SP1, SIRT1, and PTEN. The miRNA with the highest numbers of interactions in the network were: miR-9, miR-16, miR-34a, miR-106a, miR-107, miR-125b, miR-146, and miR-181c. The analysis revealed seven subnetworks, representing disease modules which have a potential for further biomarker development. The obtained MTI network is not yet complete, and additional studies are needed for the comprehensive understanding of the AD-associated miRNA targetome.

scholarly journals A Comprehensive Analysis Identified Hub Genes and Associated Drugs in Alzheimer’s Disease

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Qi Jing ◽  
Hui Zhang ◽  
Xiaoru Sun ◽  
Yaru Xu ◽  
Silu Cao ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Interaction Analysis ◽  
Gene Interaction ◽  
The Elderly ◽  
Machine Learning Algorithms ◽  
Sustained Remission ◽  
Protein Protein Interaction ◽  
Interaction Database ◽  
Normal Individuals

Alzheimer’s disease (AD) is the most common neurodegenerative disease among the elderly and has become a growing global health problem causing great concern. However, the pathogenesis of AD is unclear and no specific therapeutics are available to provide the sustained remission of the disease. In this study, we used comprehensive bioinformatics to determine 158 potential genes, whose expression levels changed between the entorhinal and temporal lobe cortex samples from cognitively normal individuals and patients with AD. Then, we clustered these genes in the protein-protein interaction analysis and identified six significant genes that had more biological functions. Besides, we conducted a drug-gene interaction analysis of module genes in the drug-gene interaction database and obtained 26 existing drugs that might be applied for the prevention and treatment of AD. In addition, a predictive model was built based on the selected genes using different machine learning algorithms to identify individuals with AD. These findings may provide new insights into AD therapy.

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