Bioinformatics Analysis of ceRNA Regulatory Network in Alzheimer’s Disease

Biophysics ◽  
2022 ◽  
Vol 10 (01) ◽  
pp. 1-13
Author(s):  
壬清 李
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Regulatory Network ◽  
Bioinformatics Analysis

scholarly journals Differential Expression of mRNAs in Peripheral Blood Related to Prodrome and Progression of Alzheimer’s Disease

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Weishuang Xue ◽  
Jinwei Li ◽  
Kailei Fu ◽  
Weiyu Teng
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Gene Expression Omnibus ◽  
Venn Diagram ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks

Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease that affects the quality of life of elderly individuals, while the pathogenesis of AD is still unclear. Based on the bioinformatics analysis of differentially expressed genes (DEGs) in peripheral blood samples, we investigated genes related to mild cognitive impairment (MCI), AD, and late-stage AD that might be used for predicting the conversions. Methods. We obtained the DEGs in MCI, AD, and advanced AD patients from the Gene Expression Omnibus (GEO) database. A Venn diagram was used to identify the intersecting genes. Gene Ontology (GO) and Kyoto Gene and Genomic Encyclopedia (KEGG) were used to analyze the functions and pathways of the intersecting genes. Protein-protein interaction (PPI) networks were constructed to visualize the network of the proteins coded by the related genes. Hub genes were selected based on the PPI network. Results. Bioinformatics analysis indicated that there were 61 DEGs in both the MCI and AD groups and 27 the same DEGs among the three groups. Using GO and KEGG analyses, we found that these genes were related to the function of mitochondria and ribosome. Hub genes were determined by bioinformatics software based on the PPI network. Conclusions. Mitochondrial and ribosomal dysfunction in peripheral blood may be early signs in AD patients and related to the disease progression. The identified hub genes may provide the possibility for predicting AD progression or be the possible targets for treatments.

scholarly journals Association of microbiota-derived propionic acid and Alzheimer’s disease; bioinformatics analysis

2020 ◽  
Author(s):  
Morteza Aliashrafi ◽  
Mohammad Nasehi ◽  
Mohammad-Reza Zarrindast ◽  
Mohammad Taghi Joghataei ◽  
Hakimeh Zali ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Propionic Acid ◽  
Bioinformatics Analysis

scholarly journals Downregulation of ATP6V1A Involved in Alzheimer’s Disease via Synaptic Vesicle Cycle, Phagosome, and Oxidative Phosphorylation

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Zhike Zhou ◽  
Jun Bai ◽  
Shanshan Zhong ◽  
Rongwei Zhang ◽  
Kexin Kang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Oxidative Phosphorylation ◽  
Synaptic Vesicle ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Functional Enrichment ◽  
Gabaergic Synapse ◽  
Vesicle Cycle ◽  
Synaptic Vesicle Cycle

Objective. The objective of this study was to investigate the potential molecular mechanisms of ATPase H+ transporting V1 subunit A (ATP6V1A) underlying Alzheimer’s disease (AD). Methods. Microarray expression data of human temporal cortex samples from the GSE118553 dataset were profiled to screen for differentially expressed genes (DEGs) between AD/control and ATP6V1A-low/high groups. Correlations of coexpression modules with AD and ATP6V1A were assessed by weight gene correlation network analysis (WGCNA). DEGs strongly interacting with ATP6V1A were extracted to construct global regulatory network. Further cross-talking pathways of ATP6V1A were identified by functional enrichment analysis. Diagnostic performance of ATP6V1A in AD prediction was evaluated using area under the curve (AUC) analysis. Results. The mean expression of ATP6V1A was significantly downregulated in AD compared with nondementia controls. A total of 1,364 DEGs were overlapped from AD/control and ATP6V1A-low/high groups. Based on these DEGs, four coexpression modules were predicted by WGCNA. The blue, brown, and turquoise modules were significantly correlated with AD and low ATP6V1A, whose DEGs were enriched in phagosome, oxidative phosphorylation, synaptic vesicle cycle, focal adhesion, and gamma-aminobutyric acidergic (GABAergic) synapse. Global regulatory network was constructed to identify the cross-talking pathways of ATP6V1A, such as synaptic vesicle cycle, phagosome, and oxidative phosphorylation. According to the AUC value of 74.2%, low ATP6V1A expression accurately predicted the occurrence of AD. Conclusions. Our findings highlighted the pleiotropic roles of low ATP6V1A in AD pathogenesis, possibly mediated by synaptic vesicle cycle, phagosome, and oxidative phosphorylation.

Plasma Exosomes as a Therapeutic Approach Prevent the Cognitive Decline by Inhibiting Tau Protein Hyperphosphorylation in Alzheimer’s Disease Mice

2021 ◽  
Vol 11 (2) ◽  
pp. 221-228
Author(s):  
Lijuan Huang ◽  
Hao Wang ◽  
Haijuan Sui ◽  
Yijie Shi ◽  
Liang Zhao
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Tau Protein ◽  
Therapeutic Approach ◽  
Bioinformatics Analysis ◽  
Cognitive Impairments ◽  
Cognitive Disorder ◽  
Pathological Process ◽  
Exosomal Mirnas ◽  
Novel Therapeutic

It was well known that circulating plasma exosomes (Pla-Exo) were enriched with multiple microRNAs (miRNAs) and participated in the regulation of biological and pathological process via exchanging information and transferring substance into targeted cells and organs. Therefore, clinical significance of Pla-Exo had been recognized and they functioned as biomarkers for the clinical diagnosis or therapeutic applications to treat diseases. We explored the possibility of using Pla-Exo as a novel therapeutic approach for ameliorating cognitive dysfunction in Alzheimer’s disease (AD) mice. Here we found that Pla-Exo freely crossed the blood-brain barrier (BBB) and was transferred into the hippocampus of mice. After following peritoneal injection (I.P.) of Pla-Exo, survival of neuron cells was enhanced and cognitive disorder was attenuated in okadaic acid (OA) treated mice via deactivating GSK-3β and down-regulating GSK-3β mediated hyperphosphorylation of Tau protein. Finally, some potential exosomal miRNAs were screened by bioinformatics analysis and confirmed their target of GSK-3β. Taken together, all data proved that Pla-Exo contributed to the amelioration of cognitive impairments.

O3-06-02: POLYGENIC SCORE ANALYSIS OF EXONIC VARIANTS IN AN IMMUNE CO-REGULATORY NETWORK IDENTIFIES NOVEL PROTEIN-ALTERING VARIANTS THAT ASSOCIATE WITH ALZHEIMER'S DISEASE

2006 ◽  
Vol 14 (7S_Part_19) ◽  
pp. P1025-P1026
Author(s):  
Joseph S. Reddy ◽  
Mariet Allen ◽  
Xue Wang ◽  
Joanna M. Biernacka ◽  
Jenkins D. Gregory ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Regulatory Network ◽  
Polygenic Score ◽  
Score Analysis ◽  
Novel Protein

scholarly journals Differential Expression of mRNAs in the Brain Tissues of Patients with Alzheimer’s Disease Based on GEO Expression Profile and Its Clinical Significance

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Guowei Ma ◽  
Mingyan Liu ◽  
Ke Du ◽  
Xin Zhong ◽  
Shiqiang Gong ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Differential Expression ◽  
Brain Tissue ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Venn Diagram ◽  
Ad Prevention ◽  
The Brain ◽  
Brain Tissues

Background. Early diagnosis of Alzheimer’s disease (AD) is an urgent point for AD prevention and treatment. The biomarkers of AD still remain indefinite. Based on the bioinformatics analysis of mRNA differential expressions in the brain tissues and the peripheral blood samples of Alzheimer’s disease (AD) patients, we investigated the target mRNAs that could be used as an AD biomarker and developed a new effective, practical clinical examination program. Methods. We compared the AD peripheral blood mononuclear cells (PBMCs) expression dataset (GEO accession GSE4226 and GSE18309) with AD brain tissue expression datasets (GEO accessions GSE1297 and GSE5281) from GEO in the present study. The GEO gene database was used to download the appropriate gene expression profiles to analyze the differential mRNA expressions between brain tissue and blood of AD patients and normal elderly. The Venn diagram was used to screen out the differential expression of mRNAs between the brain tissue and blood. The protein-protein interaction network map (PPI) was used to view the correlation between the possible genes. GO (gene ontology) and KEGG (Kyoto Gene and Genomic Encyclopedia) were used for gene enrichment analysis to determine the major affected genes and the function or pathway. Results. Bioinformatics analysis revealed that there were differentially expressed genes in peripheral blood and hippocampus of AD patients. There were 4958 differential mRNAs in GSE18309, 577 differential mRNAs in GSE4226 in AD PBMCs sample, 7464 differential mRNAs in GSE5281, and 317 differential mRNAs in GSE129 in AD brain tissues, when comparing between AD patients and healthy elderly. Two mRNAs of RAB7A and ITGB1 coexpressed in hippocampus and peripheral blood were screened. Furthermore, functions of differential genes were enriched by the PPI network map, GO, and KEGG analysis, and finally the chemotaxis, adhesion, and inflammatory reactions were found out, respectively. Conclusions. ITGB1 and RAB7A mRNA expressions were both changed in hippocampus and PBMCs, highly suggested being used as an AD biomarker with AD. Also, according to the results of this analysis, it is indicated that we can test the blood routine of the elderly for 2-3 years at a frequency of 6 months or one year. When a patient continuously detects the inflammatory manifestations, it is indicated as a potentially high-risk AD patient for AD prevention.

scholarly journals The role of microRNAs regulatory network in Alzheimer’s disease: a bioinformatics analysis

2021 ◽  
Author(s):  
Chenjing Sun ◽  
Xiaokun Qi ◽  
Jianguo Liu ◽  
Feng Duan ◽  
Lin Cong
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Bioinformatics Analysis ◽  
Time Window ◽  
Bioinformatic Analysis ◽  
Preclinical Phase ◽  
Wide Range ◽  
Important Time ◽  
Brain Tissues

IntroductionAlzheimer’s disease (AD) is a neurodegenerative disease which presents with an earlier onset age and increased symptom severity. The objective of this study was to evaluate the relationship between regulation of miRNAs and AD.Material and methodsWe completed the bioinformatic analysis of miRNAs-AD studies through multiple databases such as TargetScan, Database for Annotation, Visualization and Integrated Discovery (DAVID), FunRich and String and assessed which miRNAs are commonly elevated or decreased in brain tissues, cerebrospinal fluid (CSF) and blood of AD. All identified articles were assessed using specific inclusion and exclusion criteria.ResultsMiRNAs related to AD of twenty-eight studies were assessed in this study. A wide range of miRNAs were up-regulated or down-regulated in tissues of AD patient’s brain, blood and CSF. 27 differentially dysregulated miRNAs have identified involved in amyloidogenesis, inflammation, tau-phosphorylation, apoptosis, synaptogenesis, neurotrophism, neurons degradation, activates cell cycle entry. Additionally, our bioinformatics analysis identified the top ten functions of common miRNAs in candidate studies. The function of common up-regulated miRNAs primarily target nucleus and common down-regulated miRNAs primarily target transcription, DNA-templated.ConclusionsComprehensive analysis of all miRNAs studies reveals cooperation in miRNA signatures whether in brain tissues or in CSF and peripheral blood. More and more studies suggest that miRNAs may play crucial roles as diagnostic biomarkers and/or as new therapeutic targets in AD. According to biomarkers, we can identify the preclinical phase early that provides an important time-window for therapeutic intervention.

Integrated Bioinformatics Analysis Identifies Hub Genes Associated with Viral Infection and Alzheimer’s Disease

2021 ◽  
pp. 1-9
Author(s):  
Xiaoru Sun ◽  
Hui Zhang ◽  
Dongdong Yao ◽  
Yaru Xu ◽  
Qi Jing ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Viral Infection ◽  
Bioinformatics Analysis ◽  
Expression Patterns ◽  
Temporal Cortex ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
Kegg Pathways ◽  
Barr Virus

Background: Alzheimer’s disease (AD) is a fatal neurodegenerative disease, the etiology of which is unclear. Previous studies have suggested that some viruses are neurotropic and associated with AD. Objective: By using bioinformatics analysis, we investigated the potential association between viral infection and AD. Methods: A total of 5,066 differentially expressed genes (DEGs) in the temporal cortex between AD and control samples were identified. These DEGs were then examined via weighted gene co-expression network analysis (WGCNA) and clustered into modules of genes with similar expression patterns. Of identified modules, module turquoise had the highest correlation with AD. The module turquoise was further characterized using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis. Results: Our results showed that the KEGG pathways of the module turquoise were mainly associated with viral infection signaling, specifically Herpes simplex virus, Human papillomavirus, and Epstein-Barr virus infections. A total of 126 genes were enriched in viral infection signaling pathways. In addition, based on values of module membership and gene significance, a total of 508 genes within the module were selected for further analysis. By intersecting these 508 genes with those 126 genes enriched in viral infection pathways, we identified 4 hub genes that were associated with both viral infection and AD: TLR2, COL1A2, NOTCH3, and ZNF132. Conclusion: Through bioinformatics analysis, we demonstrated a potential link between viral infection and AD. These findings may provide a platform to further our understanding of AD pathogenesis.

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