Influence of N6-methyladenosine (m6A) modification on cell phenotype in Alzheimer's disease.

OBJECTIVE: Recent research has suggested that m6A modification takes on critical significance to Neurodegeneration. As indicated by the genome-wide map of m6A mRNA, genes in Alzheimer's disease model achieved significant m6A methylation. This study aimed to investigate the hub gene and pathway of m6A modification in the pathogenesis of AD. Moreover, possible brain regions with higher gene expression levels and compounds exerting potential therapeutic effects were identified. Thus, this study can provide a novel idea to explore the treatment of AD. METHODS: Differential expression genes (DEGs) of GSE5281 and GSE48350 from the Gene Expression Omnibus (GEO) database were screened using the Limma package. Next, the enrichment analysis was conducted on the screened DEGs. Moreover, the functional annotation was given for N6-methyladenosine (m6A) modification gene. The protein-protein interaction network (PPI) analysis and the visualization analysis were conducted using STRING and Cytoscape. The hub gene was identified using CytoHubba. The expression levels of Hub genes in different regions of brain tissue were analyzed based on Human Protein Atlas (HPA) database and Bgee database. Subsequently, the candidate drugs targeting hub genes were screened using cMAP. RESULTS: A total of 42 m6A modified genes were identified in AD (20 up-regulated and 22 down-regulated genes). The above-described genes played a certain role in biological processes (e.g., retinoic acid, DNA damage response and cysteine-type endopeptidase activity), cellular components (e.g., mitochondrial protein complex), and molecular functions (e.g., RNA methyltransferase activity and ubiquitin protein ligase). KEGG results suggested that the above-mentioned genes were primarily involved in the Hippo signaling pathway of neurodegeneration disease. A total of 10 hub genes were screened using the protein-protein interaction network, and the expression of hub genes in different regions of human brain was studied. Furthermore, 10 compounds with potential therapeutic effects on AD were predicted. CONCLUSION: This study revealed the potential role of the m6A modification gene in Alzheimer's disease through the bioinformatics analysis. The biological changes may be correlated with retinoic acid, DNA damage response and cysteine-type endopeptidase activity, which may occur through Hippo signaling pathway. The hub genes (SOX2, KLF4, ITGB4, CD44, MSX1, YAP1, AQP1, EGR2, YWHAZ and TFAP2C) and potential drugs may provide novel research directions for future prognosis and precise treatment.

Mechanism of Tianma Gouteng Decoction in the treatment of Parkinson's disease based on network pharmacology and molecular docking.

OBJECTIVE: To explore the pharmacological mechanism and molecular targets of Tianma Gouteng Decoction (TMGTD) in the treatment of Parkinson's disease (PD). METHODS: We applied network pharmacology to screen the active components of TMGTD and predict target genes in multiple Chinese herbal medicine databases and compound databases, and built a drug-ingredient-target network. Then, we used the CytoHubba plug-in to filter out the core components of TMGTD according to the order of degree value. We screened PD-related pathogenic targets in the DrugBank, Genecard and OMIM databases from high to low in Betweenness Centrality (BC) value and Closeness Centrality (CC) value. Subsequently, we determined the intersection target of TMGTD and PD by Venn diagram and performed protein-protein interaction (PPI) analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on core molecules and intersection targets. Finally, molecular docking was performed to verify the binding of the top three core molecules of TMGTD with the top three core targets of PD. RESULTS: The core components of TMGTD are quercetin, kaempferol and palmitic acid. The main targets of TMGTD in the treatment of PD are ALB, GAPDH and AKT1. GO analysis and KEGG analysis showed that the biological process of TMGTD in the treatment of PD is closely related to the activities of neurotransmitter receptors, G protein-coupled receptors and dopamine neurotransmitter receptors. TMGTD possesses therapeutic effects on PD mainly through the PI3K-Akt signaling pathway and MAPK signaling pathway. Molecular docking shows the high affinity of the quercetin, kaempferol and palmitic acid with PD core targets. CONCLUSION: TMGTD plays a pivotal role in the treatment of PD through multiple components, multiple targets and multiple pathways. The results provide a research direction for the subsequent exploration of the mechanism of TMGTD in PD treatment.