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Published on: September 27, 2024
Bioinformatics and Gene Expression Omnibus Analysis of Key Candidate Genes and Pathways Associated with Femoral Head
Yuanjing Ding1, Yuxia Ma2, Heng Yan3
1Department of Joint Surgery, Central Hospital Affiliated to Shandong First Medical University, Shandong, China.
Background:
Femoral head necrosis (FHN) is a debilitating bone disease affecting an estimated 8 million people worldwide. Although specific drugs for FHN have limitations, targeted therapies have shown promising results. The significance of this study is underscored by the high prevalence of FHN, the limitations of current treatments, and the potential of targeted drugs and natural compounds for effective therapeutic interventions.
Objectives:
This study aimed to explore the genetic landscape and associated pathways of FHN through bioinformatics analysis of Gene Expression Omnibus (GEO) data and molecular docking simulations targeting specific enzymes implicated in FHN.
Methods:
Differentially expressed genes (DEGs) in FHN samples were identified from GEO datasets, specifically accession number GSE123568 (Platform: GPL15207). Functional enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to identify enriched pathways and Gene Ontology (GO) terms. Additionally, a protein-protein interaction (PPI) network was constructed using the STITCH (search tool for interaction of chemicals) database, which helped identify top hub genes and proteins. Molecular docking was conducted against key proteins using compounds from the topical chinese herbal medicine (TCHM) database associated with FHN.
Results:
The study provided a comprehensive bioinformatics analysis of key candidate genes and pathways associated with FHN, which may serve as potential therapeutic targets. It was found that FHN is associated with mitogen-activated protein kinases (MAP4K4/ MAPK8/ MAPK9) and interleukins (IL1b/ IL19/ IL26). Molecular docking results showed strong interactions of traditional Chinese herbal compounds through hydrogen bonding and electrostatic interactions at the active sites of the top ten target proteins associated with FHN.
Conclusions:
The study confirmed that FHN is linked with enzymes such as mitogen-activated protein kinases (MAPKs), interleukins, tumor necrosis factors (TNFs), and VEGFA (vascular endothelial growth factor A). Molecular docking simulations demonstrated that hesperidin, naringin, and curcumin exhibit potent inhibition against key proteins involved in FHN. Future research will focus on elucidating the specific roles of genes associated with FHN and exploring potential therapeutic targets using natural compounds.
Insights
Femoral head necrosis (FHN) is linked to specific genes and pathways, including mitogen-activated protein kinases and interleukins. Natural compounds like hesperidin show potential for FHN treatment by inhibiting key proteins.
Area of Science:
- Bioinformatics
- Genomics
- Pharmacology
Background:
- Femoral head necrosis (FHN) affects millions globally, with current treatments having limitations.
- Targeted therapies and natural compounds offer promising therapeutic avenues for FHN.
- This study addresses the need for effective interventions due to FHN's prevalence and treatment challenges.
Purpose of the Study:
- To investigate the genetic basis and molecular pathways of FHN using bioinformatics.
- To identify potential therapeutic targets through gene expression analysis and molecular docking.
- To explore the efficacy of natural compounds against FHN-associated proteins.
Main Methods:
- Analysis of Gene Expression Omnibus (GEO) datasets (GSE123568) to identify differentially expressed genes (DEGs) in FHN.
- Functional enrichment analysis (DAVID) and protein-protein interaction (PPI) network construction (STITCH) to identify key pathways and hub genes.
- Molecular docking simulations using traditional Chinese herbal medicine (TCHM) database compounds against FHN-related proteins.
Main Results:
- Identified key candidate genes and pathways associated with FHN, including mitogen-activated protein kinases (MAPKs) and interleukins (ILs).
- Discovered strong interactions between traditional Chinese herbal compounds and FHN target proteins via molecular docking.
- Highlighted hesperidin, naringin, and curcumin as potent inhibitors of FHN-associated proteins.
Conclusions:
- Confirmed FHN's association with MAPKs, interleukins, tumor necrosis factors (TNFs), and VEGFA.
- Demonstrated the potential of natural compounds (hesperidin, naringin, curcumin) in inhibiting key FHN proteins.
- Proposed further research into specific gene roles and natural compound-based therapeutic strategies for FHN.
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