Machine Learning-Driven Identification of Exosome-Related Genes in Head and Neck Squamous Cell Carcinoma for Prognostic Evaluation and Drug Response Prediction

Background: This study integrated four Gene Expression Omnibus (GEO) datasets to identify disease-specific feature genes in head and neck squamous cell carcinoma (HNSCC) through differential expression analysis with batch effect correction. Methods: The GeneCards database was used to find genes related to exosomes, and samples were categorized into groups with high and low expression levels based on these feature genes. Functional and pathway enrichment analyses (GO, KEGG, and GSEA) were used to investigate the possible biological mechanisms underlying feature genes. A predictive model was produced by using machine learning algorithms (LASSO regression, SVM, and random forest) to find disease-specific feature genes. Receiver operating characteristic (ROC) curve analysis was used to assess the model’s effectiveness. The diagnostic model showed excellent predictive accuracy through external data GSE83519 validation. Results: This analysis highlighted 22 genes with significant differential expression. A predictive model based on five important genes (AGRN, TSPAN6, MMP9, HBA1, and PFN2) was produced by using machine learning algorithms. MMP9 and TSPAN6 showed relatively high predictive performance. Using the ssGSEA algorithm, three key genes (MMP9, AGRN, and PFN2) were identified as strongly linked to immune regulation, immune response suppression, and critical signaling pathways involved in HNSCC progression. Matching HNSCC feature gene expression profiles with DSigDB compound signatures uncovered potential therapeutic targets. Molecular docking simulations identified ligands with high binding affinity and stability, notably C5 and Hoechst 33258, which were prioritized for further validation and potential drug development. Conclusions: This study employs a novel diagnostic model for HNSCC constructed using machine learning technology, which can provide support for the early diagnosis of HNSCC and thus contribute to improving patient treatment plans and clinical management strategies.