Identification and validation of the important role of YAP in the development and progression of Osteosarcoma

Abstract Aim This study aims to explore the molecular mechanisms of osteosarcoma by integrating multi-omics data to identify key genes and pathways, with a focus on the Hippo pathway, and to validate the association of YAP expression with tumor malignancy progression. Methods This study integrates multi-omics data to conduct a systematic analysis of osteosarcoma. We obtained whole-exome sequencing (WES) data from 106 patients from the National Genomics Data Center (NGDC) and collected clinical data from 3,115 osteosarcoma patients from the SEER database. Univariate Cox regression analysis was performed using the survival analysis package in R to construct a time-dependent covariate model for chemotherapy efficacy. WES data were analyzed using tools such as HISAT2 and SAMtools to identify copy number variations (CNVs) in genes and genomic regions. KEGG and GO enrichment analyses were conducted using the KOBAS-i and Metascape platforms. Gene-drug interaction data were retrieved from the Drug Gene Interaction (DGI) database and visualized using the igraph package in R. Additionally, RNA sequencing data were obtained to analyze the expression levels of the YAP1 gene, and its expression was further validated by immunohistochemical staining, with phosphate-buffered saline as the negative control and a known positive marker as the positive control. Results Clinical data analysis indicates that both surgery and chemotherapy significantly reduce mortality rates, with chemotherapy demonstrating significant early efficacy. However, this efficacy diminishes over time, while radiotherapy notably increases the risk of mortality. Genomic analysis using WES identified 3,215 genes with copy number alterations, including 826 amplifications and 2,389 deletions. Functional enrichment revealed key pathways like immune response and cancer metabolism, with the Hippo pathway showing significant alterations, particularly in YAP1, a core regulatory gene. YAP1 exhibited recurrent copy number gains in osteosarcoma, and 35 Hippo-related genes showed distinct CNA patterns. Pharmacogenomic analysis identified 1,299 drug-gene interactions involving 73 Hippo pathway genes, suggesting potential therapeutic targets. These findings highlight the importance of the Hippo pathway, especially YAP1, in osteosarcoma and its potential as a therapeutic target. The positive expression rate of YAP was 78.84% (41/52), while the expression rate in osteochondroma was 30% (6/20). The expression rate in osteosarcoma was significantly higher than that in osteochondroma (P = 0.000). The positive expression rate of YAP was not significantly associated with gender or age, but showed a statistically significant correlation with tumor size, staging, and metastasis status. Notably, analysis revealed a positive correlation between YAP positive expression and both Enneking staging and distant metastasis in osteosarcoma patients. Conclusion Our study demonstrated that chemotherapy efficacy in osteosarcoma patients diminishes over time, identifies significant copy number variations in osteosarcoma tissues, and highlights the elevated expression of YAP1, particularly in osteosarcoma compared to osteochondroma, suggesting its potential role in tumorigenesis and therapeutic targeting.