Uncovering differential gene expression between mtRNA-positive and -negative osteosarcoma cells: implications beyond mitochondrial function.

Background: Long-term clinical outcomes for patients with osteosarcoma have shown little improvement over the past few decades. Identifying novel molecular targets to inhibit osteosarcoma cell growth remains an urgent challenge.

Methods: Explore the function of mtRNA in the occurrence and development of osteosarcoma utilizing bioinformatics analysis of the Gene Expression Omnibus (GEO) microarray dataset. The Network Analyst tool was used to analyze GSE73120. Differentially expressed genes (DEGs) were identified using GEO2R and analyzed using NetworkAnalyst. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed using Metascape and WebGestalt. A protein-protein interaction (PPI) network was constructed through the STRING database and visualized with Cytoscape. The MCODE algorithm was used to identify key modules, and CytoHubba was applied to determine hub genes. Validation of hub genes was conducted using the GEPIA database.

Results: A total of 104 DEGs were identified, including 89 upregulated and 15 downregulated genes. GO and KEGG analyses revealed that these DEGs were enriched in pathways related to connective tissue development, collagen trimer, and extracellular matrix structural components. The PPI network analysis identified seven hub genes. Among them, COL1A1, PDGFRB, and SPARC were confirmed as sarcoma-related genes using the GEPIA database.

Conclusion: Our findings suggest that COL1A1, PDGFRB, and SPARC may be involved in mtRNA-driven tumorigenesis and could serve as promising therapeutic targets for osteosarcoma.