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Analysis of Transcriptomic Similarity between Osteosarcoma Cell Lines and Primary Tumors

Background: Osteosarcoma (OS) cell lines are commonly used to mimic tumors for in vitro experiments. The present study explores the resemblance of OS cell lines to OS primary tumors in regard to gene expression. Methods: Transcriptomic data were retrieved from published data sets for 18 primary tumor samples and 13 commonly used OS cell lines. Tumor purity was accounted for when correlating tumor and cell line gene expression. Differentially expressed genes between tumors and cell lines were discovered and gene ontology analysis was performed. Results: Certain commonly used cell lines, including NY, NOS1, and U2OS, display less resemblance to OS tumors than do other cell lines. For genes overexpressed in tumors, and consequently underexpressed in cell lines, gene ontology analysis enriched pathways related to cell-cell adhesion and stimulus detection. Conclusion: The pathways dysregulated between cell lines and tumors have been implicated in OS pathogenesis. Therefore, the findings suggest that the transcriptome of OS cell lines may not be completely representative of OS primary tumors’ gene expression and the disease process.