Proteome-wide Multi-omics Profiling of Osteosarcoma Transcription Factor Networks

Osteosarcoma (OS) is an aggressive bone cancer that most commonly affects children and young adults. OS exhibits a high degree of genomic complexity, as well as cellular plasticity, and dynamic transcriptional regulation is suggested to contribute to treatment resistance and metastasis. Cell lines are well characterised as models to advance our knowledge on OS biology. HOS and U2OS cells have increased invasiveness and higher migratory ability compared with MG63. In this study, we employed a tandem array of consensus transcription factor response elements (catTFREs) proteomic approach to characterise transcription factor (TF) regulatory networks related to OS aggressiveness. We mapped 7355 proteins and enriched 504 TFs and coregulators. When we integrated proteomics with cell line specific gene expression, H3K27ac marked enhancers and chromatin accessibility, we classified the TFs and coregulators common for HOS and U2OS and specific for the individual cell lines. We demonstrate that RUNX2 and MYBL2 are specifically enriched in HOS and U2OS. RUNX2 and MYBL2 exhibited an increase in expression in metastatic compared to primary OS tumours and may be linked to cell aggressiveness. ETV5, TBX15, and USF1 were among TFs specific to the lower migratory cell line MG63 and these genes were more expressed in primary OS tumours. Our analysis provides a comprehensive understanding of the transcriptional drivers that shape OS cell line regulatory landscapes and may have implications as markers pending further validation.