Prognostic Transcriptional Regulatory Programs Reveal Pharmacologically Targetable Vulnerabilities in Treatment-Naive Osteosarcoma

Osteosarcoma is an aggressive malignancy whose treatment has changed little over the past decades, and outcomes remain poor. Although transcriptomic studies have provided insights into osteosarcoma biology, many include metastatic or post-treatment tumours, potentially obscuring transcriptional programs associated with intrinsic tumour aggressiveness. To address this limitation, we analysed transcriptomic profiles exclusively from treatment-naive, non-metastatic osteosarcoma patients to reconstruct prognostic transcriptional regulons associated with outcome. We identified distinct transcriptional programs associated with favourable and unfavourable outcomes. Tumours linked to poor prognosis were characterized by coordinated proliferative and metabolic transcriptional programs controlled by three regulatory hubs: CTCF, E2F4, and SP1, whose regulon enrichments showed strong associations with patient survival. To explore whether these regulatory networks could be pharmacologically modulated, molecular docking and dynamics simulations were performed, revealing potentially stable interactions between the hesperidin and the DNA-binding domains of these key transcription factors. Transcriptomic analysis of osteosarcoma cells treated with hesperidin revealed alterations in the identified regulons’ composition and decreased transcription factor activity. Together, these findings identify a transcriptional regulatory architecture underlying aggressive osteosarcoma, revealing novel prognostic biomarkers and suggesting that pharmacological modulation of master regulators such as CTCF, E2F4, and SP1, may represent a strategy to target transcriptional vulnerabilities in this malignancy.