A patient-derived organoid model identifies TP53-dependent gemcitabine sensitivity in spinal chordoma

BACKGROUND: Chordoma is a rare malignant bone tumor with limited effective systemic treatment options. Conventional chemotherapy generally shows minimal benefit, highlighting the need for predictive preclinical models to explore therapeutic vulnerabilities. Patient-derived organoids (PDOs) have emerged as a promising three-dimensional culture system that preserves tumor architecture and molecular features while enabling functional testing. However, mechanistic studies linking pathway activity to drug response in chordoma PDOs remain limited. METHODS: Fresh surgical specimens from five patients with primary spinal chordoma were used to attempt generation of three-dimensional PDO cultures, of which primary three-dimensional cultures were successfully established. Organoids were characterized by histology, immunohistochemistry, and quantitative PCR analysis of chordoma-associated markers. Functional drug screening was performed using a panel of clinically relevant agents in a representative PDO model, followed by dose-response testing of gemcitabine. The role of TP53 in drug response was examined using small interfering RNA-mediated knockdown, with assessment of cell viability, Ki-67 expression, and DNA-damage response-related proteins. Statistical analyses were performed using one-way analysis of variance, with p < 0.05 considered statistically significant. RESULTS: The established PDOs recapitulated the histopathological and molecular characteristics of their matched primary tumors and maintained stable growth across six passages. Among the screened agents, gemcitabine showed the strongest growth-inhibitory effect in PDO-based functional assays. Dose-response experiments confirmed significant gemcitabine-induced growth suppression. Importantly, TP53 knockdown markedly attenuated gemcitabine-induced cytotoxicity, increased proliferative activity, and reduced activation of DNA-damage response signaling, indicating a TP53-dependent vulnerability. CONCLUSIONS: This study establishes a spinal chordoma PDO platform for functional precision oncology. Our findings identify a TP53-dependent DNA-damage vulnerability engaged by gemcitabine in patient-derived three-dimensional models, supporting biomarker-informed hypothesis generation rather than routine chemotherapy in unselected patients. This PDO-based approach provides a translational framework for exploring pathway-defined therapeutic susceptibilities in rare tumors such as chordoma.