Transcriptomic Characterization of Doxorubicin Resistance in Bone Sarcoma Organoids

Tumor organoids have emerged as the most promising avatar to model cancer in vitro and to be used as drug testing platform in personalized medicine protocols. The derivation of organoids from epithelial tumors is well established, and their use has proven useful for biomarker discovery, drug screening, and clinical decision support. However, the generation of organoids from sarcomas is much less developed and current protocols require further optimization to fully harness their research and clinical potential. In this study, we explored the challenges of generating basement membrane extract (BME)-based organoids from patient-derived sarcoma samples. Of the 19 samples processed, 3D structures formed in 7 (37%), yet none of these organoids could be propagated beyond the first passage. As an alternative approach, we successfully generated 3D organoids with long-term growth potential from sarcoma xenografts. Of the 14 xenograft samples tested, 7 (50%) could be maintained through at least three passages and were successfully biobanked. Specifically, organoids derived from xenografts grown from parental and doxorubicinresistant 143B osteosarcoma cells could be maintained as long-term cultures and used as a 3D platform to investigate drug resistance in osteosarcoma. Transcriptomic profiling and functional assays performed in these models identified the nonreceptor protein tyrosine kinase SRC as a key mediator of resistance to doxorubicin in osteosarcoma. Importantly, we demonstrated that inhibition of SRC signaling using dasatinib restores doxorubicin sensitivity in osteosarcoma cells by suppressing c-JUN–driven ABCB1 expression.