Drug screening reveals differential drug response in primary and metastatic clear cell sarcoma

Clear Cell Sarcoma (CCS) are ultra-rare fusion-translocated soft-tissue tumours occurring mainly in young adults with poor prognosis. Their aggressiveness and resistance to conventional chemotherapy, especially in a metastatic setting, characterize these tumours. A functional drug screen consisting of 80 drugs was performed on patient-derived CCS cell lines. Top candidates were validated in 3D cell culture and in vivo models, allowing comparison of drug responses among CCS cell lines, including one matched pair (MUG Lucifer cell lines) representing primary and metastatic disease from the same patient. Underlying mechanisms were evaluated with RNA Seq, fluorescence/luminescence based assays, Western blot and IHC. In vitro experiments in CCS spheroids highlighted the transcription inhibitor lurbinectedin to be the best overall candidate which was further confirmed in mouse xenografts, albeit to a lesser extent than observed in vitro, especially in the metastatic CCS model. Transcriptional and functional analyses revealed heterogeneous drug responses and differences in cell death mechanisms across CCS lines, reflecting patient-specific variability. Furthermore, we explored combination treatment of lurbinectedin with selinexor. Synergistic effects were confirmed in a novel autologous co-culture model incorporating cancer-associated fibroblasts, providing a more physiologically relevant system for drug testing. This study identified promising therapeutic avenues by highlighting key vulnerabilities in CCS, considering both inter-tumour heterogeneity, tumour plasticity and the stromal influence on drug response.