Systematic analyses of RNA-binding proteins uncover therapeutically promising vulnerabilities in osteosarcoma

Osteosarcoma (OS) is the most common primary malignant bone tumor with a strong tendency to metastasize, limiting the prognosis of affected patients. Genomic, epigenomic and transcriptomic analyses have demonstrated the exquisite molecular complexity of this tumor, but haven't sufficiently defined the underlying mechanisms or identified promising therapeutic targets. To systematically explore RNA-protein interactions relevant to OS, we defined the RNA interactomes together with the full proteome and the transcriptome of cells from five malignant bone tumors (four osteosarcomata and one malignant giant cell tumor of the bone) and from normal mesenchymal stem cells and osteoblasts. These analyses uncovered both systematic changes of RNA-binding activity common to all osteosarcomata and individual alterations that were observed in only a subset of tumors. Functional analyses especially revealed a vulnerability of these tumors to translation inhibition and a positive feedback circuit involving the RNA-binding protein IGF2BP3 and the transcription factor Myc which affected cellular translation and OS cell viability. Our results provide novel and potentially clinically relevant insights into a previously uncharted molecular landscape of osteosarcoma. To investigate the RNA-protein interactome in osteosarcoma, four patient-derived osteosarcoma (OS) cell lines and one giant cell tumor of bone (GCTB) were used for enhanced RNA interactome capture (eRIC) and full proteome analysis in comparison with normal osteoblasts (OB) and bone mesenchymal cells (MSC). Total RNA was also isolated from the seven cell types and used for RNAseq. Differential gene expression analysis was done for the OS and GCTB cells in comparison with the OB and MSC in order to determine upregulated and downregulated mgenes in the OS and GCTB cells