A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [Human_RNAseq_bulk]

Rhabdomyosarcoma (RMS), the most common soft-tissue sarcoma occurring in the pediatric population, arises from the skeletal muscle compartment. Several transcriptional and post-transcriptional regulators lock the tumor in a continuous undifferentiated state and prevent the cells from returning to quiescence. MicroRNAs (miRNAs) are short non-coding RNAs that modulate cell identity by means of post-transcriptional regulation of messenger RNAs. In this study, we aimed at identifying miRNAs that could affect FN-RMS cell identity. Thus, we analyzed publicly available datasets and identified miR-449a and miR-340 as the main regulators of cell cycle and p53 signaling. Using miR-eCLIP technology, we identified the direct effects of miRNAs in FN-RMS cell lines, and an overall rewiring of cell identity at the transcriptomic, epigenetic and metabolic level. We observed that miR-449a+340 directly and indirectly targeted glycolysis and pyruvate entry into mitochondria by inhibiting mitochondrial pyruvate complex (MPC) inhibition. The pharmacological inhibition of MPC resulted in a similar metabolic shift with cell cycle exit and a significant reduction in metastatic potential of FN-RMS models. In conclusion, the combination of miR-449 and miR-340 play a pivotal role in orchestrating the cell identity of FN-RMS, and the modulation of MPC emerges as a key factor in redirecting FN-RMS towards a quiescent, non-tumorigenic state. Human fusion-negative rhabdomyosarcoma (FN-RMS) cell line RD18 was transfected with either lipofectamine or miR-449a + miR-340 for 60 hours, and subsequently bulk RNAseq was performed