mRNA/sRNA Co-Sequencing Reveals Multiple New Targeted Therapy Candidates in Rhabdomyosarcoma [miRNA-seq]

There have been few studies investigating the transcriptional-driver landscape of rhabdomyosarcoma (RMS). In this study, we performed genome-wide mRNA and sRNA co-sequencing from the same RMS and wildtype tissues to identify differentially expressed and differentially regulated genes involved in the molecular pathology of RMS. One key finding is the upregulation of RUNX2 transcription factor, which is normally under the negative control of HDAC4 transcriptional silencer, but this is lost in these tissues. Similar to bone sarcomas, we propose that HDAC4 itself was under the negative regulated of miR-140, i.e., upregulation of miR-140 silences HDAC4, allowing for the expression of RUNX2. The data showed that most miRNAs known to target HDAC4 (e.g. miR-1, miR-206) including miR-140 were downregulated, with the exception of miR-155. There might be the possibility that miR-140/HDAC4/RUNX2 signalling pathway is specific to bone sarcoma but here, the miR-155/HDAC4/RUNX2 signalling pathway is specific to muscle sarcomas. Further studies are required to test this hypothesis. Overall design: In total, 14 human biopsy samples were used; 5 alveolar RMS, 4 embryonal RMS and 5 control skeletal muscle samples. Total RNA was extracted and then sRNA was sequenced. This contains the sRNA-seq data while the mRNA-seq data, which includes the same samples and additional RMS/control samples, is provided separately.