Systematic profiling of synovial sarcoma transcriptome

We systematically explored the transcriptome of 10 synovial sarcoma (SS) patients. We detected a large number of upregulated and downregulated genes in SS compared to normal tissues, which were mainly involved in cell cycle, metabolic and P53 signaling pathways. Moreover, we identified a multitude of differentially alternative spliced genes, indicating that the deregulation of alternative splicing could be one of main factors contribute to the tumorigenesis of SS. A set of tumor-specific gene fusion pairs were identified in SS. We also detected dozens of differentially expressed circRNAs and their parental genes were enriched in muscle related biological process. The interaction network constructed based on circRNAs, miRNAs and corresponding target genes showed that the differentially expressed circRNAs in SS have the potential to regulate the expression of a number of SS related genes. Collectively, we systematically investigated the abnormal expression profile of SS and gain insights into the molecular mechanism from different views of transcriptome expression changes. Overall design: Investigation of the transcriptome changes of synovia sarcoma from different aspects.