TFE3 fusion proteins drive oxidative metabolism, ferroptosis resistance and general RNA synthesis in translocation renal cell carcinoma. [RNA-seq]

The oncogenic mechanisms by which TFE3 fusion proteins drive translocation renal cell carcinoma (tRCC) are poorly characterised. Here, we integrated loss and gain of function experiments with multi-omics analyses in tRCC cell lines and patient tumors. High nuclear accumulation of NONO-TFE3 or PRCC-TFE3 fusion proteins promotes their broad binding across the genome, engaging a core set of M/E-box-containing regulatory elements to activate specific gene expression programs as well as promiscuous binding to active promoters to stimulate mRNA synthesis. Within the core program, TFE3 fusions directly regulate genes involved in ferroptosis resistance and oxidative phosphorylation metabolism (OxPhos) increasing functional OxPhos levels. Consequently, human tRCC tumors display high OxPhos scores that persist during their epithelial to mesenchymal transition (EMT). EMT of tRCC tumours was further associated with presence of mesenchymal tRCC cancer cells and myofibroblast cancer-associated fibroblasts (myCAFs) that are both hallmarks of poor prognostic outcomes. We provide unique insights into how broad genomic binding of TFE3 fusion proteins promotes tRCC tumourigenesis by regulating OxPhos and ferroptosis resistance and more generally stimulating RNA synthesis. RNA-seq was performed in triplicates for 4 tRCC cell lines (UOK109, TF1, UOK120 and UOK146) following siCtrl or siTFE3 and in HEK293T following overexpression of GFP, TFE3, NONO-TFE3 or PRCC-TFE3.