The fusion oncogene ASPSCR1‐TFE3 directs epigenetic‐induced autophagy in alveolar soft part sarcoma

Altered metabolism is considered to be one of the new hallmarks of cancer. Autophagy is one major avenue of altered cancer metabolism, enabling cell survival under metabolic stress and promoting chemoresistance. The nuclear localization of MiTF/TFE3 family transcription factors has associated with upregulated transcription of autophagy genes in pancreatic cancer. Alveolar soft part sarcoma (ASPS) is a rare but deadly soft‐tissue sarcoma, with a predilection for adolescent and young adult victims. ASPS is noteworthy for its resistance to traditional cytotoxic chemotherapies. It consistently associates with a t(X;17) chromosomal translocation that produces the ASPSCR1‐TFE3 target gene, bearing the DNA‐binding domain from TFE3 and protein interaction domains from ASPSCR1. We have demonstrated that conditional expression of ASPSCR1‐TFE3 is sufficient to drive alveolar soft part sarcomagenesis in the mouse with complete penetrance. Mouse tumors recapitulate human ASPS histology and transcriptomes. Our objective was to identify the direct targets of ASPSCR1‐TFE3 and how these targets confer resistance to doxorubicin. The human cell lines ASPS‐1 and FUUR‐1, as well as mouse tumors driven by expression of ASPSCR1‐TFE3 were subjected to nuclear fractionation and chromatin immunoprecipitation using antibodies against ASPSCR1 and RNAPol2. Cells and tumors were further characterized for their presence of auotphagic flux by detection of LC3‐II and abundance of lysosomal proteins LAMP1 and CTSD. Furthermore, cells treated with doxorubicin were analyzed by gas‐chromatography mass spectrometry (GC‐MS) for metabolites involved in cellular respiration and glycolysis. Lastly, mice were treated with either control, monotherapy of chloroquine (15 mg/kg) or doxorubicin (10 mg/kg), or combination therapy for up to 5 months. Mice on combination therapy showed a stastical improvement in survival of 3 months over control and doxorubicin treatments. We report not only the first genome‐wide localization of the ASPSCR1‐TFE3 oncoprotein on chromatin from ASPS cell lines and mouse tumors, but also its association with actively transcribed genes. Among these are found many genes related to autophagy. We demonstrate high expression of autophagy‐related proteins at baseline conditions in human tumors, cell lines and mouse tumors. We also demonstrate active autophagic flux even in the absence of stress conditions. Inhibition of autophagy strongly synergizes with chemotherapy to kill ASPS cells, suggesting a mechanism for resistance. Furthermore, mice treated with combination therapy of chloroquine and chemotherapy significantly extends life 3 months beyond control mice. We have therefore demonstrated the direct targets of ASPSCR1‐TFE3 in ASPS, including a number of autophagy genes that are expressed in these tumors. Inhibition of autophagy in ASPS causes the tumor cells to be more susceptible to chemotherapeutic stress. Support or Funding Information Alex's Lemonade Stand Foundation Sarcoma Foundation of America Huntsman Cancer FoundationChromatin immunoprecipitation of ASPSCR1‐TFE3 peaks from the entire mouse genome.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .