Characterizing and targeting the oncogenic program in Alveolar Soft Part Sarcoma

Approximately 20% of sarcomas are driven by oncogenic translocations, which commonly involve transcriptional regulators. Alveolar soft part sarcoma (ASPS) is a sarcoma most commonly diagnosed in young adults and characterized by a translocation involving the gene ASPSCR1 and the transcription factor TFE3. Current therapies for ASPS target angiogenesis or the immune microenvironment, but do not directly target the fusion protein or its cellular dependencies. In this project, we propose to perform integrative studies of the transcriptional and epigenetic landscapes of ASPS, using this information to identify novel therapeutic targets. In Aim 1, we will perform integrative computational comparisons of transcriptional (RNA-seq) and chromatin (H3K27ac ChIP-seq) data from ASPS tumors, patient-derived xenograft and cell lines, and draw comparisons to other sarcomas to identify features unique to this disease. To further identify exceptional aspects of ASPS biology, we will perform transcriptional and biochemical profiling of ASPS cells engineered with a fusion protein that can be rapidly degraded using a genetic and chemical proteolysis targeting chimera (PROTAC) system. Using this system, rapid chemical-induced degradation of ASPSCR1::TFE3 will reveal genes acutely regulated by the fusion protein and identify cancer-associated growth programs it controls. Results of these studies will identify global patterns of gene expression and chromatin organization in ASPS, and mechanistic studies using the degradable fusion protein will identify genes it directly regulates which may be most relevant for disease biology. In Aim 2, we will identify novel dependencies in ASPS. Using the proximity proteomics-based strategy BioID, we have genetically tagged the ASPSCR1::TFE3 fusion protein with a biotin ligase, leading to covalent modification of interacting proteins with biotin. Following purification and mass spectrometry sequencing of interacting proteins, we have discovered that the ASPSCR1::TFE3 fusion protein interacts with the NuA4 Histone Acetyltransferace Complex, the Mediator Complex, and the Transcription Initiation Complex. We will utilize small molecule inhibitors targeting each of these complexes to determine how their disruption alters the ASPSCR1::TFE3 gene expression program. Finally, in preliminary studies described in Aim 1, we have identified uniquely elevated expression of Cyclin D1 in ASPS compared to other sarcomas, which is driven by the ASPSCR1::TFE3 oncoprotein. We will evaluate the targeted disruption of the Cyclin D1-driven growth program using CDK4/6 inhibitors, assaying cell proliferation, cell cycle and apoptosis assays. We will further perform RNA-seq in ASPS cell lines to evaluate the transcriptional effects of CDK4/6 inhibitors. These innovative studies will greatly enhance our understanding of ASPS, produce data sets valuable to the global sarcoma community, and identify urgently needed targeted therapies for ASPS patients.