(P 46) INVESTIGATING THE IMPACT OF SARCOMA FUSION PROTEINS ON EPIGENETIC AND DNA-DEPENDENT PROCESSES THROUGH INTERACTOME PROFILING

Objective: Around 30 % of sarcomas carry oncogenic fusions as primary drivers of tumorigenesis. The resulting chimeric proteins often lack proper regulatory domains, leading to inappropriate functional roles and disruption of cellular homeostasis. While these fusion proteins are studied for their role in cell signaling, their impact on epigenetic regulation and other DNA-dependent processes remains poorly explored.

Methods: Our study aims to elucidate how sarcoma fusion proteins interact with cellular machineries that govern chromatin organization, DNA replication, and repair in order to define biomarkers and potential sarcoma vulnerabilities. Patients’ representative fusion genes (122 fusions recurrent for 20 sarcoma subtypes) have been designed and ectopically expressed in relevant cell models. Chimeric protein complexes, along with their interacting partners, are being identified using Tandem Affinity Purification/Mass Spectrometry (TAP/MS).

Results: Analysis of the interactomes of Ewing sarcoma fusions (9 fusions recurring in this subtype) showed that their interactomes are interconnected. The results show that Ewing fusions shared interactions with three transcription factors (TFs), ZEB1, BCL11A and TRPS1. As a proof of concept for the significance of these common TFs in the oncogenic activity of Ewing fusions, we analyzed survival of Ewing patients with high vs low mRNA expression of these TFs. High expression levels were associated with lower survival rates of patients. Further, to understand the underlying molecular mechanisms, we identified genes that are positively correlated with ZEB1, BCL11A and TRPS1 and subjected these factors to pathway enrichment analysis. This resulted in enrichment of PI3K/AKT and MAPK pathways. Moreover, to assess validity of these pathways in Ewing sarcoma, we analyzed publicly available drug screening data of Ewing sarcoma cell line (A673 with endogenous EWSR1-FLI1). A673 cells were significantly sensitive to PI3K and GSK3B inhibitors.

Conclusion: Future analyses will focus on identifying interactors across sarcoma subtypes and validating how these interactions modulate chromatin and DNA-dependent pathways to support tumor survival. Linking the oncogenic activity of chimeras to vulnerabilities in epigenetic regulation and genome maintenance could uncover new therapeutic opportunities in sarcoma.