Dissolving Fusion Oncoprotein Condensates to Reverse Aberrant Gene Expression

Area of Science:

• Oncology
• Molecular Biology
• Biochemistry

Background:

• Many cancer-associated fusion proteins share a common structure: an N-terminal phase separation-prone region (PS) and a C-terminal DNA-binding domain (DBD).
• This PS-DBD topology resembles transcription factors, suggesting these fusions may drive cancer by forming aberrant transcriptional condensates via phase separation.

Purpose of the Study:

• To investigate the role of phase separation in the oncogenic function of PS-DBD fusion proteins.
• To identify compounds capable of dissolving these aberrant condensates and reversing their oncogenic effects.

Main Methods:

• High-throughput screening using time-lapse, high-content imaging to identify condensate-dissolving compounds.
• Cellular condensate assays and transcriptomic data analysis to validate findings.
• Investigation of compound mechanisms, including effects on lysosome formation.

Main Results:

• A significant fraction of cancer-associated fusion proteins exhibit a PS-DBD topology, forming aberrant condensates.
• A high-throughput screen identified 114 compounds that dissolve condensates formed by FUS::ERGmut.
• LY2835219 dissolved condensates from FUS::ERGmut and EWS::FLI1 by promoting lysosome formation and reversed aberrant gene expression driven by EWS::FLI1.

Conclusions:

• Aberrant condensate formation by PS-DBD fusions plays a likely role in oncogenesis.
• Mechanistically unbiased screening can identify compounds that modulate fusion protein-driven condensates.
• LY2835219 demonstrates proof of principle for targeting these condensates therapeutically, though its specific targeting mechanism requires further elucidation.