ASPSCR1-TFE3 reprograms transcription by organizing enhancer loops around hexameric VCP/p97

Area of Science:

• Oncology
• Molecular Biology
• Genetics

Background:

• Alveolar soft part sarcoma (ASPS) and Xp11-rearranged renal cell carcinoma (RCC) are rare cancers driven by the ASPSCR1::TFE3 fusion oncoprotein resulting from a t(X;17) translocation.
• Identifying specific therapeutic targets for these cancers has been challenging due to the unique genetic driver.
• Understanding the molecular mechanisms and co-factors involved in ASPSCR1::TFE3 oncogenesis is crucial for developing novel treatments.

Purpose of the Study:

• To identify molecular partners and co-factors of the ASPSCR1::TFE3 oncoprotein.
• To elucidate the functional role of identified co-factors in the oncogenic activity of ASPSCR1::TFE3.
• To evaluate the therapeutic potential of targeting these co-factors in ASPS and Xp11-RCC.

Main Methods:

• Proteomic analysis, including co-immunoprecipitation, was used to identify proteins interacting with ASPSCR1::TFE3.
• Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and HiChIP were employed to study the genomic distribution and chromatin conformation.
• In vitro and in vivo (mouse models) assays were performed to assess the impact of VCP on cancer cell proliferation and tumorigenesis.

Main Results:

• Proteomic analysis revealed significant enrichment of VCP/p97, an AAA+ ATPase, in nuclear complexes with ASPSCR1::TFE3.
• VCP was demonstrated to be an obligate co-factor of ASPSCR1::TFE3, co-localizing with it on chromatin and enhancers genome-wide.
• VCP's enzymatic function and hexameric assembly were shown to be critical for orchestrating the oncogenic transcriptional signature of ASPSCR1::TFE3 by facilitating higher-order chromatin structures.
• Co-depedency between ASPSCR1::TFE3 and VCP was observed for cancer cell proliferation and tumorigenesis in both in vitro and in vivo models.

Conclusions:

• VCP/p97 acts as a crucial co-factor for the ASPSCR1::TFE3 oncoprotein in ASPS and Xp11-RCC.
• VCP plays a key role in regulating chromatin architecture and transcriptional programs driven by ASPSCR1::TFE3.
• VCP represents a promising and novel therapeutic target for alveolar soft part sarcoma and Xp11-rearranged renal cell carcinoma.