Uncovering the formation and function of fusion oncoprotein condensates in translocation renal cell carcinoma

Translocation renal cell carcinoma (tRCC) is an aggressive type of kidney cancer lacking effective treatments. It is mostly seen in children, making up 40% of all pediatric and adolescent renal cell carcinomas (RCCs). tRCC is characterized by the chromosomal rearrangements involving the microphthalmia-associated transcriptional factor family, most prevalent of which is the TFE3 transcription factor. Our understanding of the molecular mechanisms of how TFE3 fusions drive tRCC remains limited, and the targeted therapies for these tRCC patients do not exist. In this work, we plan to discover molecular mechanisms by which TFE3 fusion oncoproteins (FOs) drive tRCC, with the goal of identifying potential drug targets and their critical dependencies in the future. Our preliminary data shows that two of the most common TFE3 FOs, NONO-TFE3 and SFPQ-TFE3 form biomolecular condensates inside the nucleus, which are membrane-less compartments organized by weak multivalent interactions. Biomolecular condensates can concentrate pathway-specific factors and change genome organization and transcription programs. Therefore, understanding how NONO-TFE3 and SFPQ-TFE3 condensates form and function can reveal important insights about how TFE3 FOs drive tRCC. Many transcription factors and FOs are known to use intrinsically-disordered regions (IDRs) to form condensates. However, interactions mediated by IDRs are usually ill-defined, hampering the efforts to target these domains in cancer therapy. We found in our preliminary study that highly structured coiled-coil domains (CCDs) and RNA-recognition motifs (RRMs) are important for NONO-TFE3 and SFPQ-TFE3 condensate formation and transcription activities, giving us unique edge to understand how TFE3 FOs form condensates and function. In this proposal, we will investigate further how CCDs and RRMs of NONO-TFE3 and SFPQ-TFE3 FOs drive condensate formation and cancer progression. We hypothesize that TFE3 FOs drive tRCC by forming biomolecular condensates, changing the transcription programs of kidney cells. We aim to: 1) understand how RNA-binding drives TFE3 FO condensate formation; 2) elucidate how TFE3 FO condensates drive tRCC tumorigenesis; and 3) investigate how TFE3 FO condensates reshape the chromatin landscape and transcription of tRCC. Our results will shed light on new therapeutic approaches that target components of FO condensates, their molecular interactions, and their downstream effectors, striving to eradicate the devastating TFE3 FO-driven tRCCs. While we use 2D and 3D in vitro models where possible, we also perform TFE3 FO-driven tumor growth and invasion studies that involve grafting tumor cells into a mouse. This approach is necessary to recapitulate the complex tumor microenvironment that affects tumor progression. Project Number: 1R01CA303867-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Danfeng Cai (+1 co-PI) | Institution: JOHNS HOPKINS UNIVERSITY, BALTIMORE, MD | Award Amount: $643,861 | Activity Code: R01 | Study Section: Cancer Genetics Study Section[CG] View on NIH RePORTER: https://reporter.nih.gov/project-details/11366037