Abstract B038: TFE3 fusion oncoprotein condensate as a mechanism in translocation renal cell carcinoma

Abstract Translocation renal cell carcinoma (tRCC) is an aggressive and understudied form of kidney cancer primarily driven by fusion oncoproteins (FOs) involving transcription factor E3 (TFE3). Although multiple TFE3 fusion partners have been reported, such as SFPQ, NONO, and PRCC, the mechanisms underlying TFE3 FO-driven oncogenesis remain elusive, hindering the development of targeted therapies. Emerging evidence suggests that biomolecular condensates—membrane-less subcellular compartments formed through multivalent, weak interactions among proteins and nucleic acids—may be a novel mechanism for oncogene activation in cancer. We hypothesized that TFE3 FOs form biomolecular condensates in tRCC, leading to aberrant transcriptional regulation and disease progression. The aim of our study was to elucidate whether, and by what mechanisms, TFE3 FOs form condensates and drive oncogenic reprogramming, with the ultimate goal of identifying new therapeutic targets. To address this, we deployed a pipeline integrating advanced imaging, optogenetics, and high-throughput sequencing. Using immunofluorescence with Zeiss AiryScan super-resolution microscopy, we visualized TFE3 FO condensates in patient-derived tRCC tumor samples and cell lines. Automated photomanipulation and the OptoDroplet optogenetic platform enabled domain mapping of condensate formation, pinpointing the coiled-coil domains (CCDs) of NONO and SFPQ as essential for this process. We further combined single-particle tracking (HiLo microscopy), CUT&RUN sequencing, and RNA-seq to assess the functional impact of condensates on chromatin association, enhancer landscape remodeling, and gene expression. Our results show that TFE3 FOs form biomolecular condensates that prolong chromatin binding, enhance genome-wide transcriptional activation, and establish novel enhancers and super-enhancers at pro-growth gene loci—effects not observed with wild-type TFE3. Disruption of condensate formation reverses these oncogenic programs. These findings reveal a previously unrecognized condensate-driven mechanism in tRCC, highlighting biomolecular condensates as actionable targets for future drug discovery. Our work not only advances the mechanistic understanding of tRCC but also pioneers a scalable, automated approach for the systematic interrogation of "undruggable" fusion oncoproteins, opening novel avenues for therapeutic intervention in kidney cancer. (Disclaimer: This abstract was drafted with the assistance of artificial intelligence (AI) to improve clarity and flow.) Citation Format: Choon Leng So, Ye Jin Lee, Bujamin H. Vokshi, Wanlu Chen, Binglin Huang, Emily De Sousa, Yangzhenyu Gao, W Marston Linehan, Hongkai Ji, Eneda Toska, Danfeng Cai. TFE3 fusion oncoprotein condensate as a mechanism in translocation renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Kidney Cancer Research: From Molecular Insights to Therapeutic Breakthroughs; 2026 Mar 13-16; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(5_Suppl_2):Abstract nr B038.