Development of a mechanistic understanding and novel therapeutic strategies for TFE3-rearranged renal cell carcinoma

Abstract

TFE3 rearranged renal cell carcinoma (TFE3-tRCC) is a rare subtype of renal cell carcinoma (RCC) harboring gene fusions that trigger oncogenic activation of TFE3 transcription factor. The frequency of this rare tumor is surprisingly high in children and young adults (20% to 75% of childhood RCCs) compared to older adults (ranges between 1% and 5%). Importantly, TFE3-tRCC can show aggressive behavior with rapid progression and little to no response to drugs commonly used for renal cancer treatment. In this project we aim to define gene expression programs of distinct TFE3 fusions to uncover molecular events driven by chimeric TFE3 and delineate their consequences for important cancer phenotypes. By identifying fusion-specific pathway alterations, we seek to propose novel therapeutic strategies tailored to the patients with these fusions. Using a cohort of 31 patients with suspected diagnosis of TFE3-tRCC, we have employed a novel customized RNA-based targeted Next generation Sequencing (NGS) panel to determine putative fusion partners of TFE3. Next, high throughput technologies like short read and long read RNA sequencing and ChIP sequencing were used to characterize the molecular landscape downstream of different fusion events. Finally, to explore the influence of the transcriptional diversity on therapeutic decisions, we aim to perform molecularly informed drug screening in our in vitro models followed by in vivo validation. With our newly developed targeted NGS panel, we have characterized our patient cohort and identified 7 distinct TFE3 fusion partners in 25 cases out of 31. The putative partners are ASPSCR1, LUC7L3, MED15, NonO, PRCC, RBM10, and SFPQ. Certain partners confer unique tumor morphologies, e.g., MED15::TFE3 fusion associates with cystic features. Our transcriptomic analysis shows tumors with same fusion tend to cluster together, driven by shared pathway upregulation (OXPHOS, lysosomal pathway, autophagy, proteasome etc.). Differential upregulation of pathways such as immune response, metabolic pathways, mitophagy, RNA splicing etc. highlight fusion specific identity, informing fusion driven molecular characteristics. Preliminary in vitro chromatin accessibility data suggests the potential involvement of the chimeric TFE3 protein in alternative splicing regulation, which is further consistent with splicing enrichment observed in our transcriptomic analysis. Different fusion partners for TFE3 likely impact the dysregulation of the chimeric protein and drives tumorigenesis. However, our limited understanding of the molecular landscape and clinical consequences of the different TFE3 fusions presents as the major obstacle towards development of targeted therapeutic strategies for this disease. In this scenario of unmet clinical needs, we seek to define the molecular features of TFE3-tRCC, thereby uncovering specific vulnerabilities of tumor cells that prompt the development of new targeted therapeutic strategies.