Dual activation of autophagy and mTOR by TFE3 fusions promotes tumorigenesis in rearranged renal cell carcinoma

TFE3-rearranged renal cell carcinoma (TFE3-RCC), an aggressive kidney cancer predominantly affecting pediatric and young adult populations, is driven by Xp11.2 rearranged generating oncogenic TFE3 fusion proteins. Although these fusions define the disease, their mechanistic roles remain elusive. Here, lentiviral-mediated overexpression of PRCC-TFE3 or NONO-TFE3 in RCC models triggered nuclear rearranged fusion proteins and significantly accelerated tumor proliferation both in vitro and in vivo. Our integrated RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analyses mechanistically revealed that TFE3 fusions directly bind to promoters of lysosome and mTOR signaling pathway genes, leading to transcriptional activation of this pathway. Moreover, the fusions aberrantly escaped canonical mTOR signaling pathway regulation and paradoxically hyperactivated phospho-mTOR signaling. Importantly, dual inhibition of the autophagy and mTOR pathways synergistically suppressed tumor growth, exceeding the efficacy of single-agent treatments. These data demonstrate that co-targeting these TFE3-regulated pathways represents a promising therapeutic strategy for this intractable malignancy.