Therapeutic targeting of TFE3/IRS-1/PI3K/mTOR axis in translocation renal cell carcinoma

Purpose: Translocation renal cell carcinoma (tRCC) represents a rare subtype of kidney cancer associated with various TFE3, TFEB, or MITF gene fusions that is not responsive to standard treatments for RCC. Therefore, the identification of new therapeutic targets represents an unmet need for this disease. Experimental Design: We have established and characterized a tRCC patient-derived xenograft (PDX), RP-R07, as a novel preclinical model for drug development by using next generation sequencing and bioinformatics analysis. We then assessed the therapeutic potential of inhibiting the identified pathway using in vitro and in vivo models. Results: The presence of a SFPQ-TFE3 fusion (t(X;1) (p11.2; p34)) with chromosomal break-points was identified by RNA-seq and validated by RT-PCR. TFE3 chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis indicated a strong enrichment for the PI3K/AKT/mTOR pathway. Consistently, microRNA microarray analysis also identified PI3K/AKT/mTOR as a highly enriched pathway in RP-R07. Upregulation of PI3/AKT/mTOR pathway in additional TFE3-tRCC models were confirmed by significantly higher expression of phospho-S6 (P<0.0001) and phospho-4EBP1 (P<0.0001) in established tRCC cell lines compared to clear cell RCC cells. Simultaneous vertical targeting of both PI3K/AKT and mTOR axis provided a greater anti-proliferative effect both in vitro (P<0.0001) and in vivo (P<0.01) compared to single node inhibition. Knockdown of TFE3 in RP-R07 resulted in decreased expression of IRS-1 and inhibited cell proliferation. Conclusions: These results identify TFE3/IRS-1/PI3K/AKT/mTOR as a potential dysregulated pathway in TFE3-tRCC, and suggest a therapeutic potential of vertical inhibition of this axis by using a dual PI3K/mTOR inhibitor for TFE3-tRCC patients.

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