Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition

Abstract

Mammalian target of rapamycin (mTOR) is a central regulator of mammalian metabolism and physiology. Aberrant hyperactivation of the mTOR pathway promotes tumor growth and metastasis, and can also promote tumor resistance to chemotherapy and cancer drugs; this makes mTOR an attractive cancer therapeutic target. mTOR inhibitors have been approved to treat cancer; however, the mechanisms underlying drug sensitivity remain poorly understood. Here, whole exome sequencing of three chromophobe renal cell carcinoma (chRCC) patients with exceptional mTOR inhibitor sensitivity revealed that all three patients shared somatic mutations in the deubiquitinase gene USP9X. The clonal characteristics of the mutations, which were amassed by studying multiple patients' primary and metastatic samples from various years, together with the low USP9X mutation rate in unselected chRCC series, reinforced a causal link between USP9X and mTOR inhibitor sensitivity. Rapamycin treatment of USP9X-depleted HeLa and renal cancer 786-O cells, along with the pharmacological inhibition of USP9X, confirmed that this protein plays a role in patients' sensitivity to mTOR inhibitors. USP9X was not found to exert a direct effect on mTORC1, but subsequent ubiquitylome analyses identified p62 as a direct USP9X target. Increased p62 ubiquitination and the augmented rapamycin effect upon bortezomib treatment, together with the results of p62 and LC3 immunofluorescence assays, suggested that dysregulated autophagy in USP9X-depleted cells can have a synergistic effect with mTOR inhibitors. In summary, we show that USP9X constitutes a potential novel Abbreviations: chRCC, chromophobe renal cell carcinoma; DAPI, 4,6-diamidino-2-phenylindole; IHC, immunohistochemistry; indels, small insertions or deletions; KO, knockout; mTOR, mammalian target of rapamycin; SNVs, single nucleotide variants; WES, whole exome sequencing.

Integrated mendelian randomization analyses highlight AFF3 as a novel eQTL-mediated susceptibility gene in renal cancer and its potential mechanisms

“…Solarek et al showed that insulin and insulin-like growth factors could serve as the intratumoral regulators of RC [ 39 ]. Roldán-Romero et al revealed that the loss of the deubiquitinase gene USP9X could sensitize RC cells to mTOR inhibition [ 40 ]. Nam et al shed light on that the TGF-β/HDAC7 pathway would suppress the metabolism of the TCA cycle in RC [ 41 ].…”