Elongin BC complex negatively regulates AXL and marks a differentiated phenotype in melanoma

Abstract High expression of the receptor tyrosine kinase AXL is implicated in epithelial-to-mesenchymal transition, cancer progression and therapy resistance. For example, AXL is abundant in BRAF mutant melanomas progressing on targeted BRAF/MEK inhibition. Therefore, AXL is thought to represent an attractive therapeutic target. This notwithstanding, little is known about the mechanisms governing expression of AXL. Here, we describe a fluorescence-activated cell sorting (FACS)-based whole genome-wide CRISPR-Cas9 screen to uncover regulators of AXL expression. We identified several genes, inactivation of which led to increased AXL expression. Most remarkable was the identification of five components that associate with the Elongin B/C heterodimer. The Elongin B/C heterodimer engages in multiple protein-protein interactions, including the transcription factor complex subunit Elongin A, the von Hippel-Lindau (VHL) tumor suppressor protein, and members of the SOCS-box protein family. The screen identified ELOB, ELOC, SOCS5, UBE2F and RNF7, each of which we demonstrate to serve as an inhibitor of AXL expression. Although the AXL promoter contains hypoxia response elements and Elongin B/C are found in the VHL complex, Elongin B/C unexpectedly regulate AXL independently of hypoxia. Instead, we demonstrate that the Elongin BC complex interacts with AXL through ELOB, and contributes to proteasomal AXL turnover. RNA-sequencing analysis of several melanoma datasets revealed a negative association between Elongin B/C and dedifferentiation. This was confirmed by immunohistochemistry in patient-derived melanoma xenografts. These results uncover the Elongin BC complex as a key determinant of AXL expression in melanoma, and that this correlates with a differentiated state.