Clear cell renal cell carcinoma (ccRCC) is characterised by frequent inactivation of the VHL tumour suppressor gene and consequent accumulation of HIF2A that drives tumourigenesis. The current clinically-approved therapies for ccRCC are those targeting the angiogenesis and mTOR signalling pathways, however, the overall patients’ objective response rates are still low, and patients rapidly develop resistance towards the administered therapies. An incomplete understanding of the underlying molecular mechanisms that support ccRCC progression has contributed to the lack of effective diagnostic and/or therapeutic strategies developed, especially for the highly mortal advanced stage ccRCC. Thus, the identification of cellular networks on which ccRCC cells are highly dependent would facilitate the development of better diagnostic and/or therapeutic approaches for ccRCC.

Super enhancers have been reported to drive the expression of critical transcription regulators in various biological contexts including the regulation of cancer phenotypes. Previously generated H3K27ac ChIP-Seq data from several ccRCC cell lines has identified KLF6, a zinc finger DNA-binding transcription factor, to be associated with one of the strongest super enhancers in ccRCC, which could signify a biological relevance to KLF6 in supporting ccRCC pathogenesis. Thus, the purpose of this present study was to interrogate the role of KLF6 in ccRCC, and dissect the KLF6-regulated transcriptional networks and how they can contribute in supporting ccRCC pathogenesis.

It was discovered that KLF6 expression was supported by a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway. In line with its regulation by the super enhancer, CRISPR-Cas9 and CRISPRi-mediated perturbation of KLF6 led to impaired ccRCC cells growth in vitro and in vivo as well as reducing the cells metastatic lung colonisation capability. KLF6 inhibition led to the deregulation of lipid homeostasis pathways in ccRCC cells. A dual KLF6 role was identified in modulating lipid homeostasis pathways in ccRCC: First, KLF6 directly regulates the expression of several important lipid homeostasis genes. Second, KLF6 promotes PDGFB expression, which activates the mTORC1 signalling pathway and the key lipid metabolism transcriptional regulators SREBF1 and SREBF2. KLF6 and mTORC1 thus co-regulate lipid homeostasis, consequently supporting ccRCC cell growth. Furthermore, findings from this study also reveal a molecular link between the PDGF and mTORC1 signalling pathways, which are the clinically relevant therapeutic targets in ccRCC. In general, the link between super enhancer-driven transcriptional networks and essential metabolic pathways described herein may provide clues to the mechanisms that maintain the stability of cell identity-defining transcriptional programmes in cancer.