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.1.Ministry of Higher Education Malaysia
2.National University of Malaysi