GSE115763
KLF6-dependent transcription in renal cancer cells
The PDGF and mTOR pathways are clinically relevant therapeutic targets in clear cell renal cell carcinoma (ccRCC), but the molecular mechanisms that lead to their activation has remained poorly understood. By chromatin and transcriptomic profiling and functional analysis we have identified Kruppel like factor 6 (KLF6), a transcription factor of the zinc-finger family, as a critical regulator of the PDGF-mTOR axis in ccRCC. KLF6 expression is supported by one of the strongest super enhancers in ccRCC cells. Inhibition of KLF6 in several ccRCC cell lines impaired cell proliferation in vitro and in vivo and reduced metastatic lung colonization. KLF6 depletion led to downregulation of lipid homeostasis pathways downstream of SREBF1 and SREBF2, suggesting a role for KLF6 as a regulator of mTOR. We find that KLF6 modulates mTORC1 activity in ccRCC via transcriptionally regulating the expression of PDGFB, an activator of the PIK3-AKT-mTOR signalling pathway. Targeting PDGFB in ccRCC inhibited mTORC1, and supplementing KLF6-depleted cells with recombinant PDGFB rescued mTORC1 activity. Our data suggest that a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway, supports an autocrine PDGFB-dependent signalling loop that promotes mTOR activity in ccRCC. These results suggest the possibility that combining low dose PDGFR and mTOR inhibition could be a viable therapeutic strategy for ccRCC. Overall design: mRNA profiling in experimental models of metastasis. 113 kb SE deletion is chr10:3793002-3906184 in hg38