A CCCTC-binding factor (CTCF)-fatty acid desaturase 1 (FADS1) axis regulates oncogenic energy metabolism in hepatocellular carcinoma

CCCTC-binding factor (CTCF) is a highly conserved DNA-binding protein crucial for 3D genome organization and gene regulation. Previous studies have shown that CTCF overexpression in hepatocellular carcinoma (HCC) is associated with poor prognosis. This study aimed to elucidate the molecular mechanisms underlying CTCF's role in HCC pathogenesis and identify the downstream effectors that mediate its oncogenic functions. We generated CTCF knockout HCC cell lines (Huh7 and PLC5) using the CRISPR-Cas9 technology. CTCF knockout significantly reduced HCC cell proliferation, colony formation, migration, and invasion capabilities while inducing cellular senescence. Chromatin immunoprecipitation-sequencing analysis revealed that CTCF knockout in HCC cells preferentially affected its binding to promoters and enhancers rather than topologically associating domain boundaries. In contrast, genes that were commonly downregulated in the two CTCF knockout cell lines were significantly enriched in the energy metabolism pathway, and fatty acid desaturase 1 (FADS1) emerging as a key CTCF target gene. We further found that CTCF and FADS1 expression levels are highly correlated in clinical HCCs with high expression levels associated with poor patient survival. FADS1 knockdown recapitulated the CTCF knockout phenotypes, including reduced ATP levels, impaired glycolysis and oxidative phosphorylation, and decreased NAD + /NADH ratios. Re-expression of FADS1 in CTCF knockout cells significantly upregulated ATP level associated with enhanced glycolytic and respiratory capacity. In vivo xenograft studies confirmed that tumor growth was significantly inhibited by CTCF or FADS1 depletion. This study highlighted a CTCF-FADS1 axis that predominately regulates energy metabolism in HCC cells with profound prognostic and therapeutic implications for HCCs.