Elucidating the functional role of CCCTC-binding factor (CTCF) in hepatocellular carcinoma

Abstract

Hepatocellular carcinoma (HCC) is the most prevalent cause of cancer and cancer death in the world, where China accounts for more than half of new cases worldwide. Despite the advances in cancer treatments, the prognosis of HCC remains poor. Therefore, a thorough understanding of the mechanisms regarding HCC growth and metastasis is essential for the development of more effective treatments. Earlier evidence suggested that CCCTC-binding factor (CTCF), a highly conserved nuclear factor involved in the maintenance of genome architecture and transcriptional regulations, plays a role in HCC cells growth and metastasis. Furthermore, overexpression of CTCF in HCC is also associated with poor prognosis of the patients. The goal of my study is to further delineate the functional role of CTCF in HCC pathogenesis. I successfully created CTCF-knockout cell models using CRISPR/Cas9 technology. I confirmed the known growth and metastatic phenotypes of CTCF deficiency using the CTCF-knockout cell models. Transcriptomic and chromatin-immunoprecipitations sequencing (ChIP-seq) analysis identified genes regulated by CTCF. Bioinformatic analysis of CTCF-regulated genes further revealed enrichment of biological pathways related to metabolic processes. Concordantly, the rate of oxidative phosphorylation, the glycolytic flux, NAD⁺/NADH ratio, and cellular ATP levels, were compromised in CTCF knockout cells, confirming a functional role of CTCF in HCC energy metabolism. Analysis of CTCF-regulated genes related to metabolic processes revealed three genes that are implicated in the regulation of cellular NAD⁺/NADH ratio, which includes fatty acid desaturase 1 (FADS1), IQ Motif Containing GTPase Activating Protein 2 (IQGAP2), and glutamic-oxaloacetic transaminase 2 (GOT2), respectively, suggesting that these genes may mediate the phenotypes of CTCF deficiency. Accordingly, a significantly reduction in cellular NAD⁺/NADH ratio was observed when FADS1 and IQGAP2 was knocked down in HCC cells respectively. Furthermore, knockdown of FADS1 and IQGAP2 respectively resulted in reduced HCC cell growth, cell migration and invasion, as well as oxidative phosphorylation and glycolytic flux, to an extent similar to the knockout CTCF knockout, suggesting that the two genes are potential players in the CTCF regulatory axis for metabolic regulation. Further works are required to confirm if ectopic expression of the two gene could rescue the phenotypes of CTCF knockout. My study has discovered a novel functional role of CTCF in HCC cells in energy homeostasis, suggested a potential HCC intervention strategy via CTCF inhibition.