Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer.

Enhancer -regulatory elements play critical roles in gene regulation at many stages of cell growth. Enhancers in cancer cells also regulate the transcription of oncogenes. In this study, we performed a comprehensive analysis of long-range chromatin interactions, histone modifications, chromatin accessibility and expression in two gastric cancer (GC) cell lines compared to normal gastric epithelial cells. We found that GC-specific enhancers marked by histone modifications can activate a population of genes, including some oncogenes, by interacting with their proximal promoters. In addition, motif analysis of enhancer-promoter interacting enhancers showed that GC-specific transcription factors are enriched. Among them, we found that is crucial for GC cell growth and activated by the enhancer with an enhancer-promoter loop and  upregulation. Clinical GC samples showed epigenetic activation of enhancers at the locus and significant upregulation of and , regardless of molecular GC subtype and clinicopathological factors. Single-cell RNA sequencing of gastric mucosa with intestinal metaplasia showed high expression of and in intestinal stem cells. When we inactivated the loop-forming enhancer at the locus using CRISPR interference (dCas9-KRAB), GC cell growth was significantly inhibited. In conclusion, we identified as an oncogene activated by a loop-forming enhancer and contributing to GC cell growth.