Multiomics analysis reveals the enhancer landscapes and 3D chromatin architecture in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most common digestive‑tract malignancy. Aberrant 3D chromatin structure contributes to enhancer landscape disruption in many cancers, but relevant research on this topic in ESCC is still lacking. In this study, CUT&Tag was performed in ESCC cell lines (KYSE30 and KYSE150) and a normal esophageal epithelial cell line (HEEC) to reveal the epigenetic landscape and identify cancer-specific enhancers. Then, we employed RNA‑seq to evaluate gene transcription and Hi‑C to explore how 3D chromatin structure regulates the epigenetic landscape and gene expression. Findings show changes in enhancer profiles and gene expression in ESCC, along with alterations in A/B compartments, TADs, and chromatin loops associated with epigenetic changes. Notably, LIMK1 , EIF4H , and ABHD11 genes exhibited enhanced chromatin interactions and coexpressed patterns in the same chromatin interaction network. Our findings uncover the ESCC 3D genomic landscape and illustrate how 3D structural changes disrupt cancer‑specific enhancers and oncogene expression, providing insights into ESCC pathogenesis.