The genomic landscape of esophageal squamous cell carcinoma cell lines

作者：Chao Zhang, Chenghao Li, Jian Su, Kuaile Zhao, Longlong Shao, Jiaying Deng · 发表于：Cancer Cell International · 年份：2025 · DOI：10.1186/s12935-025-03686-1 · 被引用次数：6 · 研究领域：Esophageal Cancer Research and Treatment、Cancer Immunotherapy and Biomarkers、Ferroptosis and cancer prognosis

BACKGROUND: Research on the genomic characteristics of common esophageal squamous cell carcinoma (ESCC) cell lines, including exome mutations and mRNA expression, is limited. This study aims to elucidate the malignancy, invasion capability, classical cancer-related signaling pathways, and immune status of ESCC cell lines, providing a detailed genomic landscape and highlighting the unique features of each cell line. METHODS: Whole exome and RNA sequencing were conducted on ESCC cell lines TE-1, ECA-109, KYSE-30, KYSE-150, KYSE-180, KYSE-450, and KYSE-510, with the normal epithelium cell line Het-1a as a comparison. Bioinformatics methods analyzed gene mutation types, mutation frequencies, RNA expression, and classical cancer-related signaling pathways. Specific analyses were also performed on tumor burden, genes related to differentiation, invasion, immunity, and gene enrichment in each cell line. RESULTS: The highest tumor mutation burden (TMB) was 70.4 mutations per megabase (mut/MB) in KYSE-150, while the lowest was 48.7 mut/MB in KYSE-510. Mutations in the Hippo, Notch, PI3K, RTK-Ras, and Wnt signaling pathways were present in all cancer cell lines. Mutations were significantly enriched in signature 3, associated with defective homologous recombination deficiency (HRD). The NRF2 signaling pathway exhibited mutations in KYSE-180, KYSE-450, and TE-1 cell lines. The cell cycle gene mutation frequency was low, occurring only in KYSE-30 and TE-1 cell lines. The expression profi...