The genomic landscape of esophageal squamous cell carcinoma cell lines.

IF 6 2区医学 Q1 ONCOLOGY

Cancer Cell International Pub Date : 2025-05-09 DOI:10.1186/s12935-025-03686-1

Chao Zhang, Chenghao Li, Jian Zhong Su, Kuaile Zhao, Longlong Shao, Jiaying Deng

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引用次数: 0

Abstract

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 profiles of KYSE-510 and ECA-109 were similar. The KYSE-150 cell line showed up-regulated invasion genes, while the KYSE-450 cell line had significantly down-regulated poor differentiation-related genes. Immune-related genes were up-regulated in the ECA-109 cell line.

Conclusion: The molecular profiles generated in this study provide detailed information on gene mutations and expression in common ESCC cell lines. The KYSE-150 cell line exhibited a prominent invasion capability, while the ECA-109 cell line showed up-regulated immune properties. This genomic landscape offers valuable insights for future research and therapeutic strategies in ESCC.

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食管鳞状细胞癌细胞系的基因组图谱。

背景：对常见食管鳞状细胞癌（ESCC）细胞系的基因组特征，包括外显子组突变和mRNA表达的研究是有限的。本研究旨在阐明ESCC细胞系的恶性、侵袭能力、经典癌症相关信号通路和免疫状态，提供详细的基因组图谱，突出每个细胞系的独特特征。方法：对ESCC细胞系TE-1、ECA-109、KYSE-30、KYSE-150、KYSE-180、KYSE-450和KYSE-510进行全外显子组和RNA测序，并与正常上皮细胞系Het-1a进行比较。生物信息学方法分析了基因突变类型、突变频率、RNA表达和经典的癌症相关信号通路。还对每个细胞系的肿瘤负荷、与分化、侵袭、免疫相关的基因和基因富集进行了具体分析。结果：KYSE-150中最高的肿瘤突变负荷（TMB）为70.4个突变/MB (mut/MB)， KYSE-510中最低的为48.7个突变/MB。所有癌细胞系中都存在Hippo、Notch、PI3K、RTK-Ras和Wnt信号通路的突变。突变显著富集于特征3，与同源重组缺陷（HRD）相关。NRF2信号通路在KYSE-180、KYSE-450和TE-1细胞系中表现出突变。细胞周期基因突变频率低，仅发生在KYSE-30和TE-1细胞系中。KYSE-510和ECA-109的表达谱相似。KYSE-150细胞系侵袭性基因上调，而KYSE-450细胞系弱分化相关基因显著下调。免疫相关基因在ECA-109细胞系中表达上调。结论：本研究生成的分子图谱提供了ESCC常见细胞系基因突变和表达的详细信息。KYSE-150细胞系表现出明显的侵袭能力，而ECA-109细胞系表现出上调的免疫特性。这一基因组图谱为ESCC的未来研究和治疗策略提供了有价值的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Cancer Cell International ONCOLOGY-

CiteScore

10.90

自引率

1.70%

发文量

360

审稿时长

1 months

期刊介绍： Cancer Cell International publishes articles on all aspects of cancer cell biology, originating largely from, but not limited to, work using cell culture techniques. The journal focuses on novel cancer studies reporting data from biological experiments performed on cells grown in vitro, in two- or three-dimensional systems, and/or in vivo (animal experiments). These types of experiments have provided crucial data in many fields, from cell proliferation and transformation, to epithelial-mesenchymal interaction, to apoptosis, and host immune response to tumors. Cancer Cell International also considers articles that focus on novel technologies or novel pathways in molecular analysis and on epidemiological studies that may affect patient care, as well as articles reporting translational cancer research studies where in vitro discoveries are bridged to the clinic. As such, the journal is interested in laboratory and animal studies reporting on novel biomarkers of tumor progression and response to therapy and on their applicability to human cancers.