Shen Feng, Liu Xing, Ding Fengjiao, Yu Zhonglin, Shi Xinyi, Cheng Lushan, Zhang Xuewei, Jing Chengbao, Zhao Zilong, Cao Hongyou, Zhao Bing, Liu Jing
Clinical Laboratory, Ankang City Central Hospital, Ankang, 725000, China.
Oncology Department, Ankang City Central Hospital, Ankang, 725000, China.
Hereditas. 2025 Mar 14;162(1):38. doi: 10.1186/s41065-025-00398-4.
Esophageal squamous cell carcinoma (ESCA) is a type of cancer that starts in the cells lining the esophagus, the tube connecting the throat to the stomach. It is known for its aggressive nature and poor prognosis. Understanding the key factors that drive this cancer is crucial for developing better diagnostic tools and treatments.
Gene expression profiles of ESCA were analyzed using Gene Expression Omnibus (GEO) datasets (GSE23400, GSE29001, GSE92396, and GSE1420) from the GEO database. Differentially expressed genes (DEGs) were identified using the limma package, and a protein-protein interaction (PPI) network was constructed using the STRING database. Hub genes were identified based on the degree method. Further validation was performed through reverse transcription quantitative PCR (RT-qPCR), mutational and copy number variation (CNV) analysis via the cBioPortal database, promoter methylation analysis using the OncoDB and GSCA databases, survival analysis, immune infiltration analysis through the GSCA database, and functional assays, including knockdown of key genes.
We identified four key hub genes, COL3A1, COL4A1, COL5A2, and CXCL8 that play significant roles in ESCA. These genes were highly expressed in ESCA tissues and cell lines, with expression levels significantly (p-value < 0.001) elevated compared to normal controls. Receiver operating characteristic (ROC) curve analysis revealed exceptional diagnostic performance for all four genes, with area under the curve (AUC) values of 1.0, indicating perfect sensitivity and specificity in distinguishing ESCA from normal controls. Mutational analysis revealed that COL3A1 was altered in 67% of ESCA samples, primarily through missense mutations, while COL5A2 exhibited alterations in 50% of the samples, including splice site and missense mutations. Additionally, gene amplification patterns were observed in all four hub genes, further validating their oncogenic potential in ESCA progression. A significant (p-value < 0.05) promoter hypomethylation was detected in these genes, suggesting a potential regulatory role in their expression. Functional assays demonstrated that knocking down COL3A1 and COL4A1 led to decreased cell proliferation, colony formation, and migration, indicating their critical roles in tumor progression. Additionally, these genes were involved in pathways related to the extracellular matrix and immune system modulation.
COL3A1, COL4A1, COL5A2, and CXCL8 are crucial in ESCA development and progression, particularly in remodeling the extracellular matrix, modulating the immune system, and promoting metastasis. These findings suggest that these genes could serve as potential biomarkers for diagnosing ESCA and targets for future therapies. Future research should focus on in vivo validation of these findings and clinical testing to assess the therapeutic potential of targeting these genes in ESCA treatment.
食管鳞状细胞癌（ESCA）是一种起源于食管（连接咽喉与胃的管道）内衬细胞的癌症。它以侵袭性强和预后差而闻名。了解驱动这种癌症的关键因素对于开发更好的诊断工具和治疗方法至关重要。
使用来自基因表达综合数据库（GEO）的GEO数据集（GSE23400、GSE29001、GSE92396和GSE1420）分析ESCA的基因表达谱。使用limma软件包鉴定差异表达基因（DEG），并使用STRING数据库构建蛋白质-蛋白质相互作用（PPI）网络。基于度方法鉴定枢纽基因。通过逆转录定量PCR（RT-qPCR）、经由cBioPortal数据库的突变和拷贝数变异（CNV）分析、使用OncoDB和GSCA数据库的启动子甲基化分析、生存分析、通过GSCA数据库的免疫浸润分析以及包括关键基因敲低在内的功能测定进行进一步验证。
我们鉴定出四个关键枢纽基因，即COL3A1、COL4A1、COL5A2和CXCL8，它们在ESCA中发挥重要作用。这些基因在ESCA组织和细胞系中高表达，与正常对照相比，表达水平显著升高（p值<0.001）。受试者工作特征（ROC）曲线分析显示这四个基因均具有出色的诊断性能，曲线下面积（AUC）值为1.0，表示在区分ESCA与正常对照时具有完美的敏感性和特异性。突变分析显示，67%的ESCA样本中COL3A1发生改变，主要通过错义突变，而50%的样本中COL5A2发生改变，包括剪接位点和错义突变。此外，在所有四个枢纽基因中均观察到基因扩增模式，进一步验证了它们在ESCA进展中的致癌潜力。在这些基因中检测到显著的（p值<0.05）启动子低甲基化，表明其在表达中可能具有调节作用。功能测定表明，敲低COL3A1和COL4A1导致细胞增殖、集落形成和迁移减少，表明它们在肿瘤进展中起关键作用。此外，这些基因参与了与细胞外基质和免疫系统调节相关的途径。
COL3A1、COL4A1、COL5A2和CXCL8在ESCA的发生和进展中至关重要，特别是在重塑细胞外基质、调节免疫系统和促进转移方面。这些发现表明，这些基因可作为诊断ESCA的潜在生物标志物以及未来治疗的靶点。未来的研究应侧重于对这些发现进行体内验证以及临床测试，以评估靶向这些基因在ESCA治疗中的治疗潜力。
