Yan Yichao, Liang Hailiang, Li Yongbai, Chen Dongbo, Li Bo, Murshed Abduh
Department of Gastroenterological Surgery, Peking University International Hospital, No.1 Life Park Road, Life Science Park of Zhong Guancun, Changping District, Beijing, P.R. China, 102206.
Department of General Surgery, Affiliated Hospital of Yangzhou University, Yangzhou, 225001, China.
Curr Cancer Drug Targets. 2025 Jan 2. doi: 10.2174/0115680096346279241203053210.
Colorectal adenocarcinoma [COAD] is a prevalent and lethal form of cancer. Understanding the molecular mechanisms underlying COAD progression is crucial for developing effective diagnostic and therapeutic strategies.
This study aims to explore wound healing-related genes in COAD and their potential roles in tumorigenesis and prognosis using in silico and in vitro methodology.
A set of 70 genes associated with the "wound healing" term ere extracted from the Gene Ontology [GO] database [GO:0042060] and a protein-protein interaction [PPI] network was constructed using the STRING database. The PPI network was analyzed with the CytoHubba plugin in Cytoscape, identifying four major hub genes: MMP2, FN1, NF1, and PTK7. We then analyzed the expression of these hub genes across 16 COAD cell lines and nine normal colon cell lines using RT-qPCR, finding significant overexpression in COAD cell lines. ROC curve analysis confirmed the diagnostic potential of these genes, with MMP2, FN1, and NF1 showing high AUC values. Expression validation using the TCGA COAD cohort, OncoDB, and HPA databases corroborated these findings, highlighting the overexpression and high protein levels of these genes in COAD. Promoter methylation analysis indicated lower methylation levels in COAD samples, suggesting dysregulation through epigenetic mechanisms. Genetic alteration analysis via cBioPortal revealed a spectrum of mutations, with FN1 being the most frequently mutated. Prognostic analysis using a KM plotter showed that high expression of the hub genes is associated with poorer overall survival [OS] and disease-free survival [DFS]. Functional state correlations via CancerSEA suggested that these genes promote cell cycle, proliferation, metastasis, and stemness in COAD. Expression analysis in immune cells and drug sensitivity analyses highlighted the roles of MMP2, FN1, and NF1 in macrophages and drug resistance. A miRNA-mRNA network constructed using miRNet identified hsa-miR-200a-3p as a central regulator. Finally, functional assays in HCT116 cells demonstrated that knockdown of MMP2 and FN1 reduced proliferation, colony formation, and wound healing, suggesting these genes as potential therapeutic targets in COAD.
In conclusion, our study identifies MMP2, FN1, NF1, and PTK7 as key wound healing-related hub genes in COAD.
结直肠癌[COAD]是一种常见且致命的癌症形式。了解COAD进展的分子机制对于制定有效的诊断和治疗策略至关重要。
本研究旨在使用计算机模拟和体外方法探索COAD中与伤口愈合相关的基因及其在肿瘤发生和预后中的潜在作用。
从基因本体论[GO]数据库[GO:0042060]中提取了一组与“伤口愈合”术语相关的70个基因，并使用STRING数据库构建了蛋白质-蛋白质相互作用[PPI]网络。使用Cytoscape中的CytoHubba插件对PPI网络进行分析，确定了四个主要的枢纽基因：MMP2、FN1、NF1和PTK7。然后，我们使用RT-qPCR分析了这16种COAD细胞系和9种正常结肠细胞系中这些枢纽基因的表达，发现它们在COAD细胞系中显著过表达。ROC曲线分析证实了这些基因的诊断潜力，其中MMP2、FN1和NF1显示出较高的AUC值。使用TCGA COAD队列、OncoDB和HPA数据库进行的表达验证证实了这些发现，突出了这些基因在COAD中的过表达和高蛋白水平。启动子甲基化分析表明COAD样本中的甲基化水平较低，提示通过表观遗传机制发生失调。通过cBioPortal进行的基因改变分析揭示了一系列突变，其中FN1是最常发生突变的基因。使用KM绘图仪进行的预后分析表明，枢纽基因的高表达与较差的总生存期[OS]和无病生存期[DFS]相关。通过CancerSEA进行的功能状态相关性分析表明，这些基因促进COAD中的细胞周期、增殖、转移和干性。免疫细胞中的表达分析和药物敏感性分析突出了MMP2、FN1和NF1在巨噬细胞和耐药性中的作用。使用miRNet构建的miRNA-mRNA网络确定hsa-miR-200a-3p为中心调节因子。最后，在HCT116细胞中进行的功能测定表明，敲低MMP2和FN1可降低增殖、集落形成和伤口愈合，提示这些基因是COAD中潜在的治疗靶点。
总之，我们的研究确定MMP2、FN1、NF1和PTK7是COAD中关键的与伤口愈合相关的枢纽基因。
