Department of Gastroenterology, Zibo Central Hospital, Zibo, 255036, Shandong, China.
Department of Clinical Laboratory, Zibo Central Hospital, Zibo, 255036, Shandong, China.
Appl Biochem Biotechnol. 2024 Sep;196(9):6253-6268. doi: 10.1007/s12010-023-04812-3. Epub 2024 Jan 31.
To explore underlying mechanisms related to the progression of colon cancer and identify hub genes associated with the prognosis of patients with colon cancer. GSE10950 and GSE62932 were downloaded from the Gene Expression Omnibus (GEO) database. GEO2R was utilized to screen out the differentially expressed genes (DEGs). Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted on DEGs. Moreover, STRING and Cytoscape software were utilized for establishing the network of protein-protein interaction (PPI) and identifying hub genes. Afterward, data from The Cancer Genome Atlas (TCGA) was utilized for identifying prognosis-related hub genes by Kaplan-Meier survival analysis. Colon cancer cell line LOVO and human normal intestinal epithelial cell line NCM-460 were exploited to demonstrate the differential expression of selected hub genes through RT-qPCR and western blot. The LOVO cells were transfected to regulate expressions of prognosis-associated genes, followed by exploring the effects of those genes on prognosis by Cell Counting Kit-8 assay and colony-forming assay for cancer cell proliferation, cell scratch test and transwell migration assay for cancer cell migration and Annexin V-PE/7-AAD double staining as well as flow cytometry for cancer cell apoptosis. In this study, 266 common DEGs were obtained from the intersection of two datasets. The GO analysis suggested the common DEGs mainly participated in the one-carbon metabolic process, cell cycle G2/M phase transition, organelle fission, cell cycle phase transition regulation, and regulation of mitotic cell cycle phase transition. The KEGG analysis demonstrated the common DEGs were related to the p53 signaling pathway, nitrogen metabolism, mineral absorption, and cell cycle. 10 hub genes including CCNB1, KIF4A, TPX2, MT1F, PRC1, PLK4, CALD1, MMP9, CLCA1, and MMP1 were identified and CCNB1, CLCA1, and PLK4 were prognosis-related. Increased expression of CCNB1, CLCA1, and PLK4 restrained proliferation as well as migration of cancer cells and induced apoptosis of cancer cells. CCNB1, KIF4A, TPX2, MT1F, PRC1, PLK4, CALD1, MMP9, CLCA1, and MMP1 were identified as hub genes and CCNB1, CLCA1, and PLK4 could inhibit the progression of colon cancer through inhibiting proliferation as well as migration of the cancer cell and promoting apoptosis of cancer cell.
为了探究与结肠癌进展相关的潜在机制，并鉴定与结肠癌患者预后相关的枢纽基因。从基因表达综合数据库（GEO）中下载 GSE10950 和 GSE62932。利用 GEO2R 筛选差异表达基因（DEGs）。对 DEGs 进行基因本体论（GO）分析和京都基因与基因组百科全书（KEGG）通路分析。此外，利用 STRING 和 Cytoscape 软件构建蛋白质-蛋白质相互作用（PPI）网络并识别枢纽基因。随后，利用癌症基因组图谱（TCGA）的数据通过 Kaplan-Meier 生存分析鉴定与预后相关的枢纽基因。利用结肠癌细胞系 LOVO 和人正常肠上皮细胞系 NCM-460 通过 RT-qPCR 和 Western blot 验证所选枢纽基因的差异表达。转染 LOVO 细胞调节与预后相关基因的表达，然后通过细胞计数试剂盒-8 测定和集落形成实验评估这些基因对癌细胞增殖的影响，细胞划痕实验和 Transwell 迁移实验评估癌细胞迁移，Annexin V-PE/7-AAD 双染和流式细胞术评估癌细胞凋亡。在本研究中，从两个数据集的交集获得了 266 个共同的 DEGs。GO 分析表明，这些共同的 DEGs 主要参与一碳代谢过程、细胞周期 G2/M 期转换、细胞器分裂、细胞周期阶段调控和有丝分裂细胞周期阶段调控。KEGG 分析表明，这些共同的 DEGs 与 p53 信号通路、氮代谢、矿物质吸收和细胞周期有关。鉴定出包括 CCNB1、KIF4A、TPX2、MT1F、PRC1、PLK4、CALD1、MMP9、CLCA1 和 MMP1 在内的 10 个枢纽基因，其中 CCNB1、CLCA1 和 PLK4 与预后相关。CCNB1、CLCA1 和 PLK4 表达增加抑制了癌细胞的增殖和迁移，诱导了癌细胞的凋亡。CCNB1、KIF4A、TPX2、MT1F、PRC1、PLK4、CALD1、MMP9、CLCA1 和 MMP1 被鉴定为枢纽基因，CCNB1、CLCA1 和 PLK4 通过抑制癌细胞的增殖和迁移以及促进癌细胞凋亡来抑制结肠癌的进展。
