| 赵小迎,林晓筠,洪瑞璟,慈兴元,陈俊.宫颈癌差异表达基因的生物信息学分析及验证[J].浙江中西医结合杂志,2024,34(11): |
| 宫颈癌差异表达基因的生物信息学分析及验证 |
| Bioinformatics analysis of cervical cancer microarray based on GEO database |
| 投稿时间：2023-10-23 修订日期：2024-10-30 |
| DOI： |
| 中文关键词: 生物信息学 宫颈癌 基因芯片 差异基因 |
| 英文关键词:Bioinformatics Cervical cancer Gene chip Differences in gene |
| 基金项目:浙江省卫健委课题（2019KY668）；杭州市医药卫生科技项目（B20210313）；国家级大学生创新创业训练计划项目（202310343070S） |
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| 中文摘要: |
| 目的 筛选宫颈癌组织与癌旁正常组织之间差异表达基因，通过分析得到互作模块中度值较大的关键基因，并探究其作用，进而探索宫颈癌的发病机制。方法 从公共基因芯片数据库（GEO）中筛选并下载3组宫颈癌及其癌旁组织基因表达谱芯片数据，运用R软件的Limma、affymetrix以及heatmap等程序包对获取的芯片数据进行分析，获取差异表达显著的基因；随后使用DAVID网站的在线分析工具对差异表达的基因进行功能分析，以获取各基因的功能及其可能参与的信号通路。同时为进一步了解各差异表达基因之间的关联性，使用了 String10.0 数据库进行蛋白互作的分析，应用Cytoscape 软件建立PPI互作模块，进而筛选到关键基因；最后运用qPCR方法在组织水平验证关键基因的表达情况。结果 （1）与癌旁组织相比共有142个基因在宫颈癌组织中表达有差异，其中表达具有显著差异的为31个，包括24个上调基因和7个下调基因；（2）GO富集结果显示， DEGs 分别在42条生物过程（Biological Process，BP）、15 条细胞组成（Cellular Component，CC）、8条分子功能（Molecular Function，MF）和 6条 KEGG 通路中富集。宫颈癌中表达上调的基因不仅在细胞生长相关的信号通路如细胞周期、DNA复制、卵母细胞减数分裂等中发挥作用，还在细胞生物学过程相关的信号通路如蛋白质结合、ATP结合、p53信号通路等中发挥作用；（3）基于String数据库型筛选出RRM2、MCM2、ASPM、MCM4和CCNB1等5个degree得分较高的关键基因，Cytoscape 软件 MCODE插件共筛选出显著模块1个，涉及基因主要富集在DNA复制、细胞周期等信号通路。（4）qPCR结果显示ASPM在宫颈癌组织中表达高于癌旁组织，与上述分析结果一致。结论 宫颈癌发生、发展可能与关键基因：RRM2、MCM2、ASPM、MCM4和CCNB1有关。这些基因主要是参与DNA复制、细胞周期、p53信号通路等在宫颈癌相关的生物过程中发挥作用。RT-qPCR的结果提示ASPM基因的差异表达参与了宫颈癌的发生。 |
| 英文摘要: |
| Objective: To screen differentially expressed genes (DEGs) between cervical cancer tissue and normal adjacent tissues, and identify key genes to explore their roles and pathogenesis. Method: Three sets of cervical cancer expression profile chip data were collected from the Public Gene Chip Database (GEO), and differential gene expression analysis was performed on the obtained chip data using R software to obtain differentially expressed genes in cervical cancer tissue and adjacent tissues. Perform Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Protein Interaction (PPI) network analysis on the differentially expressed genes obtained. Use Cytoscape to establish a PPI interaction module and screen for key genes. Verify the expression of key genes in cervical cancer and adjacent tissues using RT qPCR method. Results (1) Through differential analysis, 31 differentially expressed genes were identified, including 24 upregulated genes and 7 downregulated genes; (2) The GO enrichment results showed that DEGs were enriched in 42 biological processes (BP), 15 cellular components (CC), 8 molecular functions (MF), and 6 KEGG pathways, respectively. The upregulated genes are mainly enriched in biological processes such as protein binding, nuclear and ATP binding, as well as signaling pathways such as cell cycle, p53 signaling pathway, DNA replication, and oocyte meiosis; (3) Based on the String database, five key genes with high degree scores, including RRM2, MCM2, ASPM, MCM4, and CCNB1, were screened. The Cytoscape software MCODE plugin screened a significant module, involving genes mainly enriched in signal pathways such as DNA replication and cell cycle. (4) The qRT PCR results showed that ASPM expression was higher in cervical cancer tissues than in adjacent tissues, consistent with the above analysis results. Conclusion: The occurrence and development of cervical cancer may be related to key genes: RRM2, MCM2, ASPM, MCM4, and CCNB1. These genes are mainly involved in DNA replication, cell cycle, p53 signaling pathways, and other biological processes related to cervical cancer. The results of RT qPCR suggest that differential expression of ASPM gene is involved in the occurrence of cervical cancer. |
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