Analysis and Identification of Hub Genes in Hepatocellular Carcinoma Based on Weighted Gene Co-expression Network and Cancer Genome Atlas Clinical Data
摘要: 背景 肝细胞癌（HCC）是全球常见的癌症相关死亡的第三大原因，约占所有原发性肝癌病例的90%，其复发率和死亡率较高，目前发生的分子机制仍不清楚。目的 探索HCC潜在的分子机制，发掘新的生物标志物。方法 从GEO数据库中下载基因表达谱GSE62232，从TCGA数据库下载RNA-seq表达数据和临床相关信息，通过差异基因表达分析正常肝脏组织与HCC组织的差异基因；对差异表达基因进行富集分析；基于TCGA中HCC和GSE62232的基因表达数据概况，使用WGCNA R包建立共表达网络，进行加权基因共表达网络分析（WGCNA），选择具有临床意义的模块，并筛选候选Hub基因；进一步分析候选Hub基因在HCC组织和正常肝脏组织显著差异表达、与HCC患者总体生存期和无病生存期是否显著相关，最终确定Hub基因；通过人类蛋白质图谱数据库对Hub基因蛋白表达进行验证。结果 本研究的基因表达数据来自50个正常肝脏组织样本和373个HCC组织样本。通过差异基因表达分析发现7 230个在HCC和正常肝脏组织之间差异表达的基因（HCC中3 691个上调基因和3 539个下调基因）。富集分析表明，上调的差异表达基因主要参与细胞周期调控和有丝分裂过程；下调的差异表达基因主要参与小分子代谢和有机酸代谢等过程。WGCNA确定了19个与HCC患者临床特征相关基因模块，通过分析模块与临床特征之间的关系，筛选出青色模块和紫色模块。青色模块基因中同时与患者总生存期和无病生存期强烈相关的前两个基因为VPS45和FAM189B；紫色模块基因中同时与患者总生存期和无病生存期强烈相关的前两个基因分别为CLEC1B和FCN3，因此将VPS45、FAM189B、CLEC1B和FCN3确定为最终的Hub基因。人类蛋白质图谱数据库免疫组织化学染色显示：VPS45和FAM189B在HCC组织中的表达高于正常肝脏组织，FCN3在HCC组织中的表达低于正常肝脏组织，CLEC1B在HCC组织和正常肝脏组织中表达差异不明显。结论 初步确定VPS45、FAM189B、CLEC1B和FCN3可能是HCC的新型潜在生物标志物，这些Hub基因可能为HCC的靶向治疗提供理论基础。
Abstract: Background Hepatocellular carcinoma（HCC） is the third leading cause of common cancer-related mortality globally，accounting for approximately 90% of all primary liver cancer cases. Its recurrence and mortality rates are high，with the underlying molecular mechanisms remaining unclear. Objective To explore potential molecular mechanisms of HCC and explore novel biomarkers. Methods Gene expression profile GSE62232 was retrieved from the GEO database，RNA-seq expression data and clinical information were retrieved from TCGA database，differential gene expression analysis was conducted between normal liver tissue and HCC tissue. Enrichment analysis on the differentially expressed genes was performed. Based on the gene expression data profiles of HCC and GSE62232 in TCGA，a co-expression network was established using the WGCNA R package，and weighted gene co-expression network analysis（WGCNA） was performed to select clinically significant modules and screen candidate Hub genes；the candidate Hub genes were further analyzed for significant differential expression in HCC tissues and normal liver tissues，and whether they were significantly correlated with the overall survival and disease-free survival of HCC patients. The hub genes were conclusively identified，and their protein expression was validated through the Human Protein Atlas database. Results The genetic expression data in this study were obtained from 50 normal liver tissue samples and 373 HCC tissue samples. Through differential gene expression analysis，a total of 7 230 genes differential expression between HCC and normal hepatic tissue，comprising 3 691 up-regulated genes and 3 539 down-regulated genes in HCC were identified. Enrichment analysis showed that the up-regulated differentially expressed genes were mainly involved in cell cycle regulation and mitotic processes；the down-regulated differentially expressed genes were mainly involved in processes such as small molecule metabolism and organic acid metabolism. WGCNA identified 19 gene modules related to the clinical features of HCC patients，the cyan and purple modules were screened by analyzing the relationship between the modules and the clinical features. The first two genes in the cyan module genes that were strongly associated with both overall survival and disease-free survival of patients were VPS45 and FAM189B. In the purple module genes，first two genes that were strongly associated with both overall survival and disease-free survival of patients were CLEC1B and FCN3，respectively；therefore，VPS45，FAM189B，CLEC1B and FCN3 were identified as the final Hub genes. Immunohistochemical staining in the Human Protein Atlas database showed that VPS45 and FAM189B were expressed higher in HCC tissues than in normal liver tissues. FCN3 was expressed in HCC tissues lower than in normal liver tissues，the difference in the expression of CLEC1B between HCC tissues and normal liver tissues was not obvious. Conclusion VPS45，FAM189B，CLEC1B and FCN3 have been preliminary identified as possible novel potential biomarkers for HCC，which may provide a theoretical basis for targeted therapy of HCC.
| [V1] | 2023-11-17 15:15:17 | ChinaXiv:202311.00139V1 | 下载全文 |
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