■RNA在肿瘤发生中起重要作用。RNA的变化可能导致生物学功能的变化。作为最广泛存在的RNA修饰,N7-甲基鸟苷(m7G)甲基化修饰在肿瘤进展中发挥不可或缺的功能。肝细胞癌(HCC)是全球范围内对人类健康的最大威胁之一。低检出率仍然是晚期疾病进展的主要原因。因此,在HCC中寻找用于预后预测和免疫治疗应答的重要生物标志物是有价值和迫切需要的。
从癌症基因组图谱(TCGA)数据库和基因表达综合(GEO)数据库获得RNA表达和临床数据。通过共识聚类完成不同亚型的筛选。用R软件进行不同的表达。通过蛋白质印迹(WB)方法验证结果。利用最小绝对收缩和选择算子(LASSO)分析鉴定具有HCC预后潜力的基因。借助我们计算的风险评分建立了预后模型。使用GeneMANIA数据库进行相关基因筛选和蛋白质-蛋白质相互作用(PPI)网络构建。使用注释数据库执行功能注释,可视化和集成发现(DAVID)数据库。此外,用R软件对关键基因和免疫浸润状态进行基因集富集分析(GSEA)。最后,免疫浸润采用cibersort方法和单样品GSEA(ssGSEA)方法进行。通过肿瘤免疫功能障碍和排除数据库(TIDE)和GEO数据库中的免疫治疗队列验证了免疫治疗的反应。
■我们发现与m7GRNA修饰相关的两种不同亚型和与m7GRNA修饰相关的四种基因在TCGA-肝细胞癌(TCGA-LIHC)数据库中差异表达。此外,根据LASSO检查这四个基因在HCC患者预后中的价值,我们选择了三个基因,包括WDR4,AGO2和NCBP2,作为预后相关基因。以这三个基因的表达为前提,我们构建了风险评分模型和列线图,以预测HCC患者的预后.我们进行了功能注释,并基于三个基因(WDR4,NCBP2和AGO2)创建了PPI网络。使用R软件,我们进行了GSEA和免疫调节分析.最后,我们预测了基因表达与免疫治疗反应之间的关系。
■我们的研究表明,m7GRNA修饰亚型的高表达与不良预后和免疫反应有关。WDR4、AGO2和NCBP2是m7GRNA修饰的关键调节因子,其可以是可用于治疗HCC的临床上有希望的生物标志物。此外,我们的风险评分模型被证明与HCC患者的OS密切相关.
UNASSIGNED: RNA plays an important role in tumorigenesis. Changes in RNA may cause changes in the biological function. The N7-methylguanosine (m7G) methylation modification performs an integral function in tumor progression as the most widely existed RNA modification. Hepatocellular carcinoma (HCC) is among the greatest threats to human health worldwide. Low detection rates remain the main cause of advanced disease progression. Therefore, finding significant biomarkers for prognosis prediction and immune therapy response in HCC is valuable and urgently needed.
UNASSIGNED: RNA expression and clinical data were acquired from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Different subtypes screening was finished by consensus cluster. Different expression was performed by R software. The results were validated by western blot (WB) methods. Genes with HCC prognostic potential were identified utilizing least absolute shrinkage and selection operator (LASSO) analyses. A prognosis model was established with the help of the risk score that we calculated. Related genes screening and protein-protein interactions (PPI) network construction were performed using the GeneMANIA database. Functional annotation was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) databases. In addition, gene set enrichment analysis (GSEA) of key genes and immune infiltration status were both done by R software. Finally, the immune infiltration was performed by cibersort method and single sample GSEA (ssGSEA) method. The response of immune therapy was validated by Tumor Immune Dysfunction and Exclusion database (TIDE) and the immune therapy cohort in GEO database.
UNASSIGNED: We found that two different subtypes related with m7G RNA modification and four genes associated with m7G RNA modification were differentially expressed in the TCGA-Liver Hepatocellular Carcinoma (TCGA-LIHC) database. Additionally, to examine the value of these four genes in the HCC patients\' prognoses according to the LASSO, we selected three genes, including WDR4, AGO2, and NCBP2, as prognostic related genes. Premised on the expression of these three genes, a risk score model and nomogram were constructed to provide a prediction of the HCC patients\' prognoses. We performed functional annotation and created a PPI network based on the three genes (WDR4, NCBP2, and AGO2). Using R software, we performed the GSEA and immune regulation analyses. Finally, we predicted the relationship between the gene expression and the response of immune therapy.
UNASSIGNED: Our study suggests that high expression of m7G RNA modification subtype is related with poor prognosis and immune response. WDR4, AGO2, and NCBP2 are key regulators of m7G RNA modification which can be clinically promising biomarkers that can be used to treat HCC. In addition, our risk score model was shown to have a strong link to OS in patients with HCC.