Cui Heteng, Yang Wenyuan
Department of Oncology, The 940Th Hospital of Joint Logistic Support Force of Chinese People's Liberation Army, 333 Nan Bin He Road, Qilihe District, Lanzhou, 730050, Gansu, China.
Discov Oncol. 2024 Dec 4;15(1):747. doi: 10.1007/s12672-024-01646-1.
Hepatocellular carcinoma (HCC) is the sixth most frequently diagnosed cancer worldwide accompanied by a low 5-year survival rate. In our study, we aimed to analyze relevant genetic features that can predict the prognosis of HCC patients by single-cell RNA sequencing (scRNA-seq).
Single-cell RNA-seq data of HCC were analyzed from the Gene Expression Omnibus (GEO) database. Using the Seurat package, we performed quality control to remove cells with low quality. After normalization, we detected highly variable genes across the single cells. Then, cell clustering and Cell type annotation were performed using highly variable genes. Then, functional enrichment analyses were performed by GO and KEGG, and cell-cell communication analysis, trajectory analysis were conducted. LASSO-Cox regression analysis was used to perform Survival analysis and ROC evaluation for high and low-risk groups. Validation of the expressions and survival prognosis of the screened genes in HCC. Expression levels of the genes were analyzed by RT-qPCR and western blot in normal liver cell line THLE-3 and HCC cell lines (HuH7, HCCLM9, and HCCLM13).
A total of 2208 up-regulated and 1447 down-regulated genes were identified in HCC samples. These differentially expressed genes (DEGs) were enriched in several cytokine-related pathways and the MIF-CD74/CXCR4 signaling pathway. By integrating large amounts of RNA sequencing data, we identified 566 prognostic genes associated with HCC cells. Eleven genes were screened using the LASSO-COX risk factor model. Stratifying patients into high- or low-risk groups based on these genes allowed us to effectively predict their survival and ROC curve. Five genes were further found to be associated with poor survival prognosis in HCC and were notably overexpressed in HCC cell lines compared to normal liver cell line.
This study revealed potential prognostic marker genes in HCC patients, providing insights into predicting patients' survival rates.
肝细胞癌（HCC）是全球第六大常见癌症，5年生存率较低。在本研究中，我们旨在通过单细胞RNA测序（scRNA-seq）分析可预测HCC患者预后的相关基因特征。
从基因表达综合数据库（GEO）分析HCC的单细胞RNA-seq数据。使用Seurat软件包进行质量控制以去除低质量细胞。标准化后，我们检测单细胞中的高变基因。然后，使用高变基因进行细胞聚类和细胞类型注释。接着，通过GO和KEGG进行功能富集分析，并进行细胞间通讯分析和轨迹分析。使用LASSO-Cox回归分析对高、低风险组进行生存分析和ROC评估。对筛选出的基因在HCC中的表达和生存预后进行验证。通过RT-qPCR和蛋白质免疫印迹分析正常肝细胞系THLE-3和HCC细胞系（HuH7、HCCLM9和HCCLM13）中这些基因的表达水平。
在HCC样本中总共鉴定出2208个上调基因和1447个下调基因。这些差异表达基因（DEGs）富集于多个细胞因子相关途径和MIF-CD74/CXCR4信号通路。通过整合大量RNA测序数据，我们鉴定出566个与HCC细胞相关的预后基因。使用LASSO-COX风险因子模型筛选出11个基因。根据这些基因将患者分为高风险或低风险组，使我们能够有效预测他们的生存情况和ROC曲线。进一步发现5个基因与HCC患者的不良生存预后相关，并且与正常肝细胞系相比，在HCC细胞系中显著过表达。
本研究揭示了HCC患者潜在的预后标志物基因，为预测患者生存率提供了见解。
