肝癌铜死亡相关基因及其与预后、免疫浸润的关系分析
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1.湖南医药学院 医学院,湖南 怀化 418000;2.湖南医药学院 基础医学院,湖南 怀化 418000;3.湖南医药学院第一附属医院 普通外科,湖南 怀化 418000

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陈伟毅,湖南医药学院讲师,主要从事消化系统肿瘤防治方面的研究。

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湖南省自然科学基金资助项目(2022JJ50290);湖南省卫生健康委科研立项课题基金资助项目(202104081483);国家级大学生创新创业训练计划基金资助项目(202212214009);2022年度湖南省大学生创新创业训练计划基金资助项目(5021)。


Analysis of cuproptosis-related genes in liver cancer and their association with prognosis and immune infiltration
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1.School of Medicine, the First Affiliated Hospital of Hunan University of Medicine, Huaihua, Hunan 418000, China;2.School of Basic Medical Sciences, Hunan University of Medicine, Huaihua, Hunan 418000, China, the First Affiliated Hospital of Hunan University of Medicine, Huaihua, Hunan 418000, China;3.Department of General Surgery, the First Affiliated Hospital of Hunan University of Medicine, Huaihua, Hunan 418000, China

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    摘要:

    背景与目的 肝癌是消化道恶性肿瘤之一,发病率高、病死率高。铜死亡是一种铜依赖、新型的细胞死亡方式,继发于铜过载诱发的线粒体功能受损。铜死亡在多种肿瘤中扮演重要作用,但其与肝癌的关系尚不清楚。因此,本研究探讨铜死亡相关基因在肝癌中的表达特征,以及与肝癌预后及免疫浸润的关系。方法 从TCGA和GTEx数据库下载肝癌和正常肝脏组织转录组数据进行差异表达和突变分析。采用R语言“clusterProfiler”包进行GO和KEGG富集分析。采用LASSO、单因素和多因素回归分析筛选影响肝癌患者预后的基因并构建风险因子图。使用R包“rms”构建列线图。使用UALCAN数据库分析铜死亡相关基因与肝癌临床病理特征的关系并验证。使用Spearman相关性分析铜死亡相关基因与免疫细胞浸润和免疫检查点的相关性。采用TIMER2.0数据库分析铜死亡相关基因表达与肿瘤相关成纤维细胞(CAF)浸润的相关性,采用TISDB数据库分析CDKN2A和DLAT表达与髓源抑制性细胞(MDSC)浸润丰度的相关性。结果 与正常肝脏组织比较,9个铜死亡相关基因在肝癌中表达显著升高,CDKN2A突变频率最高。铜死亡相关基因主要参与蛋白质脂酰化、三羧酸循环、柠檬酸循环等生物过程。基于LASSO、单因素与多因素回归分析筛选出影响肝癌患者总体生存率(OS)的基因CDKN2A和DLAT,并以此构建风险因子图,时间依赖性受试者工作特征曲线显示其具有较好的预测能力。通过单因素和多因素回归分析筛选出CDKN2A、DLAT、T分期和肿瘤状态是影响肝癌患者OS的独立预后因素,基于上述因素构建了列线图,校正曲线显示该列线图预测和实际观察之间有很好的一致性。UALCAN数据库分析发现CDKN2A、DLAT与肝癌临床分期、肿瘤分级有关,且GEO数据库、HPA数据库及肝癌细胞中的验证结果与之一致。相关性分析显示,CDKN2A和DLAT表达与免疫细胞浸润和免疫检查点表达相关;TIMER2.0数据库分析显示,DLAT表达与CAF浸润明显正相关;TISDB数据库分析显示,CDKN2A和DLAT表达与MDSC浸润丰度无相关性。结论 铜死亡相关基因CDKN2A、DLAT可能是肝癌新的预后生物标志物和免疫治疗的新靶点。

    Abstract:

    Background and Aims Liver cancer is one of the malignant tumors of the digestive system, characterized by high incidence and mortality rates. Cuproptosis, a novel copper-dependent form of cell death, occurs as a result of mitochondrial dysfunction induced by copper overload. Cuproptosis plays a significant role in various tumors, but its relationship with liver cancer remains unclear. Therefore, this study was conducted to investigate the expression characteristics of cuproptosis-related genes in liver cancer and their association with prognosis and immune infiltration.Methods Transcriptome data of liver cancer and normal liver tissues were downloaded from TCGA and GTEx databases for differential expression and mutation analysis. The R language "clusterProfiler" package was used for GO and KEGG enrichment analysis. LASSO, univariate, and multivariate regression analyses were employed to screen genes affecting the prognosis of liver cancer patients and a risk factor graph was constructed. A nomogram was constructed using the "rms" package in R. The UALCAN database was used to analyze the relationship between cuproptosis-related genes and clinicopathologic features of liver cancer and then the findings were validated. Spearman correlation analysis was used to examine the correlation between cuproptosis-related genes and immune cell infiltration and immune checkpoint expressions. TIMER2.0 database was used to analyze the correlation between the expressions of copper cuproptosis-related genes and cancer-associated fibroblast (CAF) infiltration, while TISDB database was utilized to analyze the correlation between CDKN2A and DLAT expression and myeloid-derived suppressor cell (MDSC) infiltration abundance.Results Compared to normal liver tissue, nine cuproptosis-related genes showed significantly increased expression in liver cancer, with CDKN2A having the highest mutation frequency. These genes were mainly involved in processes such as protein lipidation, tricarboxylic acid cycle, and citric acid cycle. Based on LASSO, univariate, and multivariate regression analysis, CDKN2A and DLAT were identified as genes influencing the overall survival (OS) of liver cancer patients, and a risk factor graph was constructed. Time-dependent ROC curves indicated their good predictive ability. Univariate and multivariate regression analysis revealed that CDKN2A, DLAT, T stage, and tumor status were independent prognostic factors for OS in liver cancer patients. A nomogram was constructed based on these factors, and calibration curves demonstrated good consistency between the predicted and observed values. UALCAN database analysis found associations of CDKN2A and DLAT with clinical stage and tumor grade in liver cancer, with validation results from GEO and HPA database as well as liver cancer cells aligning with these findings. Correlation analysis indicated that the expressions of CDKN2A and DLAT were correlated with immune cell infiltration and immune checkpoint expressions. TIMER2.0 database analysis revealed a significant positive correlation between DLAT expression and CAF infiltration, while TISDB database analysis showed no correlation of CDKN2A and DLAT expression with MDSC infiltration abundance.Conclusion Cuproptosis-related genes CDKN2A and DLAT may serve as novel prognostic biomarkers and potential targets for immunotherapy in liver cancer.

    表 1 TCGA-LIHC数据集中肝癌患者的临床信息[n(%)]Table 1 The clinical information of liver cancer patients in the TCGA-LIHC dataset [n (%)]
    表 2 单因素和多因素Cox回归分析筛选OS相关因素Table 2 Univariate and multivariate Cox regression analysis of factors for OS
    图1 铜死亡相关基因在肝癌中的表达、相关性和突变情况 A:铜死亡相关基因在肝癌组织和正常肝组织中的表达差异;B:铜死亡相关基因的相关性分析;C:DLAT与MTF1的相关性;D-E:铜死亡相关基因的突变频率和突变类型Fig.1 Expression pattern, correlation and mutation of cuproptosis-related genes in liver cancer A: The expression of cuproptosis-related genes in liver cancer and normal tissues; B: Correlation between the expression of cuproptosis-related genes; C: Correlation between the expression of DLAT and MTF1; D-E: Mutation frequency and classification of cuproptosis-related genes in liver cancer
    图2 GO、KEGG富集分析和PPI网络 A:GO富集分析;B:KEGG 富集分析;C:PPI网络Fig.2 GO, KEGG pathway enrichment and PPI network analysis A: GO enrichment analysis; B: KEGG pathway enrichment analysis; C: PPI network analysis
    图3 铜死亡相关基因LASSO回归分析Fig.3 Cuproptosis-related genes screened by the Lasso cox regression analysis
    图4 基于铜死亡相关基因的风险因子图构建 A:基于CDKN2A和DLAT的风险因子图;B:Kaplan-Meier生存曲线比较高风险组和低风险组患者OS;C:时间依赖ROC曲线评估风险因子图模型预测能力;D-F: CDKN2A、DLAT、GLS高表达组和低表达组患者Kaplan-Meier生存曲线比较Fig.4 Construction of the risk score model of cuproptosis-related genes in liver cancer A: The risk score model based on CDKN2A and DLAT; B: Kaplan-Meier survival analysis of the high-risk group and low-risk group; C: Time-dependent ROC curves assessing the prediction ability of the risk score model; D-F: Comparison of Meier survival curves between patients with high and low CDKN2A, DLAT and GLS expressions
    图5 基于铜死亡相关基因肝癌患者预后列线图构建 A:单因素回归分析;B:多因素回归分析;C:列线图预测肝癌患者1、3、5年OS;D:校准曲线Fig.5 Construction of nomogram for prognosis in liver cancer patients A: Univariate analysis; B: Multivariate analysis; C: Nomogram for predicting 1-, 3-, and 5-year OS in liver cancer patients; D: The calibration curves for the nomogram
    图6 CDKN2A和DLAT在肝癌不同临床病理特征中的表达 A-B:CDKN2A在肝癌各临床分期和肿瘤分级中的表达;C-D:DLAT在肝癌各临床分期和肿瘤分级中的表达Fig.6 Expression of CDKN2A and DLAT in liver cancer with different clinicopathologic features A-B: CDKN2A expressions in different clinical stages and tumor grades; C-D: DLAT expressions in different clinical stages and tumor grades
    图7 CDKN2A和DLAT在肝癌中的表达验证 A-D:CDKN2A和DLAT在GSE144269/GSE207435中的表达分析;E-F:HPA数据库分析CDKN2A和DLAT在肝癌组织中的表达;G-H:Western blot检测CDKN2A和DLAT表达Fig.7 Validation of differential expression of CDKN2A and DLAT in liver cancer A-D: CDKN2A and DLAT expressions in GSE144269 and GSE207435; E-F: CDKN2A and DLAT expression in HPA dataset; G-H: The protein expressions of CDKN2A and DLAT measured by Western blot analysis
    图8 CDKN2A和DLAT与免疫细胞浸润的相关性 A:CDKN2A;B:DLAT;C-D:CDKN2A和DLAT与CAF细胞浸润相关性;E-F:CDKN2A和DLAT与MDSC细胞浸润丰度相关性Fig.8 Correlation of CDKN2A and DLAT with immune cell infiltration in liver cancer A: CDKN2A; B: DLAT; C-D: The correlation of CDKN2A and DLAT with CAF infiltration; E-F: The correlation of CDKN2A and DLAT with MDSC infiltration abundance
    图9 CDKN2A和DLAT与免疫检查点的相关性 A-F:CDKN2A;G-J:DLATFig.9 The correlation of CDKN2A and DLAT with immune checkpoints A-F: CDKN2A; G-J: DLAT
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陈伟毅,胡柯,刘雨,彭靖,李小成,段绍毅,陈立军,杨骐彰.肝癌铜死亡相关基因及其与预后、免疫浸润的关系分析[J].中国普通外科杂志,2024,33(1):74-87.
DOI:10.7659/j. issn.1005-6947.2024.01.009

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  • 收稿日期:2023-10-07
  • 最后修改日期:2023-12-21
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  • 在线发布日期: 2024-02-05