[关键词]
[摘要]
目的 基于生物信息学探究细胞焦亡相关基因在乳腺癌中的作用及临床意义,并筛选可对细胞焦亡起调控作用的中药。方法 从TCGA、GEO数据库中获取乳腺癌相关数据集;使用R、Perl语言对细胞焦亡相关基因在乳腺癌细胞中的表达、变异进行评估;对数据集分别进行细胞焦亡基因分型及预后差异基因分型,并对各分型进行多组学分析;构建预后模型、进行风险评分,按照风险评分分组进行亚组多组学分析并检验对生存的预测能力;以细胞焦亡基因为靶点,利用TCMSP数据库及Cytoscape软件构建“细胞焦亡靶点-成分-中药”网络并进行拓扑学分析,进而得出核心中药及其相关属性。结果 大多数细胞焦亡基因在乳腺癌中表达异常并具有拷贝数变异,细胞肿瘤抗原(cellular tumor antigen p53,TP53)等11个基因发生了体细胞突变;细胞焦亡分型中A亚型预后好、细胞焦亡基因及免疫相关通路高表达、免疫细胞含量高;B型与之相反,且A、B两亚型差异明显,其分型差异基因有1223个。将不同的焦亡基因重新聚类,得到3个基因型,乳腺癌细胞焦亡预后差异基因分型中I组预后最好,II组最差,I组主要为基因及细胞焦亡基因高表达,II组主要呈现低表达。预后模型风险评分将患者分为高、低风险组,低风险组细胞焦亡基因高表达、预后好,高风险组相反,通过列线图可对患者不同临床特征进行预后评估;免疫细胞与风险评分相关性大多呈负相关;肿瘤微环境中基质细胞、免疫细胞及总评分均为高风险组更低,肿瘤突变负荷则高风险组更高;干细胞与风险得分呈正相关。“细胞焦亡靶点-成分-中药”网络得出木蝴蝶、红花等17味中药为核心药物,其性味主要为苦寒,次以辛温,辅以甘平之品,主要调节肝、肺、脾、胃等脏腑。结论 细胞焦亡基因在乳腺癌的免疫中发挥重要作用,与乳腺癌患者预后具有明显相关性,调控细胞焦亡基因的中药主要有木蝴蝶、红花等17味药物,可为乳腺癌的诊疗及中药干预研究提供思路与参考。
[Key word]
[Abstract]
Objective To explore the role and clinical significance of pyroptosis related genes in breast cancer and screen traditional Chinese medicines (TCMs) that can regulate pyroptosis based on bioinformatics. Methods Breast cancer related data sets were obtained from TCGA and GEO databases; The expression and variation of pyroptosis related genes in breast cancer was evaluate by R and Perl language; Pyroptosis genotyping and prognostic differential genotyping were performed on the data sets, and multi-omics analysis was performed for each genotype; The prognostic model were constructed, risk scores were performed, and sub-group multi-omics analysis was carried out according to risk scores to test the predictive power of survival. Finally, the pyroptosis related genes were used as the targets, and the TCMSP database and Cytoscape software were used to construct "target-component-Chinese herbal medicine" network and topological analysis to obtain core TCMs and their related attributes. Results Most genes related to pyroptosis were abnormally expressed in breast cancer and had copy number variation; Eleven genes such as cellular tumor antigen p53 (TP53) had somatic mutations. The A subtype of pyroptosis had good prognosis, high expression of pyroptosis genes and immune-related pathways, and high content of immune cells. Type B was the opposite, and type A and B had obvious differences, the number of differential genes was 1223. The differential genes of pyroptosis were reclustered to generate three genotypes. Among them, group I had the best prognosis, group II had the worst prognosis, and pyroptosis related genes were mainly highly expressed in group I, and lowly expressed in group II. The patients were divided into high and low risk groups according to risk scores of prognostic model. The low risk group showed high expression of pyroptosis gene and good prognosis, while the high risk group showed the opposit. The prognostic evaluation of different clinical characteristics of patients could be carried out through the nomogram; The correlation analysis of immune cells and risk scores showed that most of them were negatively correlated; In the tumor microenvironment, the stromal cell score, immune cell score and total score were lower in all high risk group, and tumor mutation burden was higher in the high risk group. Stem cells were also positively correlated with the risk score. The network of "target of pyroptosis-component-TCMs" obtained 17 TCMs, such as Muhudie (Oroxyli Semen) and Honghua (Carthami Flos). Their nature and flavor were mainly bitter and cold, followed by pungent and warm, supplemented by sweet and light medicines, which mainly regulate the liver, lungs, spleen and stomach, etc. Conclusion The pyroptosis genes play an important role in the immunity of breast cancer, and have obvious correlation with the prognosis of breast cancer patients. The main TCMs that regulate pyroptosis include 17 medicines such as Oroxyli Semen and Carthami Flos. The conclusion can provide ideas and references for further research.
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[基金项目]
国家重点研发计划“中医药现代化研究”项目(2018YFC1707400);中国中医科学院科技创新工程中医临床基础学科创新团队项目(CI2021B003);2021年岐黄学者支持项目