基于机器学习筛选食管鳞状细胞癌的特征基因与免疫细胞浸润分析及中药预测

Screen of key characteristic genes of ESCC base on machine learning,analysis of immune cell infiltration and prediction of traditional Chinese medicine

目的:探索食管鳞状细胞癌(ESCC)可能的作用靶点及其发病机制,并利用生物信息学技术预测潜在治疗ESCC的中药。方法:通过检索GEO数据库获取ESCC的基因芯片,从中筛选出差异基因。利用R软件包“ColorsESCCE、Stringi、GGplot2、Bioconductor”对基因本体(GO)、京都基因和基因组百科全书(KEGG)进行差异基因的富集分析。使用R软件包“E1071,PreProcessCore”将获得的差异基因基于CiberSort算法对22个免疫细胞进行浸润分析,了解免疫浸润细胞与特征基因之间的相关性。通过Coremine和Herb数据库检索特征基因治疗ESCC的潜在中药。结果:得到UBL3、KIF4A、KIF14、GPX3共4个食管鳞状细胞癌特征基因。免疫细胞浸润分析结果显示,在食管鳞状细胞癌患者体内CD4^(+)T细胞、M0巨噬细胞、M2巨噬细胞、活化的树突状细胞显著上调;静息的肥大细胞、活化的肥大细胞显著下调。丹参、香橼、西红花、枸杞子、茯苓、人参、鳖甲等中药是潜在治疗食管鳞状细胞癌的药物。结论:特征基因与ESCC的病程进展相关,并预测丹参、香橼、西红花、枸杞子、茯苓、人参、鳖甲等中药是ESCC潜在靶向特征基因的治疗药物,为ESCC的临床诊治和药物开发提供了新的方向,同时也为ESCC患者提供了更多的治疗方法和途径。

Objective Explore the potential targets and pathogenesis of esophageal squamous cell carcinoma(ESCC),and further use bioinformatics technology to predict potential traditional Chinese medicine treatments for ESCC.Methods ESCC gene chip was obtained by searching GEO database,and the different genes were screened.Perform Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis on differentially expressed genes using the R software"colorsESCCe,stringi,ggplot2,Bioconductor".Using the R software"e1071,preprocessCore",the differential genes obtained were subjected to infiltration analysis on 22 types of immune cells based on the CIBERSORT algorithm,and the correlation between immune infiltration cells and characteristic genes was analyzed.Retrieve potential traditional Chinese medicine for characteristic gene therapy of ESCC through Coremine and Herb databases.Results Obtained 4 characteristic genes for ESCC,including UBL3,KIF4A,KIF14,and GPX3.The results of immune cell infiltration analysis showed that CD4^(+)T cells,M0 macrophages,M2 macrophages,and activated dendritic cells were significantly upregulated in ESCC patients;Resting mast cells and activated mast cells were significantly downregulated.Chinese herbal medicines such as salvia miltiorrhiza,citron,saffron,gouqizi,poria cocos,ginseng,biejia are potential drugs for ESCC.Conclusion The characteristic genes are related to the progress of ESCC,and it is predicted that traditional Chinese medicines such as Salvia miltiorrhiza,grapefruit,saffron,gouqizi,poria cocos,ginseng and turtle shell may be potential drugs for the treatment of ESCC with targeted characteristic genes.This provides a new direction for the clinical diagnosis,treatment,and drug development of ESCC,and is expected to bring more accurate and effective treatment methods to ESCC patients.