Screen of key characteristic genes and analysis of immune cell infiltration in metastatic nasopharyngeal carcinoma base on machine learning
10.16098/j.issn.0529-1356.2024.03.008
- VernacularTitle:基于机器学习转移性鼻咽癌关键特征基因的筛选及其免疫细胞浸润分析
- Author:
Jin LU
1
;
Yun-Fan CHEN
;
Hao-Xuan ZHANG
;
Xue-Ying HUANG
Author Information
1. 安徽医科大学人体解剖学教研室,合肥 230032;蚌埠医学院人体解剖学教研室,安徽 蚌埠 233030;数字医学与智慧健康安徽省重点实验室,安徽 蚌埠 233030
- Keywords:
Metastatic nasopharyngeal carcinoma;
Immune cell infiltration;
Bioinformatics;
Machine learning
- From:
Acta Anatomica Sinica
2024;55(3):311-318
- CountryChina
- Language:Chinese
-
Abstract:
Objective To screen the key characteristic genes of metastatic nasopharyngeal carcinoma(mNPC)and analyze the immune cell infiltration in tumor microenvironment using machine learning algorithm.Methods Firstly,the training set GSE103611 was downloaded from the GEO database,and the data were subjected to differential expression gene(DEGs)screening,Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genome(KEGG)and immune cell infiltration analysis.Second,the predicted genes in DEGs were screened by least absolute shrinkage and selector operation(LASSO)regression,and the characteristic genes were screened by using the expression level of the predicted genes and receiver operating characteristic(ROC).Third,the correlation between characteristic genes and immune cells was further analyzed to determine the key characteristic genes.Finally,the expression levels of key characteristic genes and ROC were verified using the reverse validation set GSE1245 data.Results A total of 136 DEGs were obtained,and their KEGG were mainly enriched in cytochrome P450,tumor necrosis factor(TNF)signaling pathway,prion disease,EB virus infection,and other pathways.GO was mainly enriched in the negative regulatory processes of peptide-based tyrosine phosphorylation modification,viral gene expression,and B cell and leukocyte activation.The difference in the degree of infiltration of the 22 immune cells in nasopharyngeal carcinoma(NPC)and mNPC was not significant.Two key characteristic genes(DAZ1 and SCCPDH)of mNPC were finally obtained by LASSO regression,and they were significantly correlated with immune cells in the mNPC microenvironment(P＜0.05).In the reverse validation data set,the differential expressions of DAZ1 and SCCPDH between non-NPC(nNPC)and NPC groups were not significant(P＞0.05),and the AUC values of ROC of both were less than 0.6.Conclusion DAZ1 and SCCPDH are the key characteristic genes of mNPC and can be used as important markers for mNPC and immunotherapy.
