Screening of DEGs in esophageal squamous cell carcinoma and correlation analysis with immune cells infiltration and prognosis
Objective:To utilize the GEO database for screening DEGs in tissues of esophageal squamous cell carcinoma.It aims to further analyze the correlation with immune cell infiltration and prognosis.Methods:The dataset GSE23400,containing data on esophageal squamous cell carcinoma,was extracted from the GEO database.DEGs analysis was subsequently performed using the Limma package in the R software.The two-platform data of GSE23400 were integrated and the immune cell infiltration in each sample was calculated by ssGSEA algorithm of GSVA package,and the correlation between immune infiltrated cells and DEGs were calculated.The association between DEGs and the overall survival of patients was investigated using the GSE53624 dataset.Furthermore,the correlation analysis between immune infiltrating cells and genes associated with patient survival was evaluated.Also,the expression levels of the survival-related genes in esophageal squamous cell carcinoma were validated using the GSE53622 dataset,and their correlation with patient prognosis was examined.Immunohistochemistry(IHC)was utilized to detect the protein expression levels of DEGs in 38 cases of esophageal squamous cell carcinoma and the corresponding non-tumor tissues.The mRNA and protein expression levels of EHF and CSTB in esophageal squamous cell carcinoma were detected using RT-qPCR and Western blot.Results:Through the analysis of data from 104 patients with esophageal squamous cell carcinoma,a total of 38 DEGs between cancerous and normal tissues were identified.In immune-infiltration analysis,the immune cell infiltration in cancerous and normal tissue was different,the 38 DEGs were related to the abundance of immune cells infiltration.It was exposed that the expressions of EHF and CSTB genes were significantly correlated with survival time of the patients with esophageal cancer through survival analysis(both P＜0.05).In GSE53624 dataset,a significant positive correlation was found between EHF gene expression and CD4+T cells,B cells.The correlation coefficients r were 0.69 and 0.67,respectively(both P＜0.01).The positively correlation between CSTB gene expression and CD8+T cells,natural killer T cells was significant,with the correlation coefficients r were 0.76 and 0.62,respectively(both P＜0.01).The survival time of patients with increased EHF and CSTB genes expression was significantly higher than that of patients with low expression level(median survival 59.1 vs.24.1;63.1 vs.23.9).The expressions of EHF and CSTB genes were decreased in GSE53622 dataset(both P＜0.01).Patients with esophageal squamous cell carcinoma who exhibited high expression of EHF and CSTB genes showed a more favorable prognosis compared to those with low expression level(median survival NA vs.29.7;NA vs.17.9,both P＜0.05).The results from IHC demonstrated a significant decrease in the protein expression levels of EHF and CSTB in esophageal squamous cell carcinoma compared to the corresponding adjacent tissues(both P＜0.05).Similarly,the results from RT-qPCR and Western blot analysis indicated a significantly lower expression of EHF and CSTB in esophageal squamous cell carcinoma cells when compared to normal esophageal squamous epithelial cells(both P＜0.05).Conclusion:EHF and CSTB genes are likely to play significant roles in tumor immunity and the prognosis of esophageal squamous cell carcinoma.These findings could potentially serve as a theoretical foundation for the development of immunotherapy strategies and prognostic evaluations.
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