Integrated bulk and single-cell transcriptomic analysis identifies BCHE and FOXM1 as oxidative-stress markers linked to prognosis and immune-microenvironment remodeling in nasopharyngeal carcinoma

Abstract Background Nasopharyngeal carcinoma (NPC), an Epstein–Barr virus–associated head-and-neck cancer, typically carries dense yet dysfunctional immune infiltrates. Oxidative stress shapes both tumor progression and immune escape; whether oxidative-stress genes (OSGs) carry prognostic and immunological information in NPC has not been examined at bulk and single-cell resolution. Methods Three NPC microarray cohorts (GSE12452, GSE53819 and GSE64634) were integrated using robust rank aggregation and ComBat-corrected limma, and genes identified by both strategies were intersected with 1,398 OSGs from GeneCards. Candidate prognostic OSGs were tested in the RNA-seq cohort GSE102349 (n = 88) using univariate Cox, LASSO and multivariable Cox regression together with Kaplan–Meier analysis, time-dependent ROC curves and a nomogram. We further applied Hallmark gene-set enrichment, CIBERSORT, an immune-cell LASSO signature, checkpoint correlation, ssGSEA and drug-sensitivity prediction, and replicated the findings in three independent cohorts and a single-cell RNA-seq dataset (GSE150430), where in-silico knockout, transcription-factor regulon, trajectory and cell–cell communication analyses were also performed. Results Of 722 consistent differentially expressed genes, 67 were NPC-specific OSGs. BCHE emerged as the consistently prognostic OSG (univariate HR = 1.85, P = 0.009; optimal-cutoff Kaplan–Meier P = 0.003, high-versus-low HR = 4.1; the sole LASSO-retained multivariable term). FOXM1 failed multivariable retention but still defined a high-risk subgroup by optimal-cutoff Kaplan–Meier (P = 0.012, HR = 4.4). Enrichment analysis tied FOXM1 to E2F/G2M/MYC proliferation programs and BCHE to epithelial–mesenchymal-transition and Wnt signaling; both genes were inversely related to interferon and complement pathways. A ten-cell immune signature and checkpoint correlations outlined an immune-suppressed compartment. At single-cell level, both genes localized to malignant cells within a shared early malignant state, and malignant–immune crosstalk was dominated by MIF- and galectin-mediated signaling. Conclusion Convergent bulk and single-cell evidence supports BCHE as a prognostic OS marker for risk stratification and FOXM1 as a proliferation-linked marker of malignant state in NPC. Both track with immune-microenvironment remodeling and await experimental and prospective validation.