ArticleDiscover oncology2025
Integrating transcriptomics and hybrid machine learning enables high-accuracy diagnostic modeling for nasopharyngeal carcinoma.
Article in Discover oncology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Article
- 1,4-dinitrosopiperazine specifically induces malignant nasopharyngeal transformation through the cytochrome P450 enzyme.Cancer cell international · 2026Article
- Hybrid Feature Selection-Based Machine Learning and Deep Learning Framework for Biomarker Prediction From RNA-seq Data During Dengue Fever to Severe Dengue Progression.Evolutionary bioinformatics online · 2026Article
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6 authors.
Funding
Abstract
backgroundNasopharyngeal carcinoma (NPC) lacks biomarkers demonstrating both high specificity and sensitivity for early diagnosis. This study aimed to develop robust machine learning (ML)-driven diagnostic models and identify key biomarkers through integrated analysis of multi-cohort transcriptomic data.
methodsSeven NPC transcriptomic datasets (GSE12452, GSE40290, GSE53819, and GSE64634 were merged to form the training cohort, while GSE13597, GSE34573, and GSE61218 served as independent external validation sets) were integrated and preprocessed using ComBat for batch effect correction. Differential expression analysis identified 293 differentially expressed genes (DEGs). Twelve ML algorithms (including Stepglm, glmBoost, and RF) were systematically combined into 113 distinct models to classify NPC versus normal tissues. Top-performing models underwent external validation. Immune infiltration patterns and functional enrichment were analyzed using CIBERSORT and GSEA/GSVA, respectively.
resultsThe Stepglm[both]-RF hybrid model demonstrated exceptional performance with AUCs of 0.999 (training set; 95% CI: 0.997-1.000), 1.000 (GSE61218/GSE34573 validation), and 0.960 (GSE13597 validation). The glmBoost-RF model showed comparable efficacy, achieving AUCs of 1.000 (training), 0.950 (GSE61218), 1.000 (GSE34573), and 0.947 (GSE13597). Single-gene analysis identified RCN1 as a promising diagnostic marker (AUC = 0.953), with elevated expression levels correlating with poor prognosis in head and neck squamous cell carcinoma (HNSCC; p < 0.05). Immune profiling revealed significant enrichment of M1 macrophages and concomitant reduction of memory B cells in NPC. Functional enrichment analysis associated RCN1 with cell cycle regulation and immune-related pathways.
conclusionThis study establishes two high-performance ML models (Stepglm[both]-RF and glmBoost-RF) with low variability for NPC diagnosis and identifies RCN1 as a dual-function biomarker with diagnostic and prognostic potential. The findings provide a scalable framework for early NPC detection and novel insights into immune microenvironment dysregulation.
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