Expression Pattern, Functional Characteristics and Prognostic Significance of NLGN1 Gene in Nasopharyngeal Carcinoma: A Comprehensive Multi-omics Analysis

Background Neuroligin 1 (NLGN1), as an important member of the cell adhesion molecule family, primarily participates in synapse formation and neuronal connection regulation. However, the role and clinical significance of NLGN1 in the development and progression of nasopharyngeal carcinoma (NPC) remain unclear. This study aims to comprehensively analyze the expression pattern, functional characteristics, and prognostic value of NLGN1 in nasopharyngeal carcinoma. Methods Based on the GSE266679 dataset, we systematically analyzed NLGN1 expression patterns using bioinformatics methods. Through multidimensional approaches including differential expression analysis, single-cell transcriptomic analysis, co-expression network construction, functional enrichment analysis, and survival analysis, we explored the biological functions of NLGN1 in nasopharyngeal carcinoma. Statistical analyses were performed using R language, employing Wilcoxon rank-sum test, Cox regression models, and other methods to assess statistical significance. Additionally, quantitative real-time PCR (qRT-PCR) was conducted in nasopharyngeal carcinoma cell lines (C666-1 and HONE1) and the normal nasopharyngeal epithelial cell line NP69 to experimentally validate the bioinformatics findings. Results NLGN1 expression levels were significantly higher in nasopharyngeal carcinoma tissues compared to normal tissues (p < 0.001). Single-cell transcriptomic analysis identified six major cell types, including epithelial cancer cells, proliferative cancer cells, immune stromal cells, inflammatory stromal cells, metabolic stromal cells, and myeloid cells. NLGN1 showed significant correlations with multiple key genes and participated in apoptosis and metabolism-related signaling pathways. Multi-cancer survival analysis revealed that NLGN1 expression levels were associated with patient prognosis, functioning as either a protective or risk factor in certain cancer types. Co-expression network analysis revealed that NLGN1 may participate in tumorigenesis and progression through regulating cell adhesion, signal transduction, and metabolic reprogramming. Consistently, qRT-PCR validation confirmed that NLGN1 mRNA levels were markedly elevated in C666-1 and HONE1 cells compared with NP69 cells, providing experimental support for its oncogenic potential. Conclusions NLGN1 is upregulated in nasopharyngeal carcinoma and may promote tumor progression through multiple molecular mechanisms, demonstrating potential value as a diagnostic biomarker and therapeutic target. This study provides important evidence for understanding the role of NLGN1 in nasopharyngeal carcinoma pathogenesis and establishes a foundation for precision medicine and personalized treatment strategies. The integration of experimental validation with multi-omics analysis strengthens the reliability of these findings and highlights NLGN1 as a promising molecular target in NPC.