# Epigenetic Regulation of NKT-Cell-Related Gene Signatures and Prognostic Implications in Oropharyngeal Squamous Cell Carcinoma

## TL;DR

This study explores how NKT-cell-related genes and their epigenetic regulation affect survival in oropharyngeal cancer patients.

## Contribution

The study identifies ITK, ZNF683, and ATF2 as novel prognostic markers linked to immune activation and epigenetic regulation in oropharyngeal cancer.

## Key findings

- High NKT cell differentiation scores are significantly associated with improved overall survival in OPSCC patients.
- Epigenetic changes like hypermethylation of ITK and hypomethylation of ZNF683 are observed in tumor samples.
- NKT-cell-related gene signatures are linked to immune microenvironment features and potential therapeutic targets.

## Abstract

This study investigates the role of natural killer T (NKT)-cell-related gene signatures and their epigenetic regulation in oropharyngeal squamous cell carcinoma (OPSCC). Transcriptomic data from 81 OPSCC patients were analysed using single-sample gene set enrichment analysis (ssGSEA), revealing that high NKT cell differentiation scores were significantly associated with improved overall survival. Three genes (ITK, ZNF683, and ATF2) emerged as key prognostic markers linked to immune activation and T-cell signalling pathways. Methylation analyses from TCGA and GEO datasets indicated hypermethylation of ITK and hypomethylation of ZNF683 in tumour samples, suggesting epigenetic regulation of these immune-related genes. The immune microenvironment showed predominant T regulatory cells, macrophages, and neutrophils, alongside high expression of IL-15, IL-18, TNFα, and TGFβ. These findings highlight NKT-cell-associated gene regulation as a potential prognostic and therapeutic target in OPSCC, emphasising the interplay between epigenetics and antitumor immunity.

Background: Oropharyngeal squamous cell carcinoma (OPSCC) is a major subtype of head and neck cancer, with prognosis increasingly influenced by the tumour immune microenvironment. Although immune checkpoint inhibitors have improved outcomes for some patients, reliable predictive biomarkers remain limited. Methods: This study aimed to investigate the prognostic relevance and epigenetic regulation of natural killer T (NKT)-cell-related gene signatures in OPSCC. Clinicopathological and transcriptomic data from 81 OPSCC patients were analysed using single-sample gene set enrichment analysis (ssGSEA) to evaluate immune-related gene set enrichment scores. Associations with overall survival and clinical features were assessed, and candidate prognostic genes were further explored through expression, methylation, and network analyses. Results: High NKT cell differentiation enrichment scores were significantly associated with improved survival and favourable clinical features. Gene-level analyses identified ITK, ZNF683, and ATF2 as key prognostic markers linked to T-cell signalling and epigenetic regulation. Methylation profiling revealed hypermethylation of ITK and hypomethylation of ZNF683 in tumour tissues, suggesting an epigenetic basis for altered gene expression. Conclusions: These findings highlight NKT cell differentiation as a strong prognostic indicator in OPSCC and support further exploration of epigenetic–immunologic interactions as potential therapeutic targets.