A novel gene-based model for prognosis prediction of head and neck squamous cell carcinoma

Yanxi Li; Peiran Li; Yuqi Liu; Wei Geng

doi:10.1016/j.heliyon.2024.e29449

A novel gene-based model for prognosis prediction of head and neck squamous cell carcinoma

Heliyon. 2024 Apr 16;10(8):e29449. doi: 10.1016/j.heliyon.2024.e29449. eCollection 2024 Apr 30.

Authors

Yanxi Li¹, Peiran Li², Yuqi Liu¹, Wei Geng¹

Affiliations

¹ Department of Dental Implant Center, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China.
² Department of Maxillofacial Surgery, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China.

Abstract

Background: Head and neck squamous cell carcinoma (HNSCC) is a significant global health challenge. The identification of reliable prognostic biomarkers and construction of an accurate prognostic model are crucial.

Methods: In this study, mRNA expression data and clinical data of HNSCC patients from The Cancer Genome Atlas were used. Overlapping candidate genes (OCGs) were identified by intersecting differentially expressed genes and prognosis-related genes. Best prognostic genes were selected using the least absolute shrinkage and selection operator Cox regression based on OCGs, and a risk score was developed using the Cox coefficient of each gene. The prognostic power of the risk score was assessed using Kaplan-Meier survival analysis and time-dependent receiver operating characteristic analysis. Univariate and multivariate Cox regression were performed to identify independent prognostic parameters, which were used to construct a nomogram. The predictive accuracy of the nomogram was evaluated using calibration plots. Functional enrichment analysis of risk score related genes was performed to explore the potential biological functions and pathways. External validation was conducted using data from the Gene Expression Omnibus and ArrayExpress databases.

Results: FADS3, TNFRSF12A, TJP3, and FUT6 were screened to be significantly related to prognosis in HNSCC patients. The risk score effectively stratified patients into high-risk group with poor overall survival (OS) and low-risk group with better OS. Risk score, age, clinical M stage and clinical N stage were regarded as independent prognostic parameters by Cox regression analysis and used to construct a nomogram. The nomogram performed well in 1-, 2-, 3-, 5- and 10-year survival predictions. Functional enrichment analysis suggested that tight junction was closely related to the cancer. In addition, the prognostic power of the risk score was validated by external datasets.

Conclusions: This study constructed a gene-based model integrating clinical prognostic parameters to accurately predict prognosis in HNSCC patients.

Keywords: Head and neck squamous cell carcinoma; Prognosis; Tight junction.