Identification of an individualized therapy prognostic signature for head and neck squamous cell carcinoma

• Published in: BMC genomics Vol. 24; no. 1; pp. 221 - 16
• Main Authors: Lin, Cheng, Chen, Yuebing, Pan, Jianji, Lu, Qiongjiao, Ji, Pengjie, Lin, Shuiqin, Liu, Chunfeng, Lin, Shaojun, Li, Meifang, Zong, Jingfeng
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 28.04.2023; BioMed Central; BMC
• Subjects: Analysis; Bioinformatics; Biomarkers; Cancer; Cancer therapies; Carcinogenesis; Carcinogens; Care and treatment; Chemotherapy; Datasets; Diagnosis; Gene expression; Genes; Genetic aspects; Genomes; Genomics; Head & neck cancer; Head and neck cancer; Head and neck carcinoma; Head and Neck Neoplasms - genetics; Head and Neck Neoplasms - therapy; Head and neck squamous cell carcinoma; Health risk assessment; Human papillomavirus; Humans; Immunotherapy; Mathematical analysis; Medical prognosis; Metastasis; Methods; Mutation; Nomograms; Performance prediction; Prognosis; Proteins; Radiation therapy; Radiotherapy sensitivity; Regression analysis; Remission; Remission (Medicine); Risk; Risk Factors; Risk groups; Software; Squamous cell carcinoma; Squamous Cell Carcinoma of Head and Neck - genetics; Statistical analysis; Subgroups; Survival; Therapeutic response; China; Therapeutic response; Head and neck squamous cell carcinoma; Radiotherapy sensitivity; Prognosis; Bioinformatics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09325-1

Head and neck squamous cell carcinoma (HNSCC) are the most common cancers in the head and neck. Therapeutic response-related genes (TRRGs) are closely associated with carcinogenesis and prognosis in HNSCC. However, the clinical value and prognostic significance of TRRGs are still unclear. We aimed to construct a prognostic risk model to predict therapy response and prognosis in TRRGs-defined subgroups of HNSCC. The multiomics data and clinical information of HNSCC patients were downloaded from The Cancer Genome Atlas (TCGA). The profile data GSE65858 and GSE67614 chip was downloaded from public functional genomics data Gene Expression Omnibus (GEO). Based on TCGA-HNSC database, patients were divided into a remission group and a non-remission group according to therapy response, and differentially expressed TRRGs between those two groups were screened. Using Cox regression analysis and Least absolute shrinkage and selection operator (LASSO) analysis, candidate TRRGs that can predict the prognosis of HNSCC were identified and used to construct a TRRGs-based signature and a prognostic nomogram. A total of 1896 differentially expressed TRRGs were screened, including 1530 upregulated genes and 366 downregulated genes. Then, 206 differently expressed TRRGs that was significantly associated with the survival were chosen using univariate Cox regression analysis. Finally, a total of 20 candidate TRRGs genes were identified by LASSO analysis to establish a signature for risk prediction, and the risk score of each patient was calculated. Patients were divided into a high-risk group (Risk-H) and a low-risk group (Risk-L) based on the risk score. Results showed that the Risk-L patients had better overall survival (OS) than Risk-H patients. Receiver operating characteristic (ROC) curve analysis revealed great predictive performance for 1-, 3-, and 5-year OS in TCGA-HNSC and GEO databases. Moreover, for patients treated with post-operative radiotherapy, Risk-L patients had longer OS and lower recurrence than Risk-H patients. The nomogram involves risk score and other clinical factors had good performance in predicting survival probability. The proposed risk prognostic signature and Nomogram based on TRRGs are novel promising tools for predicting therapy response and overall survival in HNSCC patients.