A Metabolic Gene Signature to Predict Overall Survival in Head and Neck Squamous Cell Carcinoma

Abstract

Background. Head and neck squamous cell carcinoma (HNSCC) is a common malignancy that emanates from the lips, mouth, paranasal sinuses, oropharynx, larynx, nasopharynx, and from other pharyngeal cancers. The availability of high-throughput expression data has made it possible to use global gene expression data to analyze the relationship between metabolic-related gene expression and clinical outcomes in HNSCC patients. Method. In this study, we used RNA sequencing (RNA-seq) data from the cancer genome atlas (TCGA), with validation in the GEO dataset to profile the metabolic microenvironment and define potential biomarkers for metabolic therapy. Results. We extracted data for 529 patients and 327 metabolic genes (198 upregulated and 129 downregulated genes) in the TCGA database. Carbonic anhydrase 9 (CA9) and CA6 had the largest logFCs in the upregulated and downregulated genes, respectively. Our Cox regression model data showed 51 prognostic-related genes with lysocardiolipin acyltransferase 1 (LCLAT1) and choline dehydrogenase (CHDH) being associated with the highest risk ( HR = 1.144 , 95% CI = 1.044 ~ 1.251 ) and the lowest risk ( HR = 0.580 , 95% CI = 0.400 ~ 0.839 ) in HNSCC, respectively. We next used the ROC curve to evaluate whether the differentially expressed metabolic-related genes could serve as early predictors of HNSCC. The findings showed an AUC of 0.745 and 0.618 in the TCGA and GEO analysis, respectively. Besides, the ability for the genes to predict clinicopathological HNSCC status was analyzed and the data showed that the AUC for age, gender, grade, stage, T, M, and N was 0.520, 0.495, 0.568, 0.606, 0.577, 0.476, and 0.673, respectively, in the TCGA dataset. On the other hand, the AUC for age, gender, stage, T, M, N, smoking, and HPV16-pos was 0.599, 0.531, 0.622, 0.606, 0.616, 0.550, 0.614, 0.519, and 0.397, respectively, in the GEO dataset. Conclusion. Taken together, our study unearths a novel metabolic gene signature for the prediction of HNSCC prognosis based on the TCGA dataset. Our signature might point out the metabolic microenvironment disorders and provides potential treatment targets and prognostic biomarkers.

The circ_0032822 Promotes the Proliferation of Head and Neck Squamous Cell Carcinoma Cells Through miR-141/EF3 Signaling Axis

“…Head and neck squamous cell carcinoma (HNSCC) refers to an epithelial malignant tumor that originates in the head and neck and over 600,000 new cases are reported every year (1,2). Although advances in technology and supportive treatment have improved the quality of life of HNSCC patients, the overall prognosis is still poor due to local recurrence and distant metastasis after surgery (3,4). Therefore, there is an urgent need to better understand the molecular mechanism of HNSCC progression to improve the prevention, diagnosis, and personalized treatment of patients.…”

Plasma cell-free circRNAs panel act as fingerprint predicts the occurrence of laryngeal squamous cell carcinoma

“…In the past decade, great progress has been made in the research and treatment of LSCC [13,14]. However, treatment resistance increases the recurrence rate of LSCC and patients who undergo total laryngectomy have a poor quality of life [15]. This study screened the differentially expressed genes to provide ideas for subsequent studies, including the exploration of potential diagnostic targets, which is conducive to the risk assessment of LSCC at an earlier stage.…”

CHDH, a key mitochondrial enzyme, plays a diagnostic role in metabolic disorders diseases and tumor progression

“…As the sixth most common cancer, head and neck squamous cell carcinoma (HNSCC) is a malignancy of head and neck origin ( Galizia et al, 2022 ). Wu et al screened HNSCC patients for differentially expressed RNA based on the TCGA database and found that patients with HNSCC with low CHDH expression had the best prognosis using univariate Cox regression models ( Wu et al, 2020 ).…”