Identification of a metabolic signature genes predicting overall survival for Head and neck squamous cell carcinoma

Abstract

Background: Head and Neck Squamous Cell Carcinoma (HNSCC) is a common head and neck malignancy that originates from lips, mouth, paranasal sinuses, oropharynx, larynx, nasopharynx, and other pharyngeal cancers. Since high-throughput expression data is now available, it is feasible 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 cancer genomic maps (TCGA) and validated in the GEO dataset to shine the dysfunctional metabolic microenvironment and given potential biomarkers for metabolic therapy.Results: TCGA database contained 529 patients and 327 metabolic genes (198 upregulated and the largest logFC is CA9; 129 downregulated and the largest logFC is CA6. Cox regression model found 51 prognosis‐related genes and we found the most high-risk gene was LCLAT1 (HR=1.144, 95% CI=1.044~1.251); the most low-risk gene was CHDH (HR=0.580, 95% CI=0.400~0.839). We next study whether metabolic-related genes patterns could serve as an early predictor of incidence of HNSCC by ROC curve and the model demonstrated an AUC of 0.745 in TCGA and 0.618 in GEO. Meanwhile, the predictor of clinicopathological in HNSCC was also analyzed and we found the AUC for age, gender, grade, stage, T, M and N were 0.520, 0.495, 0.568, 0.606, 0.577, 0.476 and 0.673, respectively in TCGA and the AUC for age, gender, stage, T, M, N, smoking and HPV16-pos were 0.599, 0.531, 0.622, 0.606, 0.616, 0.550, 0.614, 0.519 and 0.397 respectively in GEO.Conclusion: Our research found a novel metabolic signature gene for HNSCC prognosis prediction based on the TCGA dataset. Our signatures may reflect metabolic microenvironment disorders and provide useful biomarkers for metabolic therapy and response treatment prediction.

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.…”

Major ceRNA regulation and key metabolic signature analysis of intervertebral disc degeneration

“…A transcriptomic signature is beneficial for clear and early diagnosis and timely treatment of patients with IDD [ 23 ], especially those that are at a high risk of IDD. Currently, the metabolic gene signature is a collection of metabolism-related genes that can characterize the outcome events; it accounts for the top differentially regulated genes in many disorders but is relatively poorly explored in IDD [ 24 , 25 ]. In the current study, we aimed to explore the key metabolic gene(s) signature and its key ceRNA regulatory systems to provide insight into IDD pathogenesis.…”