Identification of potential biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma by bioinformatics analysis

Abstract

The purpose of this study was to find disease-associated genes and potential mechanisms in head and neck squamous cell carcinoma (HNSCC) with deoxyribonucleic acid microarrays. The gene expression profiles of GSE6791 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were obtained with packages in R language and STRING constructed protein–protein interaction (PPI) network of the DEGs with combined score >0.8. Subsequently, module analysis of the PPI network was performed by Molecular Complex Detection plugin and functions and pathways of the hub gene in subnetwork were studied. Finally, overall survival analysis of hub genes was verified in TCGA HNSCC cohort. A total of 811 DEGs were obtained, which were mainly enriched in the terms related to extracellular matrix (ECM)–receptor interaction, ECM structural constituent, and ECM organization. A PPI network was constructed, consisting of 401 nodes and 1,254 edges and 15 hub genes with high degrees in the network. High expression of 4 genes of the 15 genes was associated with poor OS of patients in HNSCC, including PSMA7, ITGA6, ITGB4, and APP. Two significant modules were detected from the PPI network, and the enriched functions and pathways included proteasome, ECM organization, and ECM–receptor interaction. In conclusion, we propose that PSMA7, ITGA6, ITGB4, and APP may be further explored as potential biomarkers to aid HNSCC diagnosis and treatment.

Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis

“… 30 We found that the turquoise module played a role in the BPs and pathways, mainly in the regulation of ECM and collagen catabolic process, which play important roles in malignancy. 31 The results were in accordance with previous reports 32 that analyzed the DEGs between normal samples and OSCC in which the function of ECM was stressed and the MMP family and laminin family play an important role in tumorigenesis of OSCC. 33 These findings revealed the function of the turquoise module in OSCC, and further research is required to identify the role of the genes in the turquoise module because they might have diverse functions in OSCC malignant phenotypes.…”

Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses

“…Potential biomarkers with high specificity and sensitivity, identified in datasets by distinct Bioinformatic methods, have been continuously explored (Sun et al, 2015). Previous studies have determined a number of target genes by filtering DEGs in datasets (Yang et al, 2017;Zhao et al, 2018). Still, given the differences in specimens and database platforms, potential markers have failed to bear a significant clinical application value, so their verification process have been far from clinical practice.…”

Weighted gene co-expression network analysis and prognostic analysis identifies hub genes and the molecular mechanism related to head and neck squamous cell carcinoma

“…Head and neck squamous cell carcinoma (HNSCC) ranks the sixth most prevalent cancer and comprises 5% of worldwide malignancies. 1,2 It is pathogenically heterogeneous and happens within oral cavity, larynx or pharynx. 3,4 People engaged in alcohol consumption, smoking or poor oral hygiene are under high risk of HNSCC.…”

“…4 About 650,000 new cases and 350,000 deaths are reported annually, with its increasing incidence. 1,4 Poor prognosis of HNSCC is evidenced by that 5-y survival is about 50%, owing to likelihood of recurrence, metastasis or therapeutic resistance. 1 Despite the discovery of a number of biomarkers, the molecular mechanisms underlying the pathogenesis of HNSCC remains elusive.…”

“…1,4 Poor prognosis of HNSCC is evidenced by that 5-y survival is about 50%, owing to likelihood of recurrence, metastasis or therapeutic resistance. 1 Despite the discovery of a number of biomarkers, the molecular mechanisms underlying the pathogenesis of HNSCC remains elusive. 4 Recent studies on HNSCC are involving bioinformatics for more comprehensive analysis.…”