Identification of biomarkers with a tumor stage-dependent expression and exploration of the mechanism involved in laryngeal squamous cell carcinoma.
The aim of this study was to identify biomarkers with a tumor stage-dependent expression manner and explore the regulatory mechanisms of laryngeal squamous cell carcinoma (LSCC) progression. Microarray data GSE59102 was used for differential analysis using a limma package. Enrichment analyses were performed for the differentially expressed genes (DEGs) between tumor tissues and normal tissues at different stages. A co-expressed network involving the overlapped DEGs in two stages was established based on Pearson's correlation coefficients. Furthermore, for the tumor stage‑dependent expressed DEGs, a protein‑protein interaction (PPI) network was constructed by mapping the genes using the STRING database. Transcription factors (TFs), oncogenes and tumor‑associated genes (TSGs) among the DEGs were predicted, following a search of the TRANSFAC, tumor-associated gene (TAG) and TSG databases. The CDT database was used to identify LSCC‑associated genes. In total, 696 DEGs from early stage and control samples and 622 DEGs from advanced sttage and control samples were selected, which were mainly enriched in the cell cycle pathway. In the co-expressed network, BUB1, TTK, E2F1 and CEP55 were prominent, with E2F1 being predicted as a TSG and CEP55 as an oncogene. The HOX family members were predicted as TFs. MMP1, MMP9, MMP3 and PLAU were the most evident nodes in the PPI network, where MMP3 was connected with MMP1. The ADH family was correlated with LSCC. Several biomarkers with tumor stage-dependent expression were identified including MMP1, MMP3, MMP9, PLAU and ADHs. Additionally, the dysregulated cell cycle pathway involving BUB1, TTK, E2F1 and CEP55, and the mediation of MMP1 by MMP3 as well as the predicted TF HOX, may all play significant roles in LSCC progression.
Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.
Lian
L
Hui
Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.
Ning
N
Yang
Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.
Huijun
H
Yang
Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.
Xing
X
Guo
Department of Otolaryngology, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China.
Xuejun
X
Jang
D014408:Biomarkers, Tumor / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology*; D019295:Computational Biology / Q000379:methods; D018450:Disease Progression; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006258:Head and Neck Neoplasms / Q000235:genetics* / Q000473:pathology*; D006801:Humans; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D000077195:Squamous Cell Carcinoma of Head and Neck
D014408:Biomarkers, Tumor