Genome-wide gene expression profiling of tongue squamous cell carcinoma by RNA-seq

• Published in: Clinical oral investigations 2018, Vol.22 (1), p.209-216
• Main Authors: Zhang, Hai Xia, Liu, Ou Sheng, Deng, Chao, He, Yan, Feng, Ye Qian, Ma, Jin An, Hu, Chun Hong, Tang, Zhan Gui
• Format: Article
• Language: English
• Subjects: Carcinoma, Squamous Cell - genetics; Collagenase 3; Dentistry; Down-Regulation; Epidermis; Epithelial cells; Gene expression; Gene Expression Profiling; Genome-Wide Association Study; Genomes; Humans; Invasiveness; Keratinization; Medicine; Molecular modelling; Mucosa; Muscle contraction; Oral cancer; Oral squamous cell carcinoma; Original Article; Polymerase chain reaction; Real-Time Polymerase Chain Reaction; Ribonucleic acid; RNA; Sequence Analysis, RNA; Squamous cell carcinoma; Tongue; Tongue Neoplasms - genetics; Up-Regulation
• ISSN: 1432-6981; 1436-3771
• DOI: 10.1007/s00784-017-2101-7

Objective Tongue squamous cell carcinoma (TSCC) is significantly more malignant than other type of oral squamous cell carcinoma (OSCC). In this study, we aimed to identify specific global gene expression signatures of TSCC to investigate the more invasive behavior of the deeply infiltrating cancer. Methods Using RNA-seq technology, we detected gene expression of 20 TSCCs, 20 matched paratumor tissues, and 10 healthy normal mucosa tissues. Enrichment analysis of gene ontology (GO) and pathway was conducted using online tools DAVID for the dysregulated genes. Additionally, we performed the quantitative real-time RT-PCR (qRT-PCR) to validate the findings of RNA-Seq in 10 samples of TSCC, matched paratumor, and normal mucosa, respectively. Results We detected 252 differentially expressed genes (DEGs) between TSCC and matched paratumor tissue, including 117 up-regulated and 135 down-regulated genes. For comparison between TSCC and normal mucosa, 234 DEGS were identified, consisting of 67 up-regulated and 167 down-regulated genes. For both two comparisons, GO categories of muscle contraction (GO: 0006936), epidermis development (GO: 0008544), epithelial cell differentiation (GO: 0030855), and keratinization (GO: 0031424) were commonly enriched. Altered gene expression affected some cancer-related pathways, such as tight junction. The qRT-PCR validation showed that gene expression patterns of FOLR1, NKX3-1, TFF3, PIGR, NEFL, MMP13, and HMGA2 were fully in concordance with RNA-Seq results. Conclusion Findings in this study demonstrated the genetic and molecular alterations associated with TSCC, providing new clues for understanding the molecular mechanisms of TSCC pathogenesis.