Identification of key candidate genes and pathways in anaplastic thyroid cancer by bioinformatics analysis

• Published in: American journal of otolaryngology 2020-05, Vol.41 (3), p.102434-102434, Article 102434
• Main Authors: Ding, Yong-Gang, Ren, Yu-Lin, Xu, Yang-Shan, Wei, Chang-Sheng, Zhang, Yong-Bin, Zhang, Shou-Kai, Guo, Chang-An
• Format: Article
• Language: English
• Subjects: Anaplastic thyroid cancer; Annotations; Bioinformatics; Bioinformatics analysis; Biomarkers; Biometrics; Biotechnology; Cancer; Carcinogenesis; Carcinogens; Cdc45 protein; Cell adhesion & migration; Cell cycle; Computer programs; Datasets; Differentially expressed genes; Enrichment; Gene expression; Genes; Genomes; Identification methods; Metabolism; Modules; Orthology; p53 Protein; Protein interaction; Proteins; Proteolysis; Quantitative real-time PCR; Signal transduction; Software; Therapeutic applications; Thyroid; Thyroid cancer; Thyroid carcinoma; Thyroid gland; Ubiquitin
• ISSN: 0196-0709; 1532-818X
• DOI: 10.1016/j.amjoto.2020.102434

Anaplastic thyroid carcinoma (ATC) is a refractory and poor prognosis tumor Present study aimed to investigate the underlying biological functions and pathways involved in the development of ATC and to identify potential hub genes and candidate biomarkers of ATC. Bioinformatics analyses were performed to identify the differentially expressed genes (DEGs) between ATC tissue samples and adjacent normal tissue samples. Protein-protein interaction (PPI) networks of the DEGs were constructed using Search Tool for the Retrieval of Interacting Genes online tool and Cytoscape software and divided into sub-networks using the Molecular Complex Detection (MCODE) plug-in. DEGs in each module was analyzed by enrichment analysis of the KEGG Orthology Based Annotation System (KOBAS) web software version 3.0. Eventually, the hub genes from bioinformatics analysis were verified by qRT-PCR assay in different ATC cell lines. Thirty hub genes were selected and three modules were built by the Cytoscape software from the PPI network. Seven genes (CDK1, CCNB2, BUB1B, CDC20, RRM2, CHEK1 and CDC45) were screened from thirty hub genes. Enrichment analysis showed that these hub genes were primarily accumulated in ‘cell cycle’, ‘p53 signaling pathway’, ‘viral carcinogenesis’, ‘pyrimidine metabolism’ and ‘ubiquitin mediated proteolysis’. The results of qRT-PCR indicated that seven hub genes were unregulated in three ATC cell lines compared with normal thyroid gland cell. These findings suggest that CDK1, CCNB2, BUB1B, CDC20, RRM2, CHEK1 and CDC45 may serve as novel diagnosis biomarkers and potential therapeutic target for ATC.