Prediction Biomarkers Associated with Lymph Node Metastasis and Prognosis were Identified in Papillary Thyroid Carcinoma via Integrated Bioinformatics Analysis

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Author(s): Siyuan Gan*, Ruifang Ye, Yanping Ha, Yinghuan Xiong, Rujia Li, Xiaoqing Di, Zhenning Zou, Yanqin Sun, Zhi Zhang

Journal Name: Combinatorial Chemistry & High Throughput Screening
Accelerated Technologies for Biotechnology, Bioassays, Medicinal Chemistry and Natural Products Research

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Background: Prediction biomarkers associated with prognosis and lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC) are needed to facilitate clinicians in choosing appropriate therapies.

Objective: We hope to identify key genes associated with LNM and prognosis in PTC.

Methods: GSE29265, GSE33630, GSE3467, GSE3678 and GSE58545 gene expression profiles were acquired from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between PTC tissues and normal thyroid tissues were selected with the GEO2R tool, and common DEGs among the five datasets were integrated with Venn software online. A protein-protein interaction (PPI) network of the common DEGs was visualized. We analyzed the PPI network and determined core genes using the Cytoscape software. Furthermore, we employed UALCAN to verify the expression and promoter methylation status of the core genes in thyroid carcinoma (THCA). Additionally, the Kaplan–Meier plotter online tool was used to analyze the relationship between overall survival and core gene expressions in THCA.

Results: TNS3, DUSP6, DUSP4 and PTPRE were identified as core genes. Expression of these 4 genes and the promoter methylation status of DUSP4 and PTPRE were strongly associated with LNM (P<0.05). High expression of 3 genes (DUSP6, DUSP4 and PTPRE) was related with significantly better survival than low expression of the 3 genes in THCA. In contrast, high TNS3 expression was related to significantly worse survival (P<0.05).

Conclusion: TNS3, DUSP6, DUSP4, PTPRE and DUSP4 and PTPRE promoter methylation status might be useful predictive biomarkers of LNM in PTC. Additionally, these genes may be prognostic biomarkers in PTC.

Keywords: Papillary thyroid carcinoma, lymph node metastasis, prognosis, Bioinformatics

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(E-pub Ahead of Print)
DOI: 10.2174/1386207323999201103205745
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