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 proteinprotein
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 to a
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.