Exploration of the Potential Biomarkers of Papillary Thyroid Cancer (PTC) Based on RT2 Profiler PCR Arrays and Bioinformatics Analysis

Ying Peng; Han-Wen Zhang; Wei-Han Cao; Ying Mao; Ruo-Chuan Cheng

doi:10.2147/CMAR.S266473

Exploration of the Potential Biomarkers of Papillary Thyroid Cancer (PTC) Based on RT² Profiler PCR Arrays and Bioinformatics Analysis

Cancer Manag Res. 2020 Sep 28:12:9235-9246. doi: 10.2147/CMAR.S266473. eCollection 2020.

Authors

Ying Peng^{1

2}, Han-Wen Zhang^{1

2}, Wei-Han Cao^{1

2}, Ying Mao^{1

3}, Ruo-Chuan Cheng²

Affiliations

¹ Kunming Medical University of Yunnan Province, Kunming, Yunnan 650500, People's Republic of China.
² Thyroid Disease Diagnosis and Treatment Center, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, People's Republic of China.
³ Thyroid Disease Diagnosis and Treatment Center, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, People's Republic of China.

Abstract

Background: Papillary thyroid carcinoma (PTC) has increased rapidly over recent years, and radiation, hormone effects, gene mutations, and others were viewed as closely related. However, the molecular mechanisms of PTC have not been cleared. Therefore, we intended to screen more accurate key genes and pathways of PTC by combining RT² profiler PCR arrays and bioinformatics methods in this study.

Materials and methods: RT² profiler PCR arrays were firstly analyzed to identify differential expression genes (DEGs) in PTC. RT-qPCR were performed to verify the most significant differential expression genes. The TCGA database was used to further verify for expanded data. Enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was analyzed. To construct the protein-protein interaction (PPI) network, we used STRING and Cytoscape to make module analysis of these DEGs.

Results: Sixteen differentially expressed genes were presented in RT² profiler PCR arrays, including 13 down-regulated DEGs (DEGs) and three up-regulated DEGs (DEGs), while 13 stable DEGs were eventually verified. A total of 155 DEGs were presented in the TCGA database, including 82 up-regulated DEGs (DEGs) and 73 down-regulated DEGs (dDEGs). A total of 29 important genes were extracted after integrating these two results, GO and KEGG analyses were used to observe the possible mechanisms of action of these DEGs. The PPI network was constructed to observe hub genes. Prognostic analysis further demonstrated the involvement of these genes in the biological processes of PTC.

Conclusion: This study identified some potential molecular targets and signal pathways, which might help us raise our awareness of the mechanisms of PTC.

Keywords: DEGs; bioinformatics; papillary thyroid cancer; qiagen RT2 profiler PCR arrays; signal pathways.

Grants and funding

This research was supported by the Association Foundation Program of Yunnan Science and Technology Department and Kunming Medical University (grant number 2018FE001(−168)).