Int J Med Sci 2021; 18(15):3478-3487. doi:10.7150/ijms.63402 This issue

Research Paper

Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer

Chang Liu1, Yu Pan1, Qinyu Li2✉, Yifan Zhang1✉

1. Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
2. Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.

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Citation:
Liu C, Pan Y, Li Q, Zhang Y. Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer. Int J Med Sci 2021; 18(15):3478-3487. doi:10.7150/ijms.63402. Available from https://www.medsci.org/v18p3478.htm

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Abstract

Graphic abstract

Background: Although the etiology of Hashimoto's thyroiditis (HT), a common autoimmune endocrine disease, is unknown, studies suggest a potential association with genetic factors and environmental conditions inducing excessive iodine intake. Additionally, HT patients have a high risk of papillary thyroid cancer (PTC), which is probably related to the chronic inflammation and autoimmune pathologic process occurring in HT, as it is thought to be associated with neoplastic transformation.

Methods: Bioinformatics approaches can identify differentially expressed genes (DEGs) and analyze DEG functions in diseases. R software was used in this study to identify DEGs in HT and PTC using data in Gene Expression Omnibus (GEO). The online tools DAVID, Reactome, and AmiGO were employed for annotation, visualization, and integration of DEGs related to HT and PTC, and the STRING database and Cytoscape software were applied to predict and visualize protein-protein networks (PPIs) for DEG-encoded proteins. Coexpressed DEGs in HT and PTC were validated by reverse transcription PCR (RT-PCR).

Results: In total, 326, 231, and 210 DEGs in HT specimens and samples of central PTC and PTC invasive areas, respectively, were detected. According to the PPI network, PTPN6, HLA-A, C3AR1, LCK and ITGB2 are hub genes among HT-DEGs, whereas FN1, CDH2, SERPINA1, and CYR61 are PTC-DEG hub genes. The shared DEGs LTF and CCL21 were validated by RT-PCR. Both bioinformatics and RT-PCR analyses showed LTF and CCL21 to be upregulated in HT tissues and downregulated in PTC tissues.

Conclusions: We identified that expression of LTF and CCL21 are significantly different in HT and PTC, suggesting an underlying association between HT and PTC.

Keywords: Papillary thyroid cancer, Gene analysis, Biomarkers, Hashimoto's thyroiditis