Abstract. Elevated levels of reactive oxygen species (ROS) have been proposed as a risk factor for the development of papillary thyroid carcinoma (PTC) in patients with Hashimoto thyroiditis (HT). However, it has yet to be proven that the total levels of ROS are sufficiently increased to contribute to carcinogenesis. We hypothesized that if the ROS levels were increased in HT, ROS-related genes would also be differently expressed in PTC with HT. To find differentially expressed genes (DEGs) we analyzed data from the Cancer Genomic Atlas, gene expression data from RNA sequencing: 33 from normal thyroid tissue, 232 from PTC without HT, and 60 from PTC with HT. We prepared 402 ROS-related genes from three gene sets by genomic database searching. We also analyzed a public microarray data to validate our results. Thirtythree ROS related genes were up-regulated in PTC with HT, whereas there were only nine genes in PTC without HT (Chisquare p-value < 0.001). Mean log 2 fold changes of up-regulated genes was 0.562 in HT group and 0.252 in PTC without HT group (t-test p-value = 0.001). In microarray data analysis, 12 of 32 ROS-related genes showed the same differential expression pattern with statistical significance. In gene ontology analysis, up-regulated ROS-related genes were related with ROS metabolism and apoptosis. Immune function-related and carcinogenesis-related gene sets were enriched only in HT group in Gene Set Enrichment Analysis. Our results suggested that ROS levels may be increased in PTC with HT. Increased levels of ROS may contribute to PTC development in patients with HT.Key words: Reactive oxygen species, Thyroid cancer, Hashimoto thyroiditis, Gene expression, Bioinformatics illary thyroid carcinoma (PTC) has been extensively studied, but the precise relationship between these two diseases is still being debated. Several analyses of surgical resection specimens have shown that PTC is frequently accompanied by HT. Interestingly, PTC with HT is associated with a lower rate of neck lymph node metastasis and has a better prognosis than PTC without thyroiditis in spite of increased incidence correlation [1][2][3][4][5][6][7][8][9][10]. In contrast, other studies conducted by fine-needle aspiration biopsy specimens and ultrasonographic findings have found no correlation between the incidences of these two diseases, with researchers insisting that HT does not increase the risk of thyroid
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