Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer.
Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer.
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生物信息学分析确定共享差异表达基因作为桥本甲状腺炎相关乳头状甲状腺癌的潜在生物标志物
DOI：
10.7150/ijms.63402
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发表时间：
2021
影响因子：
3.6
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Liu C;Pan Y;Li Q;Zhang Y
背景：尽管桥本甲状腺炎（HT）是一种常见的自身免疫性内分泌疾病，其病因尚不清楚，但研究表明，桥本甲状腺炎与遗传因素和环境条件导致碘摄入过多存在潜在关联。此外，HT患者患甲状腺乳头状癌（PTC）的风险很高，这可能与HT发生的慢性炎症和自身免疫病理过程有关，因为它被认为与肿瘤转化有关。方法：生物信息学方法可以识别差异表达基因 (DEG) 并分析 DEG 在疾病中的功能。本研究中使用 R 软件利用基因表达综合 (GEO) 中的数据来识别 HT 和 PTC 中的 DEG。采用在线工具 DAVID、Reactome 和 AmiGO 对 HT 和 PTC 相关的 DEG 进行注释、可视化和集成，并应用 STRING 数据库和 Cytoscape 软件对 DEG 编码的蛋白质进行预测和可视化蛋白质-蛋白质网络 (PPI)。通过逆转录 PCR (RT-PCR) 验证了 HT 和 PTC 中共表达的 DEG。结果：在 HT 标本、中央 PTC 样本和 PTC 侵袭区样本中，总共检测到了 326、231 和 210 个 DEG。根据PPI网络，PTPN6、HLA-A、C3AR1、LCK和ITGB2是HT-DEG中的枢纽基因，而FN1、CDH2、SERPINA1和CYR61是PTC-DEG中的枢纽基因。共享的 DEG LTF 和 CCL21 通过 RT-PCR 进行了验证。生物信息学和 RT-PCR 分析均显示 LTF 和 CCL21 在 HT 组织中上调，在 PTC 组织中下调。结论：我们发现 HT 和 PTC 中 LTF 和 CCL21 的表达显着不同，表明 HT 和 PTC 之间存在潜在关联。
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.
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影响因子：
5.6
作者：
Bizzaro N;Antico A;Villalta D
通讯作者：
Villalta D
影响因子：
4.1
作者：
de Morais, Nathalie Silva;Stuart, Jessica;Alexander, Erik K.
通讯作者：
Alexander, Erik K.
影响因子：
6.6
作者：
Dow, KH;Ferrell, BR;Anello, C
通讯作者：
Anello, C
DOI：
10.1093/bioinformatics/btn615
发表时间：
2009-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Carbon S;Ireland A;Mungall CJ;Shu S;Marshall B;Lewis S;AmiGO Hub;Web Presence Working Group
通讯作者：
Web Presence Working Group
影响因子：
6.2
作者：
Haugen, Bryan R.
通讯作者：
Haugen, Bryan R.