Otolaryngology Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China.
Radiology Department, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China.
Mol Med Rep. 2017 Nov;16(5):5954-5964. doi: 10.3892/mmr.2017.7346. Epub 2017 Aug 24.
As the predominant thyroid cancer, papillary thyroid cancer (PTC) accounts for 75‑85% of thyroid cancer cases. This research aimed to investigate transcriptomic changes and key genes in PTC. Using RNA‑sequencing technology, the transcriptional profiles of 5 thyroid tumor tissues and 5 adjacent normal tissues were obtained. The single nucleotide polymorphisms (SNPs) were identified by SAMtools software and then annotated by ANNOVAR software. After differentially expressed genes (DEGs) were selected by edgR software, they were further investigated by enrichment analysis, protein domain analysis, and protein‑protein interaction (PPI) network analysis. Additionally, the potential gene fusion events were predicted using FusionMap software. A total of 70,172 SNPs and 2,686 DEGs in the tumor tissues, as well as 83,869 SNPs in the normal tissues were identified. In the PPI network, fibronectin 1 (FN1; degree=31) and transforming growth factor β receptor 1 (TGFβR1; degree=22) had higher degrees. A total of 7 PPI pairs containing the non‑synonymous risk SNP loci in the interaction domains were identified. Particularly, the interaction domains involved in the interactions of FN1 and 5 other proteins (such as FN1‑tenascin C, TNC) had non‑synonymous risk SNP loci. Furthermore, 11 and 4 gene fusion events were identified in all of the tumor tissues and normal tissues, respectively. Additionally, the NK2 homeobox 1‑surfactant associated 3 (NKX2‑1‑SFTA3) gene fusion was identified in both tumor and normal tissues. These results indicated that TGFβR1 and the NKX2‑1‑SFTA3 gene fusion may be involved in PTC. Furthermore, FN1 and TNC containing the non‑synonymous risk SNP loci might serve a role in PTC by interacting with each other.
作为最常见的甲状腺癌，甲状腺乳头状癌（papillary thyroid cancer，PTC）占甲状腺癌病例的 75%-85%。本研究旨在探讨 PTC 中的转录组变化和关键基因。采用 RNA 测序技术，获得了 5 例甲状腺肿瘤组织和 5 例相邻正常组织的转录谱。利用 SAMtools 软件识别单核苷酸多态性（single nucleotide polymorphisms，SNP），然后利用 ANNOVAR 软件进行注释。通过 edgR 软件选择差异表达基因（differentially expressed genes，DEGs）后，进一步进行富集分析、蛋白结构域分析和蛋白-蛋白相互作用（protein-protein interaction，PPI）网络分析。此外，利用 FusionMap 软件预测潜在的基因融合事件。在肿瘤组织中鉴定出 70172 个 SNP 和 2686 个 DEGs，在正常组织中鉴定出 83869 个 SNP。在 PPI 网络中，纤维连接蛋白 1（fibronectin 1，FN1；degree=31）和转化生长因子β受体 1（transforming growth factor β receptor 1，TGFβR1；degree=22）具有较高的度。鉴定出 7 个包含相互作用域中非同义风险 SNP 位点的 PPI 对。特别是 FN1 与其他 5 种蛋白（如 FN1-腱糖蛋白 C、TNC）相互作用的相互作用域中存在非同义风险 SNP 位点。此外，在所有肿瘤组织和正常组织中分别鉴定出 11 个和 4 个基因融合事件。此外，在肿瘤和正常组织中均鉴定出 NK2 同源盒 1-表面活性剂相关蛋白 3（NK2 homeobox 1-surfactant associated 3，NKX2-1-SFTA3）基因融合。这些结果表明，TGFβR1 和 NKX2-1-SFTA3 基因融合可能参与 PTC。此外，含有非同义风险 SNP 位点的 FN1 和 TNC 可能通过相互作用在 PTC 中发挥作用。
