Nanjing Medical University, Nanjing, China.
Department of General Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China.
J Clin Lab Anal. 2021 Mar;35(3):e23664. doi: 10.1002/jcla.23664. Epub 2020 Dec 17.
The incidence of thyroid cancer has been on a rise. Papillary thyroid cancer (PTC) is the most common type of malignant thyroid tumor and accounts for approximately 85% of thyroid cancer cases. Although the genetic background of PTC has been studied extensively, relatively little is known about the role of small noncoding RNAs (sncRNAs) in PTC. tRNA-derived fragments (tRFs) represent a newly discovered class of sncRNAs that exist in many species and play key roles in various biological processes.
In this study, we used high-throughput next-generation sequencing technology to analyze the expression of tRFs in samples from PTC tissues and normal tissues. We selected four tRFs to perform qPCR to determine the expression levels of these molecules and make bioinformatic predictions.
We identified 53 unique tRFs and transfer RNA halves (tsRNAs). The 10 most upregulated tRFs and tsRNAs were tRF-39-I6D3887S1RMH5MI2, tRF-21-2E489B3RB, tRF-18-JMRPFQDY, tRF-17-202L2YF, tRF-17-VBY9PYJ, tRF-18-YRRHQFD2, tRF-21-WE884U1DD, tRF-41-EX2Z10I9BZBZOS4YB, tRF-39-HPDEXK7S1RNS9MI2, and tRF-20-1SS2P46I. The 10 most downregulated tRFs and tsRNAs were tRF-31-HQ9M739P8WQ0B, tRF-43-5YXENDBP1IUUK7VZV, tRF-38-RZYQHQ9M739P8WD8, tRF-25-9M739P8WQ0, tRF-33-V6Z3M8ZLSSXUD6, tRF-27-MY73H3RXPLM, tRF-26-DBNIB9I1KQ0, tRF-38-Z9HMI8W47W1R7HX, tRF-40-Z6V6Z3M8ZLSSXUOL, and tRF-39-YQHQ9M739P8WQ0EB. qPCR verification of cell lines and tissue samples yielded results consistent with the sequencing analysis. As tRF-39 expression showed the maximum difference between PTC cells and normal cells, we chose this tRF to predict targets and perform functional tRF and tsRNA enrichment analysis.
In this study, we provided a comprehensive catalog of tRFs involved in PTC and assessed the abnormal expression of these fragments. Through qPCR verification, tRF-39-0VL8K87SIRMM12E2 was found to be the most significantly upregulated tRF. Further tRF and enrichment analysis revealed that tRF-39 was mostly enriched in the "metabolic pathways." These preliminary findings can be used as the basis for further research studies based on the functional role of tRFs in patients with PTC.
甲状腺癌的发病率一直在上升。甲状腺癌（PTC）是最常见的恶性甲状腺肿瘤，约占甲状腺癌病例的 85%。尽管 PTC 的遗传背景已经得到了广泛的研究，但关于小非编码 RNA（sncRNA）在 PTC 中的作用，人们知之甚少。tRNA 衍生片段（tRFs）是一种新发现的 sncRNA 类，存在于许多物种中，在各种生物过程中发挥着关键作用。
在这项研究中，我们使用高通量下一代测序技术分析了 PTC 组织和正常组织样本中的 tRFs 表达。我们选择了四个 tRFs 进行 qPCR，以确定这些分子的表达水平，并进行生物信息学预测。
我们鉴定了 53 个独特的 tRFs 和转移 RNA 片段（tsRNAs）。上调最明显的 10 个 tRFs 和 tsRNAs 是 tRF-39-I6D3887S1RMH5MI2、tRF-21-2E489B3RB、tRF-18-JMRPFQDY、tRF-17-202L2YF、tRF-17-VBY9PYJ、tRF-18-YRRHQFD2、tRF-21-WE884U1DD、tRF-41-EX2Z10I9BZBZOS4YB、tRF-39-HPDEXK7S1RNS9MI2 和 tRF-20-1SS2P46I。下调最明显的 10 个 tRFs 和 tsRNAs 是 tRF-31-HQ9M739P8WQ0B、tRF-43-5YXENDBP1IUUK7VZV、tRF-38-RZYQHQ9M739P8WD8、tRF-25-9M739P8WQ0、tRF-33-V6Z3M8ZLSSXUD6、tRF-27-MY73H3RXPLM、tRF-26-DBNIB9I1KQ0、tRF-38-Z9HMI8W47W1R7HX、tRF-40-Z6V6Z3M8ZLSSXUOL 和 tRF-39-YQHQ9M739P8WQ0EB。细胞系和组织样本的 qPCR 验证结果与测序分析一致。由于 tRF-39 在 PTC 细胞和正常细胞之间的表达差异最大，我们选择了这个 tRF 来预测靶点，并进行功能 tRF 和 tsRNA 富集分析。
在这项研究中，我们提供了一个全面的 PTC 相关 tRFs 目录，并评估了这些片段的异常表达。通过 qPCR 验证，发现 tRF-39-0VL8K87SIRMM12E2 是上调最明显的 tRF。进一步的 tRF 和富集分析表明，tRF-39 主要富集在“代谢途径”中。这些初步发现可以作为进一步研究的基础，基于 tRF 在 PTC 患者中的功能作用。
