Shiting Shan1,2, Yuting Wang2,3, Chunfu Zhu2. 1. Nanjing Medical University, Nanjing, China. 2. Department of General Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China. 3. Dalian Medical University, Dalian, China.
Abstract
BACKGROUND: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.
BACKGROUND: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.
Authors: Afaf T Ibrahiem; Amin K Makhdoom; Khalid S Alanazi; Abdulaziz M Alanazi; Abdulaziz M Mukhlef; Saad H Elshafey; Eman A Toraih; Manal S Fawzy Journal: J Clin Lab Anal Date: 2022-04-07 Impact factor: 3.124