tRNA-derived fragments (tRFs) contribute to podocyte differentiation

et al. 2020

Preprint

Background: Recently, the incidence of cholangiocarcinoma (CCA) has gradually increased. As CCA has a poor prognosis, the ideal survival rate is scarce for patients. The abnormal expressed tsRNA may regulate the progression of a variety of tumors, and tsRNA is expected to become a new diagnostic marker of cancer. However, the expression of tsRNA is obscure and should be elucidated in CCA.Methods: We collected CCA tissues and adjacent normal tissues from three patients. High-throughput RNA-seq was utilized to determine the overall expression profiles of tsRNA in CCA and adjacent normal tissues and to screen the tsRNAs that were differentially expressed. The biological effects and potential signaling pathways of dysregulated tsRNAs between the CCA and adjacent normal tissues were explored by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.Results: High-throughput RNA-seq totally demonstrated 535 dysregulated tsRNAs, of which 241 tsRNAs were upregulated and 294 tsRNAs were downregulated in CCA compared with adjacent normal tissues (|log2 (fold change)| >=1 and p value< 0.05). GO and KEGG enrichment analyses indicated that the target genes of dysregulated tRFs (tRF-34-JJ6RRNLIK898HR, tRF-38-0668K87SERM492V, tRF-39-0668K87SERM492E2) were mainly enriched in the Notch signaling pathway, Hippo signaling pathway, and cAMP signaling pathway and in growth hormone synthesis, secretion and action.Conclusion: Differentially expressed tRFs in CCA are enriched in many pathways associated with neoplasms, which may impact the progression of CCA.

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

RNA-sequencing reveals the expression profiles of tsRNAs and their potential carcinogenic role in cholangiocarcinoma

Yan

et al. 2020

Preprint

“…tRFs can regulate gene expression through competitive binding with AGO (Argonaute) family proteins, thereby affecting the silencing efficiency of target genes [9]. In addition, tRFs and its analogs can replace the tumor gene mRNA binding protein YBX1, blocking its interaction with oncogenic mRNA and destabilizing oncogene mRNAs, resulting in inhibition of tumor cell infiltration [10]. tRFs can also regulate protein biosynthesis by affecting the translation mechanism and can regulate ribosome biogenesis at different levels.…”

Section: Introductionmentioning

confidence: 99%

A Comprehensive Expression Profile of tRNA-Derived Fragments in Papillary Thyroid Cancer

Shan

Zhu

2020

JSO

Objective: In recent years, the incidence of thyroid cancer has been increasing. Papillary thyroid cancer (PTC) is the most common type of malignant thyroid tumor, accounting 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 non-coding RNA (sncRNA) in this disease. tRNA-derived fragments (tRFs) represent a newly discovered class of sncRNAs that exist in many species and play a role in many biological processes. Methods: In this study, we used RNA sequencing to analyse the expression of tRFs in fresh frozen specimens from PTC tissues and normal tissues adjacent to the tumors. Through this analysis, we identified 49 unique tRFs and transfer RNA halves and then performed quantitative PCR to determine the expression levels of these molecules and to make bioinformatic predictions. Conclusion: In this report, we provide a comprehensive catalog of tRFs in PTC and assess the abnormal expression of these fragments. These preliminary findings can be used as the basis for further research regarding the functional role of tRFs in patients with PTC.

A comprehensive expression profile of tRNA‐derived fragments in papillary thyroid cancer

Shan

Clinical Laboratory Analysis

Zhu

2020

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-HQ 9M739P-8WQ0B, 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. K E Y W O R D S expression profile, papillary thyroid cancer, tRNA-derived fragments This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. How to cite this article: Shan S, Wang Y, Zhu C. A comprehensive expression profile of tRNA-derived fragments in papillary thyroid cancer.