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      tRNA-derived RNA fragments in cancer: current status and future perspectives

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          Abstract

          Non-coding RNAs (ncRNAs) have been the focus of many studies over the last few decades, and their fundamental roles in human diseases have been well established. Transfer RNAs (tRNAs) are housekeeping ncRNAs that deliver amino acids to ribosomes during protein biosynthesis. tRNA fragments (tRFs) are a novel class of small ncRNAs produced through enzymatic cleavage of tRNAs and have been shown to play key regulatory roles similar to microRNAs. Development and application of high-throughput sequencing technologies has provided accumulating evidence of dysregulated tRFs in cancer. Aberrant expression of tRFs has been found to participate in cell proliferation, invasive metastasis, and progression in several human malignancies. These newly identified functional tRFs also have great potential as new biomarkers and therapeutic targets for cancer treatment. In this review, we focus on the major biological functions of tRFs including RNA silencing, translation regulation, and epigenetic regulation; summarize recent research on the roles of tRFs in different types of cancer; and discuss the potential of using tRFs as clinical biomarkers for cancer diagnosis and prognosis and as therapeutic targets for cancer treatment.

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          Current Challenges in Cancer Treatment.

          In this review, we highlight the current concepts and discuss some of the current challenges and future prospects in cancer therapy. We frequently use the example of lung cancer.
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            Efficient and quantitative high-throughput transfer RNA sequencing

            Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. We achieve efficient and quantitative tRNA sequencing using engineered demethylases to remove base methylations and a highly processive thermostable group II intron reverse transcriptase to overcome these obstacles (DM-TGIRT-seq). Our method should be applicable to investigations of tRNA in all organisms.
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              ARM-Seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

              High throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, but RNAs containing modified nucleosides may escape detection when those modifications interfere with reverse transcription during RNA-seq library preparation. Here we describe AlkB-facilitated RNA Methylation sequencing (ARM-Seq) which uses pre-treatment with Escherichia coli AlkB to demethylate 1-methyladenosine, 3-methylcytidine, and 1-methylguanosine, all commonly found in transfer RNAs. Comparative methylation analysis using ARM-Seq provides the first detailed, transcriptome-scale map of these modifications, and reveals an abundance of previously undetected, methylated small RNAs derived from tRNAs. ARM-Seq demonstrates that tRNA-derived small RNAs accurately recapitulate the m1A modification state for well-characterized yeast tRNAs, and generates new predictions for a large number of human tRNAs, including tRNA precursors and mitochondrial tRNAs. Thus, ARM-Seq provides broad utility for identifying previously overlooked methyl-modified RNAs, can efficiently monitor methylation state, and may reveal new roles for tRNA-derived RNAs as biomarkers or signaling molecules.
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                Author and article information

                Contributors
                yanlu76@zju.edu.cn
                Journal
                J Hematol Oncol
                J Hematol Oncol
                Journal of Hematology & Oncology
                BioMed Central (London )
                1756-8722
                4 September 2020
                4 September 2020
                2020
                : 13
                : 121
                Affiliations
                [1 ]GRID grid.13402.34, ISNI 0000 0004 1759 700X, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Zhejiang University School of Medicine, ; Zhejiang, 310029 Hangzhou China
                [2 ]GRID grid.13402.34, ISNI 0000 0004 1759 700X, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women’s Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women’s Hospital and Institute of Translational Medicine, , Zhejiang University School of Medicine, ; Hangzhou, China
                [3 ]GRID grid.417397.f, ISNI 0000 0004 1808 0985, Department of Head and Neck Surgery, , Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, ; Hangzhou, China
                [4 ]GRID grid.30760.32, ISNI 0000 0001 2111 8460, Center of Systems Molecular Medicine, Department of Physiology, , Medical College of Wisconsin, ; Milwaukee, WI 53226 USA
                Article
                955
                10.1186/s13045-020-00955-6
                7487644
                32887641
                e5fa4751-7abe-47e3-8e0c-69353488cf92
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 13 July 2020
                : 24 August 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81871864 and 81772766
                Award Recipient :
                Categories
                Review
                Custom metadata
                © The Author(s) 2020

                Oncology & Radiotherapy
                biomarkers,cancer,epigenetic regulation,rna silencing,translation regulation,trna-derived fragments

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