1
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Tesarova T, Fiala O, Hora M, Vaclavikova R. Non-coding transcriptome profiles in clear-cell renal cell carcinoma. Nat Rev Urol 2024:10.1038/s41585-024-00926-3. [PMID: 39242964 DOI: 10.1038/s41585-024-00926-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
Clear-cell renal cell carcinoma (ccRCC) is a common urological malignancy with an increasing incidence. The development of molecular biomarkers that can predict the response to treatment and guide personalized therapy selection would substantially improve patient outcomes. Dysregulation of non-coding RNA (ncRNA) has been shown to have a role in the pathogenesis of ccRCC. Thus, an increasing number of studies are being carried out with a focus on the identification of ncRNA biomarkers in ccRCC tissue samples and the connection of these markers with patients' prognosis, pathological stage and grade (including metastatic potential), and therapy outcome. RNA sequencing analysis led to the identification of several ncRNA biomarkers that are dysregulated in ccRCC and might have a role in ccRCC development. These ncRNAs have the potential to be prognostic and predictive biomarkers for ccRCC, with prospective applications in personalized treatment selection. Research on ncRNA biomarkers in ccRCC is advancing, but clinical implementation remains preliminary owing to challenges in validation, standardization and reproducibility. Comprehensive studies and integration of ncRNAs into clinical trials are essential to accelerate the clinical use of these biomarkers.
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Affiliation(s)
- Tereza Tesarova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Ondrej Fiala
- Department of Oncology and Radiotherapeutics, Faculty of Medicine in Pilsen and University Hospital, Charles University, Pilsen, Czech Republic
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milan Hora
- Department of Urology, Faculty of Medicine in Pilsen and University Hospital, Charles University, Pilsen, Czech Republic
| | - Radka Vaclavikova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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2
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Kazimierczyk M, Fedoruk-Wyszomirska A, Gurda-Woźna D, Wyszko E, Swiatkowska A, Wrzesinski J. The expression profiles of piRNAs and their interacting Piwi proteins in cellular model of renal development: Focus on Piwil1 in mitosis. Eur J Cell Biol 2024; 103:151444. [PMID: 39024988 DOI: 10.1016/j.ejcb.2024.151444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Piwi proteins and Piwi interacting RNAs, piRNAs, presented in germline cells play a role in transposon silencing during germline development. In contrast, the role of somatic Piwi proteins and piRNAs still remains obscure. Here, we characterize the expression pattern and distribution of piRNAs in human renal cells in terms of their potential role in kidney development. Further, we show that all PIWI genes are expressed at the RNA level, however, only PIWIL1 gene is detected at the protein level by western blotting in healthy and cancerous renal cells. So far, the expression of human Piwil1 protein has only been shown in testes and cancer cells, but not in healthy somatic cell lines. Since we observe only Piwil1 protein, the regulation of other PIWI genes is probably more intricated, and depends on environmental conditions. Next, we demonstrate that downregulation of Piwil1 protein results in a decrease in the rate of cell proliferation, while no change in the level of apoptotic cells is observed. Confocal microscopy analysis reveals that Piwil1 protein is located in both cellular compartments, cytoplasm and nucleus in renal cells. Interestingly, in nucleus region Piwil1 is observed close to the spindle during all phases of mitosis in all tested cell lines. It strongly indicates that Piwil1 protein plays an essential role in proliferation of somatic cells. Moreover, involvement of Piwil1 in cell division could, at least partly, explain invasion and metastasis of many types of cancer cells with upregulation of PIWIL1 gene expression. It also makes Piwil1 protein as a potential target in the anticancer therapy.
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Affiliation(s)
- Marek Kazimierczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | | | - Dorota Gurda-Woźna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland
| | - Agata Swiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland.
| | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan 61-704, Poland.
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3
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Xiong Q, Zhang Y, Xu Y, Yang Y, Zhang Z, Zhou Y, Zhang S, Zhou L, Wan X, Yang X, Zeng Z, Liu J, Zheng Y, Han J, Zhu Q. tiRNA-Val-CAC-2 interacts with FUBP1 to promote pancreatic cancer metastasis by activating c‑MYC transcription. Oncogene 2024; 43:1274-1287. [PMID: 38443680 PMCID: PMC11035144 DOI: 10.1038/s41388-024-02991-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Cumulative studies have established the significance of transfer RNA-derived small RNA (tsRNA) in tumorigenesis and progression. Nevertheless, its function and mechanism in pancreatic cancer metastasis remain largely unclear. Here, we screened and identified tiRNA-Val-CAC-2 as highly expressed in pancreatic cancer metastasis samples by tsRNA sequencing. We also observed elevated levels of tiRNA-Val-CAC-2 in the serum of pancreatic cancer patients who developed metastasis, and patients with high levels of tiRNA-Val-CAC-2 exhibited a worse prognosis. Additionally, knockdown of tiRNA-Val-CAC-2 inhibited the metastasis of pancreatic cancer in vivo and in vitro, while overexpression of tiRNA-Val-CAC-2 promoted the metastasis of pancreatic cancer. Mechanically, we discovered that tiRNA-Val-CAC-2 interacts with FUBP1, leading to enhanced stability of FUBP1 protein and increased FUBP1 enrichment in the c-MYC promoter region, thereby boosting the transcription of c-MYC. Of note, rescue experiments confirmed that tiRNA-Val-CAC-2 could influence pancreatic cancer metastasis via FUBP1-mediated c-MYC transcription. These findings highlight a potential novel mechanism underlying pancreatic cancer metastasis, and suggest that both tiRNA-Val-CAC-2 and FUBP1 could serve as promising prognostic biomarkers and potential therapeutic targets for pancreatic cancer.
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Affiliation(s)
- Qunli Xiong
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yaguang Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yongfeng Xu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Yang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhiwei Zhang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ying Zhou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lian Zhou
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaojuan Yang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhu Zeng
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinlu Liu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ying Zheng
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qing Zhu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
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4
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Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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5
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Yang N, Li R, Liu R, Yang S, Zhao Y, Xiong W, Qiu L. The Emerging Function and Promise of tRNA-Derived Small RNAs in Cancer. J Cancer 2024; 15:1642-1656. [PMID: 38370372 PMCID: PMC10869971 DOI: 10.7150/jca.89219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/20/2024] Open
Abstract
Fragments derived from tRNA, called tRNA-derived small RNAs (tsRNAs), have attracted widespread attention in the past decade. tsRNAs are widespread in prokaryotic and eukaryotic transcriptome, which contains two main types, tRNA-derived fragments (tRFs) and tRNA-derived stress-inducing RNA (tiRNAs), derived from the precursor tRNAs or mature tRNAs. According to differences in the cleavage position, tRFs can be divided into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, whereas tiRNAs can be divided into 5'-tiRNA and 3'-tiRNA. Studies have found that tRFs and tiRNAs are abnormally expressed in a variety of human malignant tumors, promote or inhibit the proliferation and apoptosis of cancer cells by regulating the expression of oncogene, and play an important role in the aggressive metastasis and progression of tumors. This article reviews the biological origins of various tsRNAs, introduces their functions and new concepts of related mechanisms, and focuses on the molecular mechanisms of tsRNAs in cancer, including breast cancer, prostate cancer, colorectal cancer, lung cancer, b-cell lymphoma, and chronic lymphoma cell leukemia. Lastly, this article puts forward some unresolved problems and future research prospects.
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Affiliation(s)
- Na Yang
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Ruijun Li
- College of Foreign Languages, Chuxiong Normal University, Chuxiong 675000, China
| | - Ruai Liu
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Shengjie Yang
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Yi Zhao
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Wei Xiong
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Lu Qiu
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
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6
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Singh A, Zahra S, Arora S, Hamid F, Kumar S. In Silico Identification of tRNA Fragments, Novel Candidates for Cancer Biomarkers, and Therapeutic Targets. Methods Mol Biol 2024; 2812:379-392. [PMID: 39068374 DOI: 10.1007/978-1-0716-3886-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The identification of a wide variety of RNA molecules using high-throughput sequencing techniques in the transcriptome pool of living organisms has revealed hidden regulatory insights in the cell. The class of non-coding RNA fragments produced from transfer RNA, or tRFs, is one such example. They are heterogeneously sized molecules with lengths ranging between 15 and 50 nt. They have a history of being dysregulated in human malignancies and other illnesses. The detection of these molecules has been made easier by a variety of bioinformatics techniques. The various types of tRFs and how they relate to cancer are covered in this chapter. It also provides a summary of the biological significance of tRFs reported in human cancer. Additionally, it emphasizes the utilities of databases and computational tools that have been created by different research teams for the investigation of tRFs. This will further aid the exploration and analysis of tRFs in cancer research and will support future advancement and a better comprehension of these molecules.
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Affiliation(s)
- Ankita Singh
- Department of Surgical Disciplines, All India Institute of Medical Science (AIIMS), New Delhi, India
| | - Shafaque Zahra
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Simran Arora
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Fiza Hamid
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India.
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7
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Pinzaru AM, Tavazoie SF. Transfer RNAs as dynamic and critical regulators of cancer progression. Nat Rev Cancer 2023; 23:746-761. [PMID: 37814109 DOI: 10.1038/s41568-023-00611-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 10/11/2023]
Abstract
Transfer RNAs (tRNAs) have been historically viewed as non-dynamic adaptors that decode the genetic code into proteins. Recent work has uncovered dynamic regulatory roles for these fascinating molecules. Advances in tRNA detection methods have revealed that specific tRNAs can become modulated upon DNA copy number and chromatin alterations and can also be perturbed by oncogenic signalling and transcriptional regulators in cancer cells or the tumour microenvironment. Such alterations in the levels of specific tRNAs have been shown to causally impact cancer progression, including metastasis. Moreover, sequencing methods have identified tRNA-derived small RNAs that influence various aspects of cancer progression, such as cell proliferation and invasion, and could serve as diagnostic and prognostic biomarkers or putative therapeutic targets in various cancers. Finally, there is accumulating evidence, including from genetic models, that specific tRNA synthetases - the enzymes responsible for charging tRNAs with amino acids - can either promote or suppress tumour formation. In this Review, we provide an overview of how deregulation of tRNAs influences cancer formation and progression.
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Affiliation(s)
- Alexandra M Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
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8
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Peng Z, Cai J, Guo X, Xu S. Brown adipocyte activation mediates lipid metabolism through exosomal tRNA-derived fragments. Biochem Biophys Res Commun 2023; 672:128-136. [PMID: 37352601 DOI: 10.1016/j.bbrc.2023.06.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023]
Abstract
Human obesity is related with intrinsic impairments of adipocyte lipolysis and ectopic lipid accumulation. Small regulatory RNAs, such as tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are enriched in exosomes and play a crucial role in lipid metabolism. To determine certain tRFs for lipolysis, brown adipocytes were treated with forskolin. Using tRFs sequencing, 207 different expressed exosomal tRFs were determined. In forskolin samples, 145 downregulated and 62 upregulated tRFs were identified. Further, qRT-PCR validated that three notably upregulated tRFs (tRF-Gly-GCC-007, tRF-Gly-GCC-008, and tRF-Gly-GCC-009) were in accordance with the sequencing result. Target genes of tRFs were involved in positive regulation of protein phosphorylation and cell adhesion process by significantly downregulating UCHL1 expression, which might participate in lipolysis. This study might provide therapeutic targets and potential diagnostic biomarkers for obesity treatment.
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Affiliation(s)
- Zhou Peng
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyang Cai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xirong Guo
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Siliang Xu
- State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
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9
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Fu M, Gu J, Wang M, Zhang J, Chen Y, Jiang P, Zhu T, Zhang X. Emerging roles of tRNA-derived fragments in cancer. Mol Cancer 2023; 22:30. [PMID: 36782290 PMCID: PMC9926655 DOI: 10.1186/s12943-023-01739-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.
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Affiliation(s)
- Min Fu
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China ,grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jianmei Gu
- grid.260483.b0000 0000 9530 8833Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226361 Jiangsu China
| | - Maoye Wang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jiahui Zhang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Yanke Chen
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Pengcheng Jiang
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China
| | - Taofeng Zhu
- Department of Pulmonary and Critical Care Medicine, Yixing Hospital Affiliated to Jiangsu University, Yixing, 214200, Jiangsu, China.
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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10
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Hou J, Li Q, Wang J, Lu W. tRFs and tRNA Halves: Novel Cellular Defenders in Multiple Biological Processes. Curr Issues Mol Biol 2022; 44:5949-5962. [PMID: 36547066 PMCID: PMC9777342 DOI: 10.3390/cimb44120405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA transcripts rather than via random degradation. tRFs and tRNA halves are highly involved in regulating transcription and translation in a canonical or non-canonical manner in response to cellular stress. In this review, we summarize the biogenesis and types of tRFs and tRNA halves, clarify the biological functions and molecular mechanisms of tRNA fragments in both physiological and pathological processes with a particular focus on their cytoprotective roles in defending against oxidation and apoptosis, and highlight their potential application as biomarkers in determining cell fate.
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Affiliation(s)
- Jiani Hou
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qianqing Li
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jun Wang
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
| | - Wenfa Lu
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
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11
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Tanvir I, Hassan A, Albeladi F. DNA Methylation and Epigenetic Events Underlying Renal Cell Carcinomas. Cureus 2022; 14:e30743. [DOI: 10.7759/cureus.30743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/05/2022] Open
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12
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Kohansal M, Ghanbarisad A, Tabrizi R, Daraei A, Kashfi M, Tang H, Song C, Chen Y. tRNA-derived fragments in gastric cancer: Biomarkers and functions. J Cell Mol Med 2022; 26:4768-4780. [PMID: 35957621 PMCID: PMC9465185 DOI: 10.1111/jcmm.17511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/14/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
tRNA‐derived fragments (tRFs), non‐coding RNAs that regulate protein expression after transcription, have recently been identified as potential biomarkers. We identified differentially expressed tRFs in gastric cancer (GC) and the biological properties of tRFs in predicting the malignancy status of GCs as possible biomarkers. Until 15 February 2022, two independent reviewers did a thorough search in electronic databases of Scopus, EMBASE and PubMed. The QUADAS scale was used for quality assessment of the included studies. Ten articles investigating the clinical significance of tRFs, including 928 patients, were analysed. In 10 GC studies, seven tRFs were considerably upregulated and five tRFs were significantly downregulated when compared to controls. Risk of bias was rated low for index test, and flow as well as timing domains in relation to the review question. The applicability of the index test, flow and timing and patient selection for 10 studies was deemed low. In this study, we review the advances in the study of tRFs in GC and describe their functions in gene expression regulation, such as suppression of translation, cell differentiation, proliferation and the related signal transduction pathways associated with them. Our findings may offer researchers new ideas for cancer treatment as well as potential biomarkers for further research in GC.
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Affiliation(s)
- Maryam Kohansal
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran.,Department of biology, Payame Noor University, Tehran, Iran
| | - Ali Ghanbarisad
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran.,Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Reza Tabrizi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mojtaba Kashfi
- Departmen of Microbiology, School of Medicine, Shahid Beheshti Univercity of Medical Sciences, Tehran, Iran
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cailu Song
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongming Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
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13
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Li G, Manning AC, Bagi A, Yang X, Gokulnath P, Spanos M, Howard J, Chan PP, Sweeney T, Kitchen R, Li H, Laurent BD, Aranki SF, Kontaridis MI, Laurent LC, Van Keuren‐Jensen K, Muehlschlegel J, Lowe TM, Das S. Distinct Stress-Dependent Signatures of Cellular and Extracellular tRNA-Derived Small RNAs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200829. [PMID: 35373532 PMCID: PMC9189662 DOI: 10.1002/advs.202200829] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 05/11/2023]
Abstract
The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA-derived small RNAs (tDRs) play pivotal roles in stress responses. However, RNA modifications present on tDRs are barriers to accurately quantifying tDRs using traditional small RNA sequencing. Here, AlkB-facilitated methylation sequencing is used to generate a comprehensive landscape of cellular and extracellular tDR abundances in various cell types during different stress responses. Extracellular tDRs are found to have distinct fragmentation signatures from intracellular tDRs and these tDR signatures are better indicators of different stress responses than miRNAs. These distinct extracellular tDR fragmentation patterns and signatures are also observed in plasma from patients on cardiopulmonary bypass. It is additionally demonstrated that angiogenin and RNASE1 are themselves regulated by stressors and contribute to the stress-modulated abundance of sub-populations of cellular and extracellular tDRs. Finally, a sub-population of extracellular tDRs is identified for which AGO2 appears to be required for their expression. Together, these findings provide a detailed profile of stress-responsive tDRs and provide insight about tDR biogenesis and stability in response to cellular stressors.
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Affiliation(s)
- Guoping Li
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Aidan C. Manning
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Alex Bagi
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Xinyu Yang
- Fangshan Hospital of BeijingUniversity of Traditional Chinese MedicineBeijing102499China
| | - Priyanka Gokulnath
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Michail Spanos
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Jonathan Howard
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Patricia P. Chan
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Thadryan Sweeney
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Robert Kitchen
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Haobo Li
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Brice D. Laurent
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Sary F. Aranki
- Division of Cardiac SurgeryDepartment of SurgeryBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Maria I. Kontaridis
- Department of Biomedical Research and Translational MedicineMasonic Medical Research InstituteUticaNY13501USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA02115USA
- Department of MedicineDivision of CardiologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMA02215USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCA92093USA
| | | | - Jochen Muehlschlegel
- Department of Anesthesiology, Perioperative and Pain MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02115USA
| | - Todd M. Lowe
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Saumya Das
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
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14
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Fu BF, Xu CY. Transfer RNA-Derived Small RNAs: Novel Regulators and Biomarkers of Cancers. Front Oncol 2022; 12:843598. [PMID: 35574338 PMCID: PMC9096126 DOI: 10.3389/fonc.2022.843598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/06/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are conventional non-coding RNAs (ncRNAs) with a length between18 and 40 nucleotides (nt) playing a crucial role in treating various human diseases including tumours. Nowadays, with the use of high-throughput sequencing technologies, it has been proven that certain tsRNAs are dysregulated in multiple tumour tissues as well as in the blood serum of cancer patients. Meanwhile, data retrieved from the literature show that tsRNAs are correlated with the regulation of the hallmarks of cancer, modification of tumour microenvironment, and modulation of drug resistance. On the other side, the emerging role of tsRNAs as biomarkers for cancer diagnosis and prognosis is promising. In this review, we focus on the specific characteristics and biological functions of tsRNAs with a focus on their impact on various tumours and discuss the possibility of tsRNAs as novel potential biomarkers for cancer diagnosis and prognosis.
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Affiliation(s)
- Bi-Fei Fu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Chao-Yang Xu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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15
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A 5’-tiRNA fragment that inhibits proliferation and migration of laryngeal squamous cell carcinoma by targeting PIK3CD. Genomics 2022; 114:110392. [DOI: 10.1016/j.ygeno.2022.110392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/24/2022] [Accepted: 05/22/2022] [Indexed: 12/24/2022]
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16
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Hu Y, Cai A, Xu J, Feng W, Wu A, Liu R, Cai W, Chen L, Wang F. An emerging role of the 5' termini of mature tRNAs in human diseases: Current situation and prospects. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166314. [PMID: 34863896 DOI: 10.1016/j.bbadis.2021.166314] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/30/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023]
Abstract
The fundamental biological roles of a class of small noncoding RNAs (sncRNAs), derived from mature tRNAs or pre-tRNAs, in human diseases have received increasing attention in recent years. These ncRNAs are called tRNA-derived fragments (tRFs) or tRNA-derived small RNAs (tsRNAs). tRFs mainly include tRF-1, tRF-5, tRF-3 and tRNA halves (tiRNAs or tRHs), which are produced by enzyme-specific cleavage of tRNAs. Here, we classify tRF-5 and 5' tiRNAs into the same category: 5'-tRFs and review the biological functions and regulatory mechanisms of 5'-tRFs in cancer and other diseases (metabolic diseases, neurodegenerative diseases, pathological stress injury and virus infection) to provide a new theoretical basis for the diagnosis and treatment of diseases.
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Affiliation(s)
- Yuhao Hu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Aiting Cai
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Jing Xu
- Department of Laboratory Medicine, School of public health, Nantong University, Jiangsu, China
| | - Wei Feng
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Anqi Wu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Ruoyu Liu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Weihua Cai
- Department of Hepatology Laboratory, Nantong Third Hospital Affiliated to Nantong University, Jiangsu, China
| | - Lin Chen
- Department of Hepatology Laboratory, Nantong Third Hospital Affiliated to Nantong University, Jiangsu, China.
| | - Feng Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Jiangsu, China.
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17
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Qiu Z, Wang Q, Liu L, Li G, Hao Y, Ning S, Zhang L, Zhang X, Chen Y, Wu J, Wang X, Yang S, Lin Y, Xu S. Riddle of the Sphinx: Emerging Role of Transfer RNAs in Human Cancer. Front Pharmacol 2021; 12:794986. [PMID: 34975491 PMCID: PMC8714751 DOI: 10.3389/fphar.2021.794986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 01/16/2023] Open
Abstract
The dysregulation of transfer RNA (tRNA) expression contributes to the diversity of proteomics, heterogeneity of cell populations, and instability of the genome, which may be related to human cancer susceptibility. However, the relationship between tRNA dysregulation and cancer susceptibility remains elusive because the landscape of cancer-associated tRNAs has not been portrayed yet. Furthermore, the molecular mechanisms of tRNAs involved in tumorigenesis and cancer progression have not been systematically understood. In this review, we detail current knowledge of cancer-related tRNAs and comprehensively summarize the basic characteristics and functions of these tRNAs, with a special focus on their role and involvement in human cancer. This review bridges the gap between tRNAs and cancer and broadens our understanding of their relationship, thus providing new insights and strategies to improve the potential clinical applications of tRNAs for cancer diagnosis and therapy.
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Affiliation(s)
- Zhilin Qiu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guozheng Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yi Hao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yihai Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiale Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinheng Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuai Yang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yaoxin Lin
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
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18
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Wen JT, Huang ZH, Li QH, Chen X, Qin HL, Zhao Y. Research progress on the tsRNA classification, function, and application in gynecological malignant tumors. Cell Death Discov 2021; 7:388. [PMID: 34907180 PMCID: PMC8671397 DOI: 10.1038/s41420-021-00789-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
A large number of small non-coding RNAs derived from tRNAs, called tRNA-derived small RNA (tsRNAs), have been identified by high-throughput RNA sequencing of cell lines. Further research has revealed that they are not produced via random tRNA degradation, but through degradation by specific nuclease cleavages, such as Elac Ribonuclease Z 2 (ELAC2)/RNase Z, RNase L, Dicer, and angiogenin (ANG), the tsRNAs can be classified into the following types based on the location from which they have been derived from the parental tRNA: tRF-1s, tRF-3s, tRF-5s, tiRNA, and tRF-2s/i-tRFs. Moreover, tsRNAs are a type of small RNAs with diverse functions, including gene expression regulation, anti-apoptosis, translation inhibition, participation in epigenetic regulation, initial virus reverse transcription, promote virus replication and cell-to-cell communication. Certain types of tsRNAs are overexpressed in cancer tissues, but are underexpressed in normal tissues. Therefore, the relationship between tsRNAs and the occurrence and development of cancer has attracted significant research attention. Research advancements have contributed to further discoveries of the biological activities of tsRNAs, but the mechanisms of their biogenesis and functions have not been fully elucidated. This article reviews the classification and biological functions of tsRNAs, and introduces the research progress in gynecological malignancies.
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Affiliation(s)
- Jing-Tao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zheng-Hao Huang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Hong-Lei Qin
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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19
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Hu F, Niu Y, Mao X, Cui J, Wu X, Simone CB, Kang HS, Qin W, Jiang L. tsRNA-5001a promotes proliferation of lung adenocarcinoma cells and is associated with postoperative recurrence in lung adenocarcinoma patients. Transl Lung Cancer Res 2021; 10:3957-3972. [PMID: 34858784 PMCID: PMC8577981 DOI: 10.21037/tlcr-21-829] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022]
Abstract
Background The biological role and clinical significance of transfer RNA-derived small RNAs (tsRNAs) remain largely unclear. The purpose of this study was to investigate the biological function, molecular mechanism, and clinical significance of tsRNA-5001a in lung adenocarcinoma. Methods The function of tsRNA-5001a on the growth of tumor cells was accessed by cell function experiments. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression of tsRNA-5001a in paired samples of lung adenocarcinoma. Cell localization of tsRNA-5001a was performed by nuclear-cytoplasmic separation assay. Transcriptome sequencing was used to screen the molecules involved in the regulatory network of tsRNA-5001a. Independent samples t-test was used to compare the two groups. Prism software (Prism 7.0) was used to analyze the statistical results. P<0.05 was considered statistically significant. Results tsRNA-5001a was significantly upregulated in lung adenocarcinoma tissues. Upregulation of tsRNA-5001a was found to increase the risk of postoperative recurrences in patients with lung adenocarcinoma and was associated with poor prognosis. Function assay showed that overexpression tsRNA-5001a could significantly promote cell proliferation. In contrast, knockdown of tsRNA-5001a significantly inhibited the proliferation of lung adenocarcinoma cells. In addition, nucleoplasmic isolation assay indicated that tsRNA-5001a was located mainly in the cytoplasm. According to the results of RNA sequencing and The Cancer Genome Atlas database (TCGA database) analysis, growth arrest and DNA damage 45G (GADD45G) was screened and may be the target gene of tsRNA-5001a. Conclusions tsRNA-5001a promotes the proliferation of lung adenocarcinoma cells and increases the risk of postoperative recurrences in lung adenocarcinoma patients.
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Affiliation(s)
- Fang Hu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Niu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Mao
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Cui
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoting Wu
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Charles B Simone
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center and New York Proton Center, New York, NY, USA
| | - Hye Seon Kang
- Division of Pulmonary, Critical Care and Allergy, Department of Internal Medicine, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, China
| | - Liyan Jiang
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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20
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Sahlolbei M, Fattahi F, Vafaei S, Rajabzadeh R, Shiralipour A, Madjd Z, Kiani J. Relationship Between Low Expressions of tRNA-Derived Fragments with Metastatic Behavior of Colorectal Cancer. J Gastrointest Cancer 2021; 53:862-869. [PMID: 34837147 DOI: 10.1007/s12029-021-00773-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Colorectal cancer (CRC) is one of the most commonly diagnosed malignant tumors and highly heterogeneous diseases. More recently, RNA expression profiles have been used as prognostic cancer markers. In this regard, the expression of small non-coding RNAs like tRNA-derived fragments (tRFs) in tumor tissue has potential diagnostic values in metastatic cancer. METHOD Sixty postoperative CRC tissue samples, consisting of 30 cancers and 30 adjacent normal tissues, were collected from cancer patients. We evaluated MINTbase database to select tRNA-derived fragments. The expression levels of miR-1280, miR1308, tRNA-ValAAC/CAC, and tRNA-AspGTC were measured by TaqMan quantitative reverse transcription PCR technology. Also, we have evaluated the correlation between the levels of tRFs gene expression and clinicopathological of CRC disease. RESULT The three tRFs derived from tRF/miR-1280, tRNA-ValAAC/CAC, and tRNA-AspGTC downregulated in tumor tissues (all, p < 0.0001). These tRFs have lower expression in stage IV in comparison with stage III. The tRFs derived from tRNA-ValAAC (p = 0.005) and tRNA-AspGTC (p = 0.034) showed the decreased expression in CRC patients with distant metastasis. CONCLUSION The present study demonstrated that low expression of tRF/miR-1280, tRNA-ValAAC/CAC, and tRNA-AspGTC was significantly associated with metastatic stage and more aggressive tumor behavior of CRC disease. Our finding promising the potential of using tRFs as biomarkers for cancer diagnosis.
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Affiliation(s)
- Maryam Sahlolbei
- Student Research Committee, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.,Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Fahimeh Fattahi
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Somayeh Vafaei
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rezvan Rajabzadeh
- Department of Epidemiology, School of Public Health, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Aref Shiralipour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran. .,Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
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21
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Li X, Liu X, Zhao D, Cui W, Wu Y, Zhang C, Duan C. tRNA-derived small RNAs: novel regulators of cancer hallmarks and targets of clinical application. Cell Death Discov 2021; 7:249. [PMID: 34537813 PMCID: PMC8449783 DOI: 10.1038/s41420-021-00647-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/19/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
tRNAs are a group of conventional noncoding RNAs (ncRNAs) with critical roles in the biological synthesis of proteins. Recently, tRNA-derived small RNAs (tsRNAs) were found to have important biological functions in the development of human diseases including carcinomas, rather than just being considered pure degradation material. tsRNAs not only are abnormally expressed in the cancer tissues and serum of cancer patients, but also have been suggested to regulate various vital cancer hallmarks. On the other hand, the application of tsRNAs as biomarkers and therapeutic targets is promising. In this review, we focused on the basic characteristics of tsRNAs, and their biological functions known thus far, and explored the regulatory roles of tsRNAs in cancer hallmarks including proliferation, apoptosis, metastasis, tumor microenvironment, drug resistance, cancer stem cell phenotype, and cancer cell metabolism. In addition, we also discussed the research progress on the application of tsRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Xizhe Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Xianyu Liu
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Weifang Cui
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Yingfang Wu
- Centre of Stomatology, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China. .,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China. .,National Clinical Research Center for Geriatric Disorders, Changsha, 410008, Hunan, P. R. China.
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China. .,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China. .,Institute of Medical Sciences, Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P. R. China.
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22
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Huang Y, Zhang H, Gu X, Qin S, Zheng M, Shi X, Peng C, Ju S. Elucidating the Role of Serum tRF-31-U5YKFN8DYDZDD as a Novel Diagnostic Biomarker in Gastric Cancer (GC). Front Oncol 2021; 11:723753. [PMID: 34497770 PMCID: PMC8419412 DOI: 10.3389/fonc.2021.723753] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 12/31/2022] Open
Abstract
Background Gastric cancer (GC) is one of the malignant tumors with the highest morbidity and mortality in the world. Early diagnosis combined with surgical treatment can significantly improve the prognosis of patients. Therefore, it is urgent to seek higher sensitivity and specificity biomarkers in GC. tRNA-derived small RNAs are a new non-coding small RNA that widely exists in tumor cells and body fluids. In this study, we explore the expression and biological significance of tRNA-derived small RNAs in GC. Materials and Methods First of all, we screened the differentially expressed tRNA-derived small RNAs in tumor tissues by high-throughput sequencing. Agarose gel electrophoresis (AGE), Sanger sequencing, and Nuclear and Cytoplasmic RNA Separation Assay were used to screen tRF-31-U5YKFN8DYDZDD as a potential tumor biomarker for the diagnosis of GC. Then, we detected the different expressions of tRF-31-U5YKFN8DYDZDD in 24 pairs of GC and paracancerous tissues, the serum of 111 GC patients at first diagnosis, 89 normal subjects, 48 superficial gastritis patients, and 28 postoperative GC patients by quantitative real-time PCR (qRT-PCR). Finally, we used the receiver operating characteristic (ROC) curve to analyze its diagnostic efficacy. Results The expression of tRF-31-U5YKFN8DYDZDD has good stability and easy detection. tRF-31-U5YKFN8DYDZDD was highly expressed in tumor tissue, serum, and cell lines of GC, and the expression was significantly related to TNM stage, depth of tumor invasion, lymph node metastasis, and vascular invasion. The expression of serum tRF-31-U5YKFN8DYDZDD in the GC patients decreased after the operation (P = 0.0003). Combined with ROC curve analysis, tRF-31-U5YKFN8DYDZDD has better detection efficiency than conventional markers. Conclusions The expressions of tRF-31-U5YKFN8DYDZDD in the tumor and paracancerous tissues, the serum of GC patients and healthy people, and the serum of GC patients before and after operation were different. tRF-31-U5YKFN8DYDZDD is not only a diagnostic biomarker of GC but also a predictor of poor prognosis.
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Affiliation(s)
- Yuejiao Huang
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, China.,Medical School of Nantong University, Nantong, China
| | - Haiyan Zhang
- Medical School of Nantong University, Nantong, China.,Department of Pathology, Affiliated Nantong Third Hospital of Nantong University, Nantong, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shiyi Qin
- Medical School of Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Ming Zheng
- Medical School of Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiangrong Shi
- Department of Medical Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Chunlei Peng
- Department of Medical Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Shaoqing Ju
- Medical School of Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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Yuan Y, Li J, He Z, Fan X, Mao X, Yang M, Yang D. tRNA-derived fragments as New Hallmarks of Aging and Age-related Diseases. Aging Dis 2021; 12:1304-1322. [PMID: 34341710 PMCID: PMC8279533 DOI: 10.14336/ad.2021.0115] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/15/2021] [Indexed: 01/02/2023] Open
Abstract
tRNA-derived fragments (tRFs), which are non-coding RNAs produced via tRNA cleavage with lengths of 14 to 50 nucleotides, originate from precursor tRNAs or mature tRNAs and exist in a wide range of organisms. tRFs are produced not by random fracture of tRNAs but by specific mechanisms. Considerable evidence shows that tRFs are detectable in model organisms of different ages and are associated with age-related diseases in humans, such as cancer and neurodegenerative diseases. In this literature review, the origin and classification of tRFs and the regulatory mechanisms of tRFs in aging and age-related diseases are summarized. We also describe the available tRF databases and research techniques and lay a foundation for the exploration of tRFs as biomarkers for the diagnosis and treatment of aging and age-related diseases.
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Affiliation(s)
- Ya Yuan
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jiamei Li
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zhi He
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaolan Fan
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xueping Mao
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingyao Yang
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Deying Yang
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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24
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Han L, Lai H, Yang Y, Hu J, Li Z, Ma B, Xu W, Liu W, Wei W, Li D, Wang Y, Zhai Q, Ji Q, Liao T. A 5'-tRNA halve, tiRNA-Gly promotes cell proliferation and migration via binding to RBM17 and inducing alternative splicing in papillary thyroid cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:222. [PMID: 34225773 PMCID: PMC8256553 DOI: 10.1186/s13046-021-02024-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 06/18/2021] [Indexed: 11/10/2022]
Abstract
Background tRNA-derived small noncoding RNAs (sncRNAs) are mainly categorized into tRNA halves (tiRNAs) and fragments (tRFs). Biological functions of tiRNAs in human solid tumor are attracting more and more attention, but researches concerning the mechanisms in tiRNAs-mediated tumorigenesis are rarely. The direct regulatory relationship between tiRNAs and splicing-related proteins remain elusive. Methods Papillary thyroid carcinoma (PTC) associated tRNA fragments were screened by tRNA fragments deep sequencing and validated by qRT-PCR and Northern Blot in PTC tissues. The biological function of tRNA fragments were assessed by cell counting kit, transwells and subcutaneous transplantation tumor of nude mice. For mechanistic study, tRNA fragments pull-down, RNA immunoprecipitation, Western Blot, Immunofluorescence, Immunohistochemical staining were performed. Results Herein, we have identified a 33 nt tiRNA-Gly significantly increases in papillary thyroid cancer (PTC) based on tRFs & tiRNAs sequencing. The ectopic expression of tiRNA-Gly promotes cell proliferation and migration, whereas down-regulation of tiRNA-Gly exhibits reverse effects. Mechanistic investigations reveal tiRNA-Gly directly bind the UHM domain of a splicing-related RNA-binding protein RBM17. The interaction with tiRNA-Gly could translocate RBM17 from cytoplasm into nucleus. In addition, tiRNA-Gly increases RBM17 protein expression via inhibiting its degradation in a ubiquitin/proteasome-dependent way. Moreover, RBM17 level in tiRNA-Gly high-expressing human PTC tissues is upregulated. In vivo mouse model shows that suppression of tiRNA-Gly decreases RBM17 expression. Importantly, tiRNA-Gly can induce exon 16 splicing of MAP4K4 mRNA leading to phosphorylation of downstream signaling pathway, which is RBM17 dependent. Conclusions Our study firstly illustrates tiRNA-Gly can directly bind to RBM17 and display oncogenic effect via RBM17-mediated alternative splicing. This fully novel model broadens our understanding of molecular mechanism in which tRNA fragment in tumor cells directly bind RNA binding protein and play a role in alternative splicing. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02024-3.
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Affiliation(s)
- Litao Han
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hejing Lai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, 200093, China
| | - Yichen Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jiaqian Hu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhe Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Weibo Xu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wanlin Liu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wenjun Wei
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Duanshu Li
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Qiwei Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, 200093, China.
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Li J, Zhu L, Cheng J, Peng Y. Transfer RNA-derived small RNA: A rising star in oncology. Semin Cancer Biol 2021; 75:29-37. [PMID: 34029740 DOI: 10.1016/j.semcancer.2021.05.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023]
Abstract
Transfer RNAs (tRNAs) participate in protein synthesis through delivering amino acids to the ribosome. Nevertheless, recent studies revealed that tRNAs can undergo cleavage by endoribonucleases to generate a heterogeneous class of small RNAs, designated as tRNA-derived small RNAs (tsRNAs). Accumulating evidence demonstrates that tsRNAs play an important role in many biological processes, and their dysregulation is associated with the progression of diseases including cancer. Abnormally expressed tsRNAs contribute to tumor initiation and development through distinct mechanisms, such as transcriptional regulation and RNA interference. In this review, we briefly summarize the current knowledge regarding classification, biogenesis and biological function of tsRNAs. Moreover, we highlight the dysregulation and critical roles of tsRNAs in cancer and discuss their potentials as diagnostic and prognostic biomarkers or therapeutic targets.
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Affiliation(s)
- Jiao Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Lei Zhu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Jian Cheng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610064, China.
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26
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Sanchez Caballero L, Gorgogietas V, Arroyo MN, Igoillo-Esteve M. Molecular mechanisms of β-cell dysfunction and death in monogenic forms of diabetes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 359:139-256. [PMID: 33832649 DOI: 10.1016/bs.ircmb.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Monogenetic forms of diabetes represent 1%-5% of all diabetes cases and are caused by mutations in a single gene. These mutations, that affect genes involved in pancreatic β-cell development, function and survival, or insulin regulation, may be dominant or recessive, inherited or de novo. Most patients with monogenic diabetes are very commonly misdiagnosed as having type 1 or type 2 diabetes. The severity of their symptoms depends on the nature of the mutation, the function of the affected gene and, in some cases, the influence of additional genetic or environmental factors that modulate severity and penetrance. In some patients, diabetes is accompanied by other syndromic features such as deafness, blindness, microcephaly, liver and intestinal defects, among others. The age of diabetes onset may also vary from neonatal until early adulthood manifestations. Since the different mutations result in diverse clinical presentations, patients usually need different treatments that range from just diet and exercise, to the requirement of exogenous insulin or other hypoglycemic drugs, e.g., sulfonylureas or glucagon-like peptide 1 analogs to control their glycemia. As a consequence, awareness and correct diagnosis are crucial for the proper management and treatment of monogenic diabetes patients. In this chapter, we describe mutations causing different monogenic forms of diabetes associated with inadequate pancreas development or impaired β-cell function and survival, and discuss the molecular mechanisms involved in β-cell demise.
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Affiliation(s)
- Laura Sanchez Caballero
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Vyron Gorgogietas
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Maria Nicol Arroyo
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Mariana Igoillo-Esteve
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/.
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27
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Tong L, Zhang W, Qu B, Zhang F, Wu Z, Shi J, Chen X, Song Y, Wang Z. The tRNA-Derived Fragment-3017A Promotes Metastasis by Inhibiting NELL2 in Human Gastric Cancer. Front Oncol 2021; 10:570916. [PMID: 33665159 PMCID: PMC7921707 DOI: 10.3389/fonc.2020.570916] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/30/2020] [Indexed: 12/24/2022] Open
Abstract
tRNA-derived fragments (tRFs) are a new classification of small non-coding RNAs (sncRNAs) derived from the specific cleavage of precursors and mature tRNAs. Accumulating recent evidence has shown that tRFs are frequently abnormal in several cancers. Nevertheless, the role of tRFs in gastric cancer and its mechanism remain unclear. In this study, we found abnormal expression of tRF-3017A (derived from tRNA-Val-TAC) in gastric cancer tissues and cell lines and confirmed its effect on promoting the invasion and migration of gastric cancer cells through functional experiments in vitro. Analysis of clinicopathologic data showed patients with higher tRF-3017A were associated with significantly higher lymph node metastasis. Mechanistic investigation implies that tRF-3017A regulates the tumor suppressor gene NELL2 through forming the RNA-induced silencing complex (RISC) with Argonaute (AGO) proteins. In this study, we found that higher tRF-3017A were associated with significantly higher lymph node metastasis in gastric cancer patients and the tRF-3017A may play a role in promoting the migration and invasion of gastric cancer cells by silencing tumor suppressor NELL2.
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Affiliation(s)
- Linhao Tong
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Weixu Zhang
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Bicheng Qu
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Fei Zhang
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Zhonghua Wu
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jinxin Shi
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaowan Chen
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yongxi Song
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Zhenning Wang
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, Shenyang, China
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Choi EJ, Wu W, Zhang K, Lee I, Kim IH, Lee YS, Bao X. ELAC2, an Enzyme for tRNA Maturation, Plays a Role in the Cleavage of a Mature tRNA to Produce a tRNA-Derived RNA Fragment During Respiratory Syncytial Virus Infection. Front Mol Biosci 2021; 7:609732. [PMID: 33604354 PMCID: PMC7884774 DOI: 10.3389/fmolb.2020.609732] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in young children. However, effective treatment against RSV is unavailable. tRNA-derived RNA fragments (tRFs) are a recently discovered family of non-coding RNAs. We made an early observation that RSV infection causes significant induction of tRFs, which are mainly derived from the 5’-end of mature tRNAs (tRF5). However, their functions and biogenesis mechanism are not fully understood. Herein, we identified an enzyme responsible for the induction of a functional tRF5 derived from tRNA-Gln-CTG (tRF5-GlnCTG). We found that tRF5-GlnCTG promotes RSV replication and its induction, assessed by Northern blot and a new qRT-PCR-based method, is regulated by ribonuclease ELAC2. ELAC2-mediated tRF5 induction has never been reported. We also found that ELAC2 is associated with RSV N and NS1 proteins. Given the fact that tRF5-GlnCTG plays a role in RSV replication, the identification of ELAC2 being responsible for tRF5-GlnCTG induction could provide new insights into therapeutic strategy development against RSV infection.
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Affiliation(s)
- Eun-Jin Choi
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Wenzhe Wu
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Ke Zhang
- Department of Chemistry, The University of Houston Clear Lake, Clear Lake, TX, United States
| | - Inhan Lee
- miRcore, Ann Arbor, MI, United States
| | - In-Hoo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Xiaoyong Bao
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States.,Sealy Center for Molecular Medicine, The University of Texas Medical Branch, Galveston, TX, United States.,The Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States.,The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United States
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29
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Kajdasz A, Majer W, Kluzek K, Sobkowiak J, Milecki T, Derebecka N, Kwias Z, Bluyssen HAR, Wesoly J. Identification of RCC Subtype-Specific microRNAs-Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data. Cancers (Basel) 2021; 13:548. [PMID: 33535553 PMCID: PMC7867039 DOI: 10.3390/cancers13030548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/17/2022] Open
Abstract
Renal cell carcinoma (RCC) is one of the most common cancers worldwide with a nearly non-symptomatic course until the advanced stages of the disease. RCC can be distinguished into three subtypes: papillary (pRCC), chromophobe (chRCC) and clear cell renal cell carcinoma (ccRCC) representing up to 75% of all RCC cases. Detection and RCC monitoring tools are limited to standard imaging techniques, in combination with non-RCC specific morphological and biochemical read-outs. RCC subtype identification relays mainly on results of pathological examination of tumor slides. Molecular, clinically applicable and ideally non-invasive tools aiding RCC management are still non-existent, although molecular characterization of RCC is relatively advanced. Hence, many research efforts concentrate on the identification of molecular markers that will assist with RCC sub-classification and monitoring. Due to stability and tissue-specificity miRNAs are promising candidates for such biomarkers. Here, we performed a meta-analysis study, utilized seven NGS and seven microarray RCC studies in order to identify subtype-specific expression of miRNAs. We concentrated on potentially oncocytoma-specific miRNAs (miRNA-424-5p, miRNA-146b-5p, miRNA-183-5p, miRNA-218-5p), pRCC-specific (miRNA-127-3p, miRNA-139-5p) and ccRCC-specific miRNAs (miRNA-200c-3p, miRNA-362-5p, miRNA-363-3p and miRNA-204-5p, 21-5p, miRNA-224-5p, miRNA-155-5p, miRNA-210-3p) and validated their expression in an independent sample set. Additionally, we found ccRCC-specific miRNAs to be differentially expressed in ccRCC tumor according to Fuhrman grades and identified alterations in their isoform composition in tumor tissue. Our results revealed that changes in the expression of selected miRNA might be potentially utilized as a tool aiding ccRCC subclass discrimination and we propose a miRNA panel aiding RCC subtype distinction.
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Affiliation(s)
- Arkadiusz Kajdasz
- Laboratory of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (K.K.); (H.A.R.B.)
| | - Weronika Majer
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (W.M.); (N.D.)
| | - Katarzyna Kluzek
- Laboratory of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (K.K.); (H.A.R.B.)
| | - Jacek Sobkowiak
- Department of Urology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285 Poznan, Poland; (J.S.); (T.M.); (Z.K.)
| | - Tomasz Milecki
- Department of Urology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285 Poznan, Poland; (J.S.); (T.M.); (Z.K.)
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (W.M.); (N.D.)
| | - Zbigniew Kwias
- Department of Urology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285 Poznan, Poland; (J.S.); (T.M.); (Z.K.)
| | - Hans A. R. Bluyssen
- Laboratory of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (K.K.); (H.A.R.B.)
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (W.M.); (N.D.)
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30
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Zhao Q, Zhang Y, Shao S, Sun Y, Lin Z. Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis. PeerJ 2021; 9:e10594. [PMID: 33552715 PMCID: PMC7821758 DOI: 10.7717/peerj.10594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC), the main type of liver cancer in human, is one of the most prevalent and deadly malignancies in the world. The present study aimed to identify hub genes and key biological pathways by integrated bioinformatics analysis. Methods A bioinformatics pipeline based on gene co-expression network (GCN) analysis was built to analyze the gene expression profile of HCC. Firstly, differentially expressed genes (DEGs) were identified and a GCN was constructed with Pearson correlation analysis. Then, the gene modules were identified with 3 different community detection algorithms, and the correlation analysis between gene modules and clinical indicators was performed. Moreover, we used the Search Tool for the Retrieval of Interacting Genes (STRING) database to construct a protein protein interaction (PPI) network of the key gene module, and we identified the hub genes using nine topology analysis algorithms based on this PPI network. Further, we used the Oncomine analysis, survival analysis, GEO data set and random forest algorithm to verify the important roles of hub genes in HCC. Lastly, we explored the methylation changes of hub genes using another GEO data (GSE73003). Results Firstly, among the expression profiles, 4,130 up-regulated genes and 471 down-regulated genes were identified. Next, the multi-level algorithm which had the highest modularity divided the GCN into nine gene modules. Also, a key gene module (m1) was identified. The biological processes of GO enrichment of m1 mainly included the processes of mitosis and meiosis and the functions of catalytic and exodeoxyribonuclease activity. Besides, these genes were enriched in the cell cycle and mitotic pathway. Furthermore, we identified 11 hub genes, MCM3, TRMT6, AURKA, CDC20, TOP2A, ECT2, TK1, MCM2, FEN1, NCAPD2 and KPNA2 which played key roles in HCC. The results of multiple verification methods indicated that the 11 hub genes had highly diagnostic efficiencies to distinguish tumors from normal tissues. Lastly, the methylation changes of gene CDC20, TOP2A, TK1, FEN1 in HCC samples had statistical significance (P-value < 0.05). Conclusion MCM3, TRMT6, AURKA, CDC20, TOP2A, ECT2, TK1, MCM2, FEN1, NCAPD2 and KPNA2 could be potential biomarkers or therapeutic targets for HCC. Meanwhile, the metabolic pathway, the cell cycle and mitotic pathway might played vital roles in the progression of HCC.
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Affiliation(s)
- Qian Zhao
- College of Information Science and Technology, Dalian Martime University, Dalian, Liaoning, China
| | - Yan Zhang
- College of Information Science and Technology, Dalian Martime University, Dalian, Liaoning, China
| | - Shichun Shao
- College of Environmental Science and Engineering, Dalian Martime University, Dalian, Liaoning, China
| | - Yeqing Sun
- College of Environmental Science and Engineering, Dalian Martime University, Dalian, Liaoning, China
| | - Zhengkui Lin
- College of Information Science and Technology, Dalian Martime University, Dalian, Liaoning, China
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Cox A, Tolkach Y, Stein J, Kristiansen G, Ritter M, Ellinger J. Otoferlin is a prognostic biomarker in patients with clear cell renal cell carcinoma: A systematic expression analysis. Int J Urol 2021; 28:424-431. [PMID: 33465825 DOI: 10.1111/iju.14486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To comprehensively investigate the role of otoferlin as a prognostic and diagnostic biomarker in clear cell renal cell carcinoma. METHODS Three independent cohorts were used to study otoferlin in clear cell renal cell carcinoma: The Cancer Genome Atlas cohort (messenger ribonucleic acid expression; clear cell renal cell carcinoma n = 514, normal renal tissue n = 81); study validation cohort (messenger ribonucleic acid expression; clear cell renal cell carcinoma n = 79, normal renal tissue n = 44); and immunohistochemistry cohort (protein expression; clear cell renal cell carcinoma n = 142, normal renal tissue n = 30). Otoferlin gene expressions were extracted from The Cancer Genome Atlas database or determined using quantitative real-time polymerase chain reaction, respectively. Protein expression was assessed using immunohistochemistry staining against otoferlin on tissue microarrays. Correlations between otoferlin messenger ribonucleic acid/protein expression and clinicopathological data/patient survival were statistically tested. RESULTS Otoferlin messenger ribonucleic acid expression was significantly upregulated in clear cell renal cell carcinoma compared with normal renal tissue. High expression levels correlated with advanced stage, higher grade and metastatic tumors, accompanied by independent prognostic significance for overall and cancer-specific survival. In contrast, otoferlin protein expression was downregulated in tumor tissue. Although, high otoferlin expression in clear cell renal cell carcinoma was positively correlated with histological grading and independently predictive of a shortened progression-free survival. CONCLUSION Our data suggest otoferlin as an indicator of tumor aggressiveness and as a prognostic biomarker for patients with clear cell renal cell carcinoma, leading to the conclusion that otoferlin could promote the malignancy of clear cell renal cell carcinoma.
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Affiliation(s)
- Alexander Cox
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Yuri Tolkach
- Institute of Pathology, University Hospital Bonn, Bonn, Germany.,Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Johannes Stein
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | | | - Manuel Ritter
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
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Luan N, Chen Y, Li Q, Mu Y, Zhou Q, Ye X, Deng Q, Ling L, Wang J, Wang J. TRF-20-M0NK5Y93 suppresses the metastasis of colon cancer cells by impairing the epithelial-to-mesenchymal transition through targeting Claudin-1. Am J Transl Res 2021; 13:124-142. [PMID: 33527013 PMCID: PMC7847510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
tRNA-derived fragments (tRFs) are derived from corresponding tRNAs and have been shown by several studies to be novel biological markers for tumour diagnosis and therapy. However, until now, the effects of tRFs on the progression of colorectal cancer (CRC) and especially on the epithelial-to-mesenchymal transition (EMT) have remained unknown. Our study aimed to assess CRC-related tRFs and examine the effects of key tRFs on CRC progression and related mechanisms. After hypoxic treatment, tRF sequencing and real-time PCR assays were performed to identify key tRFs. Then, functional tests were designed to verify the effects and evaluate the mechanism after cell transfection under normoxic conditions. A total of 14 tRFs were differentially expressed in the hypoxia and control groups. Based on the results of PCR assay verification and conditional selection, tRF-20-M0NK5Y93 could be a promising target for exploration, as its expression was significantly lower under hypoxic conditions than under control conditions. tRF-20-M0NK5Y93 inhibited CRC cell migration and invasion partly by targeting Claudin-1, an EMT-related molecule. The results of the present study suggest that tRF-20-M0NK5Y93 promotes CRC cell migration and invasion partly by regulating Claudin-1 during EMT.
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Affiliation(s)
- Na Luan
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Yiquan Chen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Qingsong Li
- Department of Radiotherapy, The Second Affiliated Hospital of Zhejiang University School of MedicineHangzhou 310009, China
| | - Yali Mu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Qin Zhou
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Xun Ye
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Qun Deng
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Limian Ling
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Jian Wang
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
| | - Jianwei Wang
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of MedicineJiefang Road 88th, Hangzhou 310016, China
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tRNA-Derived Fragments (tRFs) in Bladder Cancer: Increased 5'-tRF-LysCTT Results in Disease Early Progression and Patients' Poor Treatment Outcome. Cancers (Basel) 2020; 12:cancers12123661. [PMID: 33291319 PMCID: PMC7762106 DOI: 10.3390/cancers12123661] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/24/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Bladder cancer (BlCa) management relies on lifelong surveillance strategies with invasive interventions that adversely affect patients’ quality-of-life and lead to a high economic burden for healthcare systems. Exploitation of bladder tumors’ molecular background could lead to modern precision medicine. tRNA-derived fragments (tRFs), rather than degradation debris, are novel functional small ncRNAs that have emerged as key regulators of cellular homeostasis. This is the first study of the clinical utility of tRFs in BlCa. Using in silico analysis of the TCGA-BLCA project, we identified 5′-tRF-LysCTT (5′-tRF of tRNALysCTT) to be significantly deregulated in BlCa, and we have studied its clinical value in our cohort of 230 BlCa patients. Elevated 5′-tRF-LysCTT levels were significantly associated with aggressive tumor phenotype as well as early disease progression and poor treatment outcome. Integration of 5′-tRF-LysCTT with established disease markers resulted in superior prediction of patients’ prognosis, supporting personalized treatment and monitoring decisions. Abstract The heterogeneity of bladder cancer (BlCa) prognosis and treatment outcome requires the elucidation of tumors’ molecular background towards personalized patients’ management. tRNA-derived fragments (tRFs), although originally considered as degradation debris, represent a novel class of powerful regulatory non-coding RNAs. In silico analysis of the TCGA-BLCA project highlighted 5′-tRF-LysCTT to be significantly deregulated in bladder tumors, and 5′-tRF-LysCTT levels were further quantified in our screening cohort of 230 BlCa patients. Recurrence and progression for non-muscle invasive (NMIBC) patients, as well as progression and patient’s death for muscle-invasive (MIBC) patients, were used as clinical endpoint events. TCGA-BLCA were used as validation cohort. Bootstrap analysis was performed for internal validation and the clinical net benefit of 5′-tRF-LysCTT on disease prognosis was assessed by decision curve analysis. Elevated 5′-tRF-LysCTT was associated with unfavorable disease features, and significant higher risk for early progression (multivariate Cox: HR = 2.368; p = 0.033) and poor survival (multivariate Cox: HR = 2.151; p = 0.032) of NMIBC and MIBC patients, respectively. Multivariate models integrating 5′-tRF-LysCTT with disease established markers resulted in superior risk-stratification specificity and positive prediction of patients’ progression. In conclusion, increased 5′-tRF-LysCTT levels were strongly associated with adverse disease outcome and improved BlCa patients’ prognostication.
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Ding L, Jiang M, Wang R, Shen D, Wang H, Lu Z, Zheng Q, Wang L, Xia L, Li G. The emerging role of small non-coding RNA in renal cell carcinoma. Transl Oncol 2020; 14:100974. [PMID: 33395751 PMCID: PMC7719974 DOI: 10.1016/j.tranon.2020.100974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
SncRNAs contribute to the progress of renal cell carcinoma. SncRNAs are promising biomarkers for diagnosis and prognosis of renal cell carcinoma. Despite the potential of sncRNA-based cancer therapy, some obstacles remain, including several severe adverse effect.
Noncoding RNAs are transcribed in the most regions of the human genome, divided into small noncoding RNAs (less than 200 nt) and long noncoding RNAs (more than 200 nt) according to their size. Compelling evidences suggest that small noncoding RNAs play critical roles in tumorigenesis and tumor progression, especially in renal cell carcinoma. MiRNA, the most famous small noncoding RNA, has been comprehensively explored for its fundamental role in cancer. And several miRNA-based therapeutic strategies have been applied to several ongoing clinical trials. However, piRNAs and tsRNAs, have not received as much research attention, because of several technological limitations. Nevertheless, some studies have revealed the presence of aberration of piRNAs and tsRNAs in renal cell carcinoma, highlighting a potentially novel mechanism for tumor onset and progression. In this review, we provide an overview of three classes of small noncoding RNA: miRNAs, piRNAs and tsRNAs, that have been reported dysregulation in renal cell carcinoma and have the potential for advancing diagnosis, prognosis and therapeutic applications of this disease.
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Affiliation(s)
- Lifeng Ding
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Minxiao Jiang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruyue Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Danyang Shen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Huan Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Zeyi Lu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Qiming Zheng
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liya Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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35
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Magee R, Rigoutsos I. On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res 2020; 48:9433-9448. [PMID: 32890397 PMCID: PMC7515703 DOI: 10.1093/nar/gkaa657] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
The fragments that derive from transfer RNAs (tRNAs) are an emerging category of regulatory RNAs. Known as tRFs, these fragments were reported for the first time only a decade ago, making them a relatively recent addition to the ever-expanding pantheon of non-coding RNAs. tRFs are short, 16-35 nucleotides (nts) in length, and produced through cleavage of mature and precursor tRNAs at various positions. Both cleavage positions and relative tRF abundance depend strongly on context, including the tissue type, tissue state, and disease, as well as the sex, population of origin, and race/ethnicity of an individual. These dependencies increase the urgency to understand the regulatory roles of tRFs. Such efforts are gaining momentum, and comprise experimental and computational approaches. System-level studies across many tissues and thousands of samples have produced strong evidence that tRFs have important and multi-faceted roles. Here, we review the relevant literature on tRF biology in higher organisms, single cell eukaryotes, and prokaryotes.
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Affiliation(s)
- Rogan Magee
- Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- To whom correspondence should be addressed. Tel: +1 215 503 4219; Fax: +1 215 503 0466;
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36
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Mechanisms of tRNA-derived fragments and tRNA halves in cancer treatment resistance. Biomark Res 2020; 8:52. [PMID: 33072328 PMCID: PMC7559774 DOI: 10.1186/s40364-020-00233-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/02/2020] [Indexed: 12/22/2022] Open
Abstract
The tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs) are newly discovered noncoding RNAs in recent years. They are derived from specific cleavage of mature and pre-tRNAs and expressed in various cancers. They enhance cell proliferation and metastasis or inhibit cancer progression. Many studies have investigated their roles in the diagnosis, progression, metastasis, and prognosis of various cancers, but the mechanisms through which they are involved in resistance to cancer treatment are unclear. This review outlines the classification of tRFs and tiRNAs and their mechanisms in cancer drug resistance, thus providing new ideas for cancer treatment.
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37
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Jia Y, Tan W, Zhou Y. Transfer RNA-derived small RNAs: potential applications as novel biomarkers for disease diagnosis and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1092. [PMID: 33145311 PMCID: PMC7575943 DOI: 10.21037/atm-20-2797] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s. tsRNAs have been reported to play essential roles and possess different biological functions in a variety of physiological activities. Recently, tsRNAs have been implicated in a large number of diseases, such as cancers (including breast cancer, ovarian cancer, lung cancer, prostate cancer, colorectal cancer, etc.), neurological disorders, viral infections, metabolic diseases and angiogenesis-related diseases. Although the biological functions of tsRNAs are still poorly understood, correlations between dysregulated tsRNA expression and disease development have been recently reported. Additionally, their capabilities as potential biomarkers for disease diagnosis and prognosis have been revealed in clinical studies. In this review, we summarize the current knowledge of tsRNAs, and discuss their potential clinical applications as biomarkers in different diseases. Although the regulation of tsRNAs is similar to miRNAs in regards to the related physiological and pathological processes, the higher stability and expression levels of tsRNAs place them as ideal biomarkers for the diagnosis and prognosis in cancer and other diseases. Therefore, it is worth to verify the possibility and reliability of these reported tsRNAs as potential biomarkers for clinical applications in disease diagnosis and prognosis.
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Affiliation(s)
- Yang Jia
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
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38
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Nechooshtan G, Yunusov D, Chang K, Gingeras TR. Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res 2020; 48:8035-8049. [PMID: 32609822 PMCID: PMC7430647 DOI: 10.1093/nar/gkaa526] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular RNAs participate in intercellular communication, and are being studied as promising minimally invasive diagnostic markers. Several studies in recent years showed that tRNA halves and distinct Y RNA fragments are abundant in the extracellular space, including in biofluids. While their regulatory and diagnostic potential has gained a substantial amount of attention, the biogenesis of these extracellular RNA fragments remains largely unexplored. Here, we demonstrate that these fragments are produced by RNase 1, a highly active secreted nuclease. We use RNA sequencing to investigate the effect of a null mutation of RNase 1 on the levels of tRNA halves and Y RNA fragments in the extracellular environment of cultured human cells. We complement and extend our RNA sequencing results with northern blots, showing that tRNAs and Y RNAs in the non-vesicular extracellular compartment are released from cells as full-length precursors and are subsequently cleaved to distinct fragments. In support of these results, formation of tRNA halves is recapitulated by recombinant human RNase 1 in our in vitro assay. These findings assign a novel function for RNase 1, and position it as a strong candidate for generation of tRNA halves and Y RNA fragments in biofluids.
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Affiliation(s)
- Gal Nechooshtan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dinar Yunusov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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A 3'-tRNA-derived fragment enhances cell proliferation, migration and invasion in gastric cancer by targeting FBXO47. Arch Biochem Biophys 2020; 690:108467. [PMID: 32592804 DOI: 10.1016/j.abb.2020.108467] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/27/2020] [Accepted: 06/07/2020] [Indexed: 12/29/2022]
Abstract
Increasing evidence demonstrates that tRNA-derived fragments (tRFs) exert important effects and are dysregulated in various human cancer types. However, their roles in gastric cancer (GC) remain unknown. Here we identified the functional effects of tRF-3019a (derived from tRNA-Ala-AGC-1-1) in GC. We demonstrated that tRF-3019a was upregulated in GC tissues and cell lines. Phenotypic studies revealed that tRF-3019a overexpression enhances GC cell proliferation, migration and invasion. Conversely, tRF-3019a knockdown inhibits GC cell malignant activities. Mechanistic investigation implies that tRF-3019a directly regulates tumor suppressor gene FBXO47. Furthermore, tRF-3019a levels may discriminate GC tissues from nontumorous tissues. Taken together, our results reveal that tRF-3019a modulates GC cell proliferation, migration and invasion by targeting FBXO47, and it may serve as a potential diagnostic biomarker for GC.
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41
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Zeng T, Hua Y, Sun C, Zhang Y, Yang F, Yang M, Yang Y, Li J, Huang X, Wu H, Fu Z, Li W, Yin Y. Relationship between tRNA-derived fragments and human cancers. Int J Cancer 2020; 147:3007-3018. [PMID: 32427348 DOI: 10.1002/ijc.33107] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
tRNA-derived fragments, a class of small noncoding RNAs (sncRNAs), have been identified in numerous studies in recent years. tRNA-derived fragments are classified into two main groups, including tRNA halves (tiRNAs) and tRNA-derived small RNA fragments (tRFs), according to different cleavage positions of the precursor or mature tRNAs. Instead of random tRNA degradation debris, a growing body of evidence has shown that tRNA-derived fragments are precise products of specific tRNA modifications and play important roles in biological activities, such as regulating protein translation, affecting gene expression, and altering immune signaling. Recently, the relations between tRNA-derived fragments and the occurrence of human diseases, especially cancers, have generated wide interest. It has been demonstrated that tRNA-derived fragments are involved in cancer cell proliferation, metastasis, progression and survival. In this review, we will describe the biogenesis of tRNA-derived fragments, the distinct expression and function of tRNA-derived fragments in the development of cancers, and their emerging roles as diagnostic and prognostic biomarkers and precise targets of future treatments.
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Affiliation(s)
- Tianyu Zeng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yijia Hua
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunxiao Sun
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuchen Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengzhu Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yiqi Yang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongmei Yin
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
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42
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Zhu P, Yu J, Zhou P. Role of tRNA-derived fragments in cancer: novel diagnostic and therapeutic targets tRFs in cancer. Am J Cancer Res 2020; 10:393-402. [PMID: 32195016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/02/2020] [Indexed: 09/28/2022] Open
Abstract
Recent studies have revealed that tRNAs are not always the terminal molecules and small RNA fragments can be mapped to precursor tRNA sequences or mature tRNA sequences. tRNA-derived fragments (tRFs) are a novel class of small RNAs in miRNA-size found in a diverse range of organisms and can be the source of small regulatory RNAs, a previously unanticipated concept. tRFs have a diverse range of effects on cells involving in cell differentiation and homeostasis. They play a critical role in pathological processes, particularly in cancer, and therefore can modulate complicated regulatory networks. Recent studies on the role of tRFs in tumorigenesis suggest that they are promising targets for diagnosis and therapeutics. Improvement in experimental and computational approaches permit a greater understanding of the regulatory networks and will have a significant impact on both basic and clinical research.
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Affiliation(s)
- Ping Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai 200032, China
| | - Jerry Yu
- Department of Medicine, University of Louisville Louisville 40292, Kentucky, USA
| | - Ping Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai 200032, China
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Rosace D, López J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol 2020; 17:1196-1213. [PMID: 32186461 DOI: 10.1080/15476286.2020.1737442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The term small non-coding RNAs (ncRNAs) refers to all those RNAs that even without encoding for a protein, can play important functional roles. Transfer RNA and ribosomal RNA-derived fragments (tRFs and rRFs, respectively) are an emerging class of ncRNAs originally considered as simple degradation products, which though play important roles in stress responses, signalling, or gene expression. They control all levels of gene expression regulating transcription and translation and affecting RNA processing and maturation. They have been linked to pivotal cellular processes such as self-renewal, differentiation, and proliferation. For this reason, mis-regulation of this novel class of ncRNAs can lead to various pathological processes such as neurodegenerative and development diseases, metabolism and immune system disorders, and cancer. In this review, we summarise the classification, biogenesis, and functions of tRFs and rRFs with a special focus on their role in immunity and cancer.
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Affiliation(s)
- Domenico Rosace
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Judith López
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
| | - Sandra Blanco
- Centro De Investigación Del Cáncer and Instituto De Biología Molecular Y Celular Del Cáncer, Consejo Superior De Investigaciones Científicas (CSIC) - University of Salamanca , Salamanca, Spain
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Dhahbi J, Nunez Lopez YO, Schneider A, Victoria B, Saccon T, Bharat K, McClatchey T, Atamna H, Scierski W, Golusinski P, Golusinski W, Masternak MM. Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5' tRNA-Val-CAC-2-1 Half. Front Oncol 2019; 9:959. [PMID: 31616639 PMCID: PMC6775249 DOI: 10.3389/fonc.2019.00959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer and, as indicated by The Oral Cancer Foundation, kills at an alarming rate of roughly one person per hour. With this study, we aimed at better understanding disease mechanisms and identifying minimally invasive disease biomarkers by profiling novel small non-coding RNAs (specifically, tRNA halves and YRNA fragments) in both serum and tumor tissue from humans. Small RNA-Sequencing identified multiple 5' tRNA halves and 5' YRNA fragments that displayed significant differential expression levels in circulation and/or tumor tissue, as compared to control counterparts. In addition, by implementing a modification of weighted gene coexpression network analysis, we identified an upregulated genetic module comprised of 5' tRNA halves and miRNAs (miRNAs were described in previous study using the same samples) with significant association with the cancer trait. By consequently implementing miRNA-overtargeting network analysis, the biological function of the module (and by "guilt by association," the function of the 5' tRNA-Val-CAC-2-1 half) was found to involve the transcriptional targeting of specific genes involved in the negative regulation of the G1/S transition of the mitotic cell cycle. These findings suggest that 5' tRNA-Val-CAC-2-1 half (reduced in serum of OSCC patients and elevated in the tumor tissue) could potentially serve as an OSCC circulating biomarker and/or target for novel anticancer therapies. To our knowledge, this is the first time that the specific molecular function of a 5'-tRNA half is specifically pinpointed in OSCC.
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Affiliation(s)
- Joseph Dhahbi
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, AdventHealth, Orlando, FL, United States
| | - Augusto Schneider
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Tatiana Saccon
- Faculdade de Nutrição, Universidade Federal de Pelotas, Pelotas, Brazil
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Krish Bharat
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Thaddeus McClatchey
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Hani Atamna
- Department of Medical Education, School of Medicine, California University of Science & Medicine, San Bernardino, CA, United States
| | - Wojciech Scierski
- Department of Otorhinolaryngology and Laryngological Oncology in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Pawel Golusinski
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Zielona Gora, Poland
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
| | - Michal M. Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznań, Poland
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznań, Poland
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Wang X, Yang Y, Tan X, Mao X, Wei D, Yao Y, Jiang P, Mo D, Wang T, Yan F. Identification of tRNA-Derived Fragments Expression Profile in Breast Cancer Tissues. Curr Genomics 2019; 20:199-213. [PMID: 31929727 PMCID: PMC6935952 DOI: 10.2174/1389202920666190326145459] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 01/12/2023] Open
Abstract
Background: In recent years, tRFs(transfer RNA-Derived Fragments) and transfer RNADerived Stress-induced RNAs (or tRNA halves) have been shown to have vital roles in cancer biology.We aimed to reveal the expression profile of tRNA-derived fragments in breast cancer tissues in the study, and to explore their potential as biomarkers of breast cancer. Methods: We characterized the tRNA-derived fragments expression profile from 6 paired clinical breast cancer tissues and adjacent normal samples. Then we selected 6 significantly expressed tRNAderived fragments and screened the genes for validation by using Quantitative Real-time PCR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes biological pathway were finally analyzed. Results: We found 30 differentially expressed tRNA-derived fragments across our dataset, out of which 17 were up-regulated, and 13 were down-regulated. Compared with 16 clinical breast cancer tissues and adjacent normal tissues by qPCR, the results demonstrated that tRF-32-Q99P9P9NH57SJ(FC = -2.6476, p = 0.0189), tRF-17-79MP9PP (FC = -4.8984, p = 0.0276) and tRF-32-XSXMSL73VL4YK (FC = 6.5781, p = 0.0226) were significantly expressed in breast cancer tissues(p < 0.001). tRF-32-XSXMSL73VL4YK was significantly up-regulated, and tRF-32-Q99P9P9NH57SJ and tRF-17-79MP9PP were significantly down-regulated in which the expressionpatterns were similar to the sequencing results. The top ten significant results of GO and KEGG pathways enrichment analysis were presented. Conclusion: Our studies have demonstrated that there were significantly expressed tRNA-derived fragments in breast cancer tissues. They are hopefully to become biomarkers and would be valuable researches in this area.
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Affiliation(s)
- Xiaoming Wang
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yining Yang
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xuyan Tan
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xuelian Mao
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Da Wei
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yufeng Yao
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Pan Jiang
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dongping Mo
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Wang
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Yan
- 1Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China; 2Department of Surgery, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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Profile analysis reveals transfer RNA fragments involved in mesangial cells proliferation. Biochem Biophys Res Commun 2019; 514:1101-1107. [PMID: 31097225 DOI: 10.1016/j.bbrc.2019.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 01/21/2023]
Abstract
Mesangial cell (MCs) proliferation is an essential component of glomerulonephritis. To find some bio-markers of mesangial cell proliferation, we investigate the relationship between transfer RNA fragments (tRFs) and proliferating mesangial cells. The model of proliferating mesangial cells was built by using transforming growth factor-1(TGF-β1) treated mesangial cells. Then we analyzed the expression of tRFs in normal mesangial cells and mesangial cells treated by TGF-β1 through high-throughput sequencing technique. qRT-PCR was conducted to validate the differently expressed tRFs in normal mesangial cells and mesangial cells treated by TGF-β1. tDR-000064 and tDR-000103 were notably down-regulated in mesangial cells treated by TGF-β1 compared with normal mesangial cells. Then we confirmed that tDR-000064 and tDR-000103 were correlated with proliferation of mesangial cells through receiver operating characteristic curve analysis. Furthermore, Gene ontology (GO) and pathway analysis demonstrated that the two dys-regulated tRFs were mostly involved in mesangial cells and TGF-β1 receptor-mediated signaling pathway. Our research provides a comprehensive analysis of tRFs in proliferating mesangial cells. (Figure 1A).
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47
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tRNA-derived fragments and tRNA halves: The new players in cancers. Cancer Lett 2019; 452:31-37. [DOI: 10.1016/j.canlet.2019.03.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 01/27/2023]
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48
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Schaffer AE, Pinkard O, Coller JM. tRNA Metabolism and Neurodevelopmental Disorders. Annu Rev Genomics Hum Genet 2019; 20:359-387. [PMID: 31082281 DOI: 10.1146/annurev-genom-083118-015334] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
tRNAs are short noncoding RNAs required for protein translation. The human genome includes more than 600 putative tRNA genes, many of which are considered redundant. tRNA transcripts are subject to tightly controlled, multistep maturation processes that lead to the removal of flanking sequences and the addition of nontemplated nucleotides. Furthermore, tRNAs are highly structured and posttranscriptionally modified. Together, these unique features have impeded the adoption of modern genomics and transcriptomics technologies for tRNA studies. Nevertheless, it has become apparent from human neurogenetic research that many tRNA biogenesis proteins cause brain abnormalities and other neurological disorders when mutated. The cerebral cortex, cerebellum, and peripheral nervous system show defects, impairment, and degeneration upon tRNA misregulation, suggesting that they are particularly sensitive to changes in tRNA expression or function. An integrated approach to identify tRNA species and contextually characterize tRNA function will be imperative to drive future tool development and novel therapeutic design for tRNA-associated disorders.
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Affiliation(s)
- Ashleigh E Schaffer
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Otis Pinkard
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| | - Jeffery M Coller
- Department of Genetics and Genome Sciences and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA;
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Dai M, Li L, Qin X. Clinical value of miRNA-122 in the diagnosis and prognosis of various types of cancer. Oncol Lett 2019; 17:3919-3929. [PMID: 30881509 PMCID: PMC6403504 DOI: 10.3892/ol.2019.10024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to systematically analyze the value of microRNA-122 (miRNA-122) in the diagnosis and prognosis of hepatocellular carcinoma (HCC) and other types of cancer. First, the reverse transcription-quantitative polymerase chain reaction method was used to detect the expression levels of miRNA-122 in the serum samples of patients with HCC, benign lesions and healthy volunteers. Next, miRNA-seq data of miRNA-122 from The Cancer Genome Atlas database were used to analyze the differential expression and overall survival rate associated with a variety of types of cancer. Meanwhile, the target gene prediction of miRNA-122 was performed using four different software programs. Finally, 353 significant target genes were identified for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis. Finally, it was demonstrated that the expression levels of miRNA-122 in the HCC group were increased compared with the healthy group (P<0.001), but decreased with respect to the benign group (P<0.001). In addition, the combination of the miRNA-122 and a fetoprotein may further improve the diagnostic accuracy between the HCC and healthy groups (area under the curve, 0.980; 95% confidence interval, 0.958–1.000). It was also demonstrated that miRNA-122 exhibited significantly differential expression and the overall survival rate was predicted for various other types of cancer, including colorectal cancer, renal carcinoma, cholangiocarcinoma, prostate cancer and thyroid carcinoma. Functional enrichment analysis demonstrated that the target genes of miRNA-122 may contribute to the composition of the nucleus and cytoplasm, and regulate a variety of biological processes, including cardiac muscle cell differentiation and glucose metabolic processes via protein biosynthesis, estrogen and glucagon associated signaling pathways. These results revealed that miRNA-122 may be an indispensable biomarker for the diagnosis, prognostic evaluation and targeted therapy in pan-cancer.
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Affiliation(s)
- Meiyu Dai
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Limin Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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Zhao C, Tolkach Y, Schmidt D, Muders M, Kristiansen G, Müller SC, Ellinger J. tRNA-halves are prognostic biomarkers for patients with prostate cancer. Urol Oncol 2018; 36:503.e1-503.e7. [DOI: 10.1016/j.urolonc.2018.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 07/05/2018] [Accepted: 08/04/2018] [Indexed: 01/25/2023]
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