1
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Lu J, Zhu P, Zhang X, Zeng L, Xu B, Zhou P. tRNA-derived fragments: Unveiling new roles and molecular mechanisms in cancer progression. Int J Cancer 2024; 155:1347-1360. [PMID: 38867475 DOI: 10.1002/ijc.35041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/17/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
tRNA-derived fragments (tRFs) are novel small noncoding RNAs (sncRNAs) that range from approximately 14 to 50 nt. They are generated by the cleavage of mature tRNAs or precursor tRNAs (pre-tRNAs) at specific sites. Based on their origin and length, tRFs can be classified into three categories: (1) tRF-1 s; (2) tRF-3 s, tRF-5 s, and internal tRFs (i-tRFs); and (3) tRNA halves. They play important roles in stress response, signal transduction, and gene expression processes. Recent studies have identified differential expression of tRFs in various tumors. Aberrantly expressed tRFs have critical clinical value and show promise as new biomarkers for tumor diagnosis and prognosis and as therapeutic targets. tRFs regulate the malignant progression of tumors via various mechanisms, primarily including modulation of noncoding RNA biogenesis, global chromatin organization, gene expression regulation, modulation of protein translation, regulation of epigenetic modification, and alternative splicing regulation. In conclusion, tRF-mediated regulatory pathways could present new avenues for tumor treatment, and tRFs could serve as promising therapeutic targets for cancer therapy.
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Affiliation(s)
- Jingjing Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong, China
| | - Ping Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiufen Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Linzi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Bujie Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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2
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Soureas K, Papadimitriou MA, Malandrakis P, Papanota AM, Adamopoulos PG, Ntanasis-Stathopoulos I, Liacos CI, Gavriatopoulou M, Sideris DC, Kastritis E, Dimopoulos MA, Scorilas A, Terpos E, Avgeris M. Small RNA-seq and clinical evaluation of tRNA-derived fragments in multiple myeloma: Loss of mitochondrial i-tRF HisGTG results in patients' poor treatment outcome. Br J Haematol 2024; 204:1790-1800. [PMID: 38414235 DOI: 10.1111/bjh.19332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/29/2024]
Abstract
Despite the substantial progress in multiple myeloma (MM) therapy nowadays, treatment resistance and disease relapse remain major clinical hindrances. Herein, we have investigated tRNA-derived fragment (tRF) profiles in MM and precursor stages (smoldering MM/sMM; monoclonal gammopathy of undetermined significance/MGUS), aiming to unveil potential MM-related tRFs in ameliorating MM prognosis and risk stratification. Small RNA-seq was performed to profile tRFs in bone marrow CD138+ plasma cells, revealing the significant deregulation of the mitochondrial internal tRFHisGTG (mt-i-tRFHisGTG) in MM versus sMM/MGUS. The screening cohort of the study consisted of 147 MM patients, and mt-i-tRFHisGTG levels were quantified by RT-qPCR. Disease progression was assessed as clinical end-point for survival analysis, while internal validation was performed by bootstrap and decision curve analyses. Screening cohort analysis highlighted the potent association of reduced mt-i-tRFHisGTG levels with patients' bone disease (p = 0.010), osteolysis (p = 0.023) and with significantly higher risk for short-term disease progression following first-line chemotherapy, independently of patients' clinical data (HR = 1.954; p = 0.036). Additionally, mt-i-tRFHisGTG-fitted multivariate models led to superior risk stratification of MM patients' treatment outcome and prognosis compared to disease-established markers. Notably, our study highlighted mt-i-tRFHisGTG loss as a powerful independent indicator of post-treatment progression of MM patients, leading to superior risk stratification of patients' treatment outcome.
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Affiliation(s)
- Konstantinos Soureas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
| | - Maria-Alexandra Papadimitriou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Malandrakis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Aristea-Maria Papanota
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Ntanasis-Stathopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Christine-Ivy Liacos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Maria Gavriatopoulou
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
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3
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Zhang L, Liu J, Hou Y. Classification, function, and advances in tsRNA in non-neoplastic diseases. Cell Death Dis 2023; 14:748. [PMID: 37973899 PMCID: PMC10654580 DOI: 10.1038/s41419-023-06250-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
tRNA-derived small RNAs (tsRNAs) are non-coding small RNAs produced by specific endonucleases following the processing and splicing of precursor or mature tRNAs upon starvation, oxidative stress, hypoxia, and other adverse conditions. tRNAs are classified into two major categories, tRNA fragments (tRFs) and tRNA-derived stress-induced small RNAs (tiRNAs), based on differences in splice sites. With the development of high-throughput sequencing technologies in recent years, tsRNAs have been found to have important biological functions, including inhibition of apoptosis, epigenetic regulation, cell-cell communication, translation, and regulation of gene expression. Additionally, these molecules have been found to be aberrantly expressed in various diseases and to be involved in several pathological processes. In this article, the classification and nomenclature, biological functions, and potential use of tsRNAs as diagnostic biomarkers and therapeutic targets in non-neoplastic diseases are reviewed. Although tsRNA research is at its infancy, their potential in the treatment of non-tumor diseases warrants further investigation.
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Affiliation(s)
- Liou Zhang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jie Liu
- Translational Research Experiment Department, Science Experiment Center, China Medical University, Shenyang, China.
| | - Yang Hou
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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4
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Christodoulou S, Katsaraki K, Vassiliu P, Danias N, Michalopoulos N, Tzikos G, Sideris DC, Arkadopoulos N. High Intratumoral i-tRF-Gly GCC Expression Predicts Short-Term Relapse and Poor Overall Survival of Colorectal Cancer Patients, Independent of the TNM Stage. Biomedicines 2023; 11:1945. [PMID: 37509584 PMCID: PMC10377136 DOI: 10.3390/biomedicines11071945] [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: 05/22/2023] [Revised: 06/22/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Colorectal cancer (CRC), one of the most prevalent types of cancer, requires the discovery of new tumor biomarkers for accurate patient prognosis. In this work, the prognostic value of the tRNA fragment i-tRF-GlyGCC in CRC was examined. Total RNA extraction from 211 CRC patient cancer tissue specimens and 83 adjacent normal tissues was conducted. Each RNA extract was subjected to in vitro polyadenylation and reverse transcription. A real-time quantitative PCR assay was used to quantify i-tRF-GlyGCC in all samples. Extensive biostatics analysis showed that i-tRF-GlyGCC levels in CRC tissues were significantly lower than in matched normal colorectal tissues. Additionally, the disease-free survival (DFS) and overall survival (OS) time intervals were considerably shorter in CRC patients with high i-tRF-GlyGCC expression. i-tRF-GlyGCC expression maintained its prognostic value independently of other established prognostic factors, as shown by the multivariate Cox regression analysis. Additionally, survival analysis after TNM stage stratification revealed that higher i-tRF-GlyGCC levels were linked to shorter DFS time intervals in patients with TNM stage II tumors, as well as an increased probability of having a worse OS for patients in TNM stage II. In conclusion, i-tRF-GlyGCC has the potential to be a useful molecular tissue biomarker in CRC, independent of other clinicopathological variables.
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Affiliation(s)
- Spyridon Christodoulou
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Katerina Katsaraki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panteleimon Vassiliu
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Nikolaos Danias
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Nikolaos Michalopoulos
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Georgios Tzikos
- Propaedeutic Department of Surgery, University General Hospital "AHEPA", Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Nikolaos Arkadopoulos
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
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5
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Christodoulou S, Sotiropoulou CD, Vassiliu P, Danias N, Arkadopoulos N, Sideris DC. MicroRNA-675-5p Overexpression Is an Independent Prognostic Molecular Biomarker of Short-Term Relapse and Poor Overall Survival in Colorectal Cancer. Int J Mol Sci 2023; 24:9990. [PMID: 37373137 DOI: 10.3390/ijms24129990] [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: 05/23/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Colorectal cancer (CRC) is the main cause of cancer-related deaths globally, highlighting the importance of accurate biomarkers for early detection and accurate prognosis. MicroRNAs (miRNAs) have emerged as effective cancer biomarkers. The aim of this study was to investigate the prognostic potential of miR-675-5p as a molecular prognostic biomarker in CRC. For this reason, a quantitative PCR assay was developed and applied to determine miR-675-5p expression in cDNAs from 218 primary CRC and 90 paired normal colorectal tissue samples. To assess the significance of miR-675-5p expression and its association with patient outcome, extensive biostatistical analysis was performed. miR-675-5p expression was found to be significantly downregulated in CRC tissue samples compared to that in adjacent normal colorectal tissues. Moreover, high miR-675-5p expression was associated with shorter disease-free (DFS) and overall survival (OS) in CRC patients, while it maintained its unfavorable prognostic value independently of other established prognostic factors. Furthermore, TNM stage stratification demonstrated that higher miR-675-5p levels were associated with shorter DFS and OS intervals, particularly in patients with CRC of TNM stage II or III. In conclusion, our findings suggest that miR-675-5p overexpression constitutes a promising molecular biomarker of unfavorable prognosis in CRC, independent of other established prognostic factors, including TNM staging.
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Affiliation(s)
- Spyridon Christodoulou
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Christina D Sotiropoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panteleimon Vassiliu
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Nikolaos Danias
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Nikolaos Arkadopoulos
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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6
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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: 35] [Impact Index Per Article: 35.0] [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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7
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A Ferroptosis Molecular Subtype-Related Signature for Predicting Prognosis and Response to Chemotherapy in Patients with Chronic Lymphocytic Leukemia. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5646275. [PMID: 35845961 PMCID: PMC9279058 DOI: 10.1155/2022/5646275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/13/2022] [Indexed: 12/21/2022]
Abstract
Ferroptosis is a type of regulated cell death catalyzed by the iron-dependent accumulation of lipid hydroperoxides to lethal levels. Chronic lymphocytic leukemia (CLL) is a chronic lymphoproliferative disorder. However, the understanding of ferroptosis in CLL remains largely poor. In this study, we investigated the stratification and prognostic role of ferroptosis-related genes in CLL patients of ICGC cohort. We obtained fourteen genes with prognostic value by screening 110 ferroptosis-related genes (FRGs). Based on the expression profiles of these 14 genes, we classified CLL patients into two clusters. Most of the FRGs were highly expressed in cluster 1, and cluster 1 was associated with better overall survival (OS). Subsequently, we developed an eight-gene signature (TP63, STEAP3, NQO1, ELAVL1, PRKAA1, HELLS, FANCD2, and CDKN2A) by using LASSO analysis. This risk signature divided CLL patients into high- and low-risk groups. We used Cox regression analysis and ROC analysis demonstrated the risk signature was reliable and robust. And we validated the risk model in an external cohort (GSE22762). We also conducted enrichment analysis and genomic mutation analysis. Finally, we explored the potential effect of chemotherapy between the two risk groups. Our study contributed to understanding the role of ferroptosis in CLL and facilitated personalized and precision treatment.
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8
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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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9
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High Expression of a tRNAPro Derivative Associates with Poor Survival and Independently Predicts Colorectal Cancer Recurrence. Biomedicines 2022; 10:biomedicines10051120. [PMID: 35625858 PMCID: PMC9138872 DOI: 10.3390/biomedicines10051120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer (CRC) is the second most lethal cause of cancer-related deaths in Europe. Fragments of tRNAPro are conserved among vertebrates, characterized by pleiotropic regulatory functions and have been found to discriminate colorectal tumors from normal colorectal mucosa. In the current study, we investigated the prognostic utility of 5′-tiRNA-ProTGG levels in CRC. For this purpose, total RNA was extracted from 155 malignant colorectal tumors and 74 adjacent non-cancerous tissue specimens, polyadenylated and reverse-transcribed using an oligo-dT adapter as primer. Real-time quantitative PCR (qPCR) was used to assess the levels of 5′-tiRNA-ProTGG. Kaplan-Meier survival analysis demonstrated that high 5′-tiRNA-ProTGG levels predict both poor disease-free survival (DFS) and overall survival (OS) of CRC patients. Of note, high 5′-tiRNA-ProTGG levels retain their unfavorable prognostic value in patients with rectal cancer and/or moderately differentiated CRC (grade II). More importantly, multivariate cox regression analysis highlighted that the overexpression of 5′-tiRNA-ProTGG constitutes an adverse prognostic factor predicting short-term relapse of CRC patients independently of the established prognosticators in CRC. Finally, bioinformatics analysis unveiled a potentially critical role of 5′-tiRNA-ProTGG regarding the maintenance of cellular homeostasis, signaling, cell communication, and cellular motility.
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10
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Weng Q, Wang Y, Xie Y, Yu X, Zhang S, Ge J, Li Z, Ye G, Guo J. Extracellular vesicles-associated tRNA-derived fragments (tRFs): biogenesis, biological functions, and their role as potential biomarkers in human diseases. J Mol Med (Berl) 2022; 100:679-695. [PMID: 35322869 PMCID: PMC9110440 DOI: 10.1007/s00109-022-02189-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 02/10/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023]
Abstract
Traditionally, transfer RNAs (tRNAs) specifically decoded messenger RNA (mRNA) and participated in protein translation. tRNA-derived fragments (tRFs), also known as tRNA-derived small RNAs (tsRNAs), are generated by the specific cleavage of pre- and mature tRNAs and are a class of newly defined functional small non-coding RNAs (sncRNAs). Following the different cleavage positions of precursor or mature tRNA, tRFs are classified into seven types, 5′-tRNA half, 3′-tRNA half, tRF-1, 5′U-tRF, 3′-tRF, 5′-tRF, and i-tRF. It has been demonstrated that tRFs have a diverse range of biological functions in cellular processes, which include inhibiting protein translation, modulating stress response, regulating gene expression, and involvement in cell cycles and epigenetic inheritance. Emerging evidences have indicated that tRFs in extracellular vesicles (EVs) seem to act as regulatory molecules in various cellular processes and play essential roles in cell-to-cell communication. Furthermore, the dysregulation of EV-associated tRFs has been associated with the occurrence and progression of a variety of cancers and they can serve as novel potential biomarkers for cancer diagnosis. In this review, the biogenesis and classification of tRFs are summarized, and the biological functions of EV-associated tRFs and their roles as potential biomarkers in human diseases are discussed.
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Affiliation(s)
- Qiuyan Weng
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Yao Wang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Yaoyao Xie
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Shuangshuang Zhang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Jiaxin Ge
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Zhe Li
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Guoliang Ye
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
| | - Junming Guo
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China. .,Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
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11
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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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12
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Wang Y, Weng Q, Ge J, Zhang X, Guo J, Ye G. tRNA-derived small RNAs: mechanisms and potential roles in cancers. Genes Dis 2022; 9:1431-1442. [PMID: 36157501 PMCID: PMC9485285 DOI: 10.1016/j.gendis.2021.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/08/2021] [Accepted: 12/18/2021] [Indexed: 11/02/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential for protein synthesis. Mature or pre-tRNAs may be cleaved to produce tRNA-derived small RNAs (tsRNAs). tsRNAs, divided into tRNA-derived stress-induced RNA (tiRNAs) and tRNA-derived fragments (tRFs), play versatile roles in a number of fundamental biological processes. tsRNAs not only play regulatory roles in gene silencing, RNA stability, reverse transcription, and translation, but are also closely related to cell proliferation, migration, cell cycle, and apoptosis. Their abnormal expression is associated with the occurrence and development of various human diseases, especially cancer. This paper reviews the classification, biogenesis, and mechanism of action of tsRNAs, and the research progress to date on tsRNAs in cancers. These findings provide new opportunities for diagnostic biomarkers and treatment targets of several types of cancers including gastric cancer, colorectal cancer, hepatocellular carcinomas, pancreatic cancer, breast cancer, prostate cancer, renal cell carcinoma, ovarian cancer, lung cancer, bladder cancer, thyroid cancer, oral cancer, and leukemia.
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13
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Gao L, Xu L, Wang X. A Systematic Review of tRNA-Derived Small non-Coding RNAs as Diagnostic and Prognostic Markers in Cancer. Technol Cancer Res Treat 2022; 21:15330338211072989. [PMID: 35506562 DOI: 10.1177/15330338211072989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objectives: tRNA-derived small non-coding RNAs (tsncRNAs) are one of mysterious small non-coding RNAs. Dysregulated tsncRNAs can led to all kinds of cancers. Recently, tsncRNAs were postulated to be potentially useful biomarkers for tumor diagnosis and prognosis. However, there were no systematic reviews of prognostic and diagnostic tsncRNAs in neoplasms. The study aimed to decipher the relationships between tsncRNAs expression, diagnostic and prognostic outcome in tumors. Methods: This study systematically searched Google Scholar, MEDLINE, Scopus, PubMed, Embase, ScienceDirect, Ovid-Medline, Chinese National Knowledge Infrastructure, WanFang and SinoMed databases for relevant articles published before September 21, 2020. Results: The study is registered in PROSPERO (CRD42020213863). Fourteen relevant studies were included in the meta-analysis: 12 on diagnosis and 5 on prognosis. The pooled add ratio, 95% confidence intervals (Cl) and hazard ratios (HR) of the studies were used to investigate the clinical parameters and overall survival (OS) of cancer patients. The area under the curve (AUC), sensitivity, and specificity was 0.79, 72%, and 73% in tumors, respectively. Though abnormally expressed tsncRNAs were associated with poor and unfavorable impacts on the OS time of cancer patients, the oncogenic tsncRNA may be a favorable impact on overall survival (OS: HR = 0.67, 95% Cl: 0.48-0.94, P = 0.02), and tumor-suppressor tsncRNA might have an unfavorable impact on overall survival (OS: HR = 1.41, 95% Cl: 0.84-2.37, P = 0.19). Conclusion: These results strongly suggested that tsncRNAs were potential novel prognostic and diagnostic indicators in tumors.
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Affiliation(s)
| | - Lin Xu
- 71220Jiujiang University, China
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tRNA GlyGCC-Derived Internal Fragment (i-tRF-GlyGCC) in Ovarian Cancer Treatment Outcome and Progression. Cancers (Basel) 2021; 14:cancers14010024. [PMID: 35008188 PMCID: PMC8750938 DOI: 10.3390/cancers14010024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022] Open
Abstract
Epithelial ovarian cancer (EOC) remains a highly-lethal gynecological malignancy, characterized by frequent recurrence, chemotherapy resistance and poor 5-year survival. Identifying novel predictive molecular markers remains an overdue challenge in the disease's clinical management. Herein, in silico analysis of TCGA-OV highlighted the tRNA-derived internal fragment (i-tRF-GlyGCC) among the most abundant tRFs in ovarian tumors, while target prediction and gene ontology (GO) enrichment analysis predicted its implication in key biological processes. Thereafter, i-tRF-GlyGCC levels were quantified in a screening EOC (n = 98) and an institutionally-independent serous ovarian cancer (SOC) validation cohort (n = 100, OVCAD multicenter study). Disease progression and patient death were used as clinical endpoints for the survival analysis. Internal validation was performed by bootstrap analysis and the clinical net benefit was estimated by decision curve analysis. The analysis highlighted the significant association of i-tRF-GlyGCC with advanced FIGO stages, suboptimal debulking and most importantly, with early progression and poor overall survival of EOC patients. The OVCAD validation cohort corroborated the unfavorable predictive value of i-tRF-GlyGCC in EOC. Ultimately, evaluation of i-tRF-GlyGCC with the established/clinically used prognostic markers offered superior patient risk-stratification and enhanced clinical benefit in EOC prognosis. In conclusion, i-tRF-GlyGCC assessment could aid towards personalized prognosis and support precision medicine decisions in EOC.
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tRNA Derivatives in Multiple Myeloma: Investigation of the Potential Value of a tRNA-Derived Molecular Signature. Biomedicines 2021; 9:biomedicines9121811. [PMID: 34944627 PMCID: PMC8698603 DOI: 10.3390/biomedicines9121811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple myeloma (MM) is a hematologic malignancy arising from the clonal proliferation of malignant plasma cells. tRNA-derived RNA fragments (tRFs) constitute a class of small non-coding RNAs, deriving from specific enzymatic cleavage of tRNAs. To the best of our knowledge, this is one of few studies to uncover the potential clinical significance of tRFs in MM. Total RNA was extracted from CD138+ plasma cells of MM and smoldering MM patients, and in vitro polyadenylated. First-strand cDNA synthesis was performed, priming from an oligo-dT-adaptor sequence. Next, real-time quantitative PCR (qPCR) assays were developed for the quantification of six tRFs. Biostatistical analysis was performed to assess the results and in silico analysis was conducted to predict the function of one of the tRFs. Our results showed that elevated levels of five out of six tRFs are indicators of favorable prognosis in MM, predicting prolonged overall survival (OS), while two of them constitute potential molecular biomarkers of favorable prognosis in terms of disease progression. Moreover, three tRFs could be used as surrogate prognostic biomarkers along with the R-ISS staging system to predict OS. In conclusion, tRFs show molecular biomarker utility in MM, while their mechanisms of function merit further investigation.
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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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A Molecular Signature of Circulating MicroRNA Can Predict Osteolytic Bone Disease in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13153877. [PMID: 34359778 PMCID: PMC8345491 DOI: 10.3390/cancers13153877] [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: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Multiple myeloma bone disease (MMBD) is one of the most important complications of multiple myeloma with a great impact on quality of life. Recent advances in the field of imaging techniques provided clinicians with a variety of imaging modalities with high sensitivity for the diagnosis of MMBD. However, no circulating biomarkers are available to support the diagnosis of MMBD in cases where the results are inconclusive. The aim of our study was to investigate the clinical utility of 19 miRNAs implicated in osteoporosis in MMBD. Our results suggest that the levels of circulating let-7b-5p, miR-143-3p, miR-17-5p, miR-335-5p, and miR-214-3p (standalone or combined in multi-miRNA models) can effectively predict the presence of MMBD in newly diagnosed MM patients. Abstract Background: Multiple myeloma bone disease (MMBD) constitutes a common and severe complication of multiple myeloma (MM), impacting the quality of life and survival. We evaluated the clinical value of a panel of 19 miRNAs associated with osteoporosis in MMBD. Methods: miRNAs were isolated from the plasma of 62 newly diagnosed MM patients with or without MMBD. First-strand cDNA was synthesized, and relative quantification was performed using qPCR. Lastly, we carried out extensive biostatistical analysis. Results: Circulating levels of let-7b-5p, miR-143-3p, miR-17-5p, miR-214-3p, and miR-335-5p were significantly higher in the blood plasma of MM patients with MMBD compared to those without. Receiver operating characteristic curve and logistic regression analyses showed that these miRNAs could accurately predict MMBD. Furthermore, a standalone multi-miRNA–based logistic regression model exhibited the best predictive potential regarding MMBD. Two of those miRNAs also have a prognostic role in MM since survival analysis indicated that lower circulating levels of both let-7b-5p and miR-335-5p were associated with significantly worse progression-free survival, independently of the established prognostic factors. Conclusions: Our study proposes a miRNA signature to facilitate MMBD diagnosis, especially in ambiguous cases. Moreover, we provide evidence of the prognostic role of let-7b-5p and miR-335-5p as non-invasive prognostic biomarkers in MM.
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Katsaraki K, Adamopoulos PG, Papageorgiou SG, Pappa V, Scorilas A, Kontos CK. A 3' tRNA-derived fragment produced by tRNA LeuAAG and tRNA LeuTAG is associated with poor prognosis in B-cell chronic lymphocytic leukemia, independently of classical prognostic factors. Eur J Haematol 2021; 106:821-830. [PMID: 33660275 DOI: 10.1111/ejh.13613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE 3' tRNA-derived fragments (3' tRFs) are important epigenetic regulators in normal and pathological conditions. In this study, we aimed to explore the potential value of a 3' tRF as a prognostic and/or screening biomarker for B-cell chronic lymphocytic leukemia (B-CLL). METHODS Publicly available next-generation sequencing data from 20 B-CLL cases were analyzed, followed by prediction of targets of the most abundantly and ubiquitously expressed 3' tRFs, leading to selection of tRF-LeuAAG/TAG . PBMCs were isolated from blood samples of 91 B-CLL patients and 43 non-leukemic donors, followed by total RNA extraction, in-vitro polyadenylation, and first-strand cDNA synthesis. Next, a real-time quantitative PCR (qPCR) assay was developed for the accurate quantification of tRF-LeuAAG/TAG and applied in all samples, prior to biostatistical analysis. RESULTS High tRF-LeuAAG/TAG levels are associated with inferior overall survival (OS) of B-CLL patients. The unfavorable significance of tRF-LeuAAG/TAG was independent of established prognostic factors in B-CLL. Stratified Kaplan-Meier OS analysis uncovered the unfavorable prognostic role of high tRF-LeuAAG/TAG levels for patients in Binet A or Rai I stage, negative CD38 expression, mutated, or unmutated IGHV genomic locus. CONCLUSION Our approach revealed the independent prognostic value of a particular 3' tRF, derived from tRNALeuAAG and tRNALeuTAG (tRF-LeuAAG/TAG ) in B-CLL.
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Affiliation(s)
- Katerina Katsaraki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens Panepistimiopolis, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens Panepistimiopolis, Athens, Greece
| | - Sotirios G Papageorgiou
- Second Department of Internal Medicine and Research Unit, University General Hospital Attikon, Athens, Greece
| | - Vasiliki Pappa
- Second Department of Internal Medicine and Research Unit, University General Hospital Attikon, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens Panepistimiopolis, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens Panepistimiopolis, Athens, Greece
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Dwivedi SKD, Rao G, Dey A, Mukherjee P, Wren JD, Bhattacharya R. Small Non-Coding-RNA in Gynecological Malignancies. Cancers (Basel) 2021; 13:1085. [PMID: 33802524 PMCID: PMC7961667 DOI: 10.3390/cancers13051085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.
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Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Biochemistry and Molecular Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
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20
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Multiple Myeloma Bone Disease: Implication of MicroRNAs in Its Molecular Background. Int J Mol Sci 2021; 22:ijms22052375. [PMID: 33673480 PMCID: PMC7956742 DOI: 10.3390/ijms22052375] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Multiple myeloma (MM) is a common hematological malignancy arising from terminally differentiated plasma cells. In the majority of cases, symptomatic disease is characterized by the presence of bone disease. Multiple myeloma bone disease (MMBD) is a result of an imbalance in the bone-remodeling process that leads to increased osteoclast activity and decreased osteoblast activity. The molecular background of MMBD appears intriguingly complex, as several signaling pathways and cell-to-cell interactions are implicated in the pathophysiology of MMBD. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate the expression of their target mRNAs. Numerous miRNAs have been witnessed to be involved in cancer and hematological malignancies and their role has been characterized either as oncogenic or oncosuppressive. Recently, scientific research turned towards miRNAs as regulators of MMBD. Scientific data support that miRNAs finely regulate the majority of the signaling pathways implicated in MMBD. In this review, we provide concise information regarding the molecular pathways with a significant role in MMBD and the miRNAs implicated in their regulation. Moreover, we discuss their utility as molecular biomarkers and highlight the putative usage of miRNAs as novel molecular targets for targeted therapy in MMBD.
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21
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Yu X, Xie Y, Zhang S, Song X, Xiao B, Yan Z. tRNA-derived fragments: Mechanisms underlying their regulation of gene expression and potential applications as therapeutic targets in cancers and virus infections. Am J Cancer Res 2021; 11:461-469. [PMID: 33391486 PMCID: PMC7681095 DOI: 10.7150/thno.51963] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
tRNA-derived fragments (tRFs) are a new category of regulatory noncoding RNAs with distinct biological functions in cancers and stress-induced diseases. Herein, we first summarize the classification and biogenesis of tRFs. tRFs are produced from pre-tRNAs or mature tRNAs. Based on the incision loci, tRFs are classified into several types: tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. Some tRFs participate in posttranscriptional regulation through microRNA-like actions or by displacing RNA binding proteins and regulating protein translation by promoting ribosome biogenesis or interfering with translation initiation. Other tRFs prevent cell apoptosis by binding to cytochrome c or promoting virus replication. More importantly, the dysregulation of tRFs has important clinical implications. They are potential diagnostic and prognostic biomarkers of gastric cancer, liver cancer, breast cancer, prostate cancer, and chronic lymphocytic leukemia. tRFs may become new therapeutic targets for the treatment of diseases such as hepatocellular carcinoma and respiratory syncytial virus infection. Finally, we point out the existing problems and future research directions associated with tRFs. In conclusion, the current progress in the research of tRFs reveals that they have important clinical implications and may constitute novel molecular therapeutic targets for modulating pathological processes.
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22
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Chen Y, Shen J. Mucosal immunity and tRNA, tRF, and tiRNA. J Mol Med (Berl) 2020; 99:47-56. [PMID: 33200232 DOI: 10.1007/s00109-020-02008-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Mucosal immunity has crucial roles in human diseases such as respiratory tract infection, inflammatory bowel diseases (IBD), and colorectal cancer (CRC). Recent studies suggest that the mononuclear phagocyte system, cancer cells, bacteria, and viruses induce the mucosal immune reaction by various pathways, and can be major factors in the pathogenesis of these diseases. Transfer RNA (tRNA) and its fragments, including tRNA-derived RNA fragments (tRFs) and tRNA-derived stress-induced RNAs (tiRNAs), have emerged as a hot topic in recent years. They not only are verified as essential for transcription and translation but also play roles in cellular homeostasis and functions, such as cell metastasis, proliferation, and apoptosis. However, the specific relationship between their biological regulation and mucosal immunity remains unclear to date. In the present review, we carry out a comprehensive discussion on the specific roles of tRNA, tRFs, and tiRNAs relevant to mucosal immunity and related diseases.
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Affiliation(s)
- Yueying Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, 160# Pu Jian Ave, Shanghai, 200127, China
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160# Pu Jian Ave, Shanghai, 200127, China
- Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai, 200127, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, 160# Pu Jian Ave, Shanghai, 200127, China.
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160# Pu Jian Ave, Shanghai, 200127, China.
- Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai, 200127, China.
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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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Pantazis TL, Giotakis AI, Karamagkiolas S, Giotakis I, Konstantoulakis M, Liakea A, Misiakos EP. Low expression of miR-20b-5p indicates favorable prognosis in laryngeal squamous cell carcinoma, especially in patients with non-infiltrated regional lymph nodes. Am J Otolaryngol 2020; 41:102563. [PMID: 32521298 DOI: 10.1016/j.amjoto.2020.102563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/24/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE Tumor recurrence and distant metastasis are very common in laryngeal squamous cell carcinoma (LSCC). In this study, we examined the potential prognostic value of microRNA-20b-5p (miR-20b-5p), a component of the tumor-related miR-106a/363 cluster. MATERIALS AND METHODS Total RNA was purified from 105 tissue specimens resected from patients having undergone surgical treatment for primary LSCC. After in vitro polyadenylation and reverse transcription, a sensitive real-time quantitative polymerase chain reaction (qPCR) methodology was applied for the relative quantification of miR-20b-5p levels. Then, we proceeded with biostatistical analysis, seeking to assess the prognostic value of miR-20b-5p expression in LSCC. RESULTS miR-20b-5p positivity constitutes a predictor of inferior DFS and OS in LSCC (P < 0.001 and P = 0.002, respectively). The significant prognostic value of miR-20b-5p expression status seems to be independent of tumor size, histological grade, and TNM stage, as revealed by the multivariate bootstrap Cox regression analysis. Kaplan-Meier survival analysis showed also that miR-20b-5p expression status can stratify LSCC patients with non-infiltrated regional lymph nodes (N0) into two subgroups with distinct prognosis (P = 0.004 and P = 0.004, respectively). CONCLUSIONS The miR-20b-5p expression status is a promising molecular tissue biomarker in LSCC, with an independent prognostic value, and thus merits further validation in larger cohorts of patients.
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Affiliation(s)
- Theodwros-Leonidas Pantazis
- First Department of Otolaryngology, Athens General Hospital "Hippokration", Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
| | - Aris I Giotakis
- First Department of Otolaryngology, Athens General Hospital "Hippokration", Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Sotirios Karamagkiolas
- First Department of Otolaryngology, Athens General Hospital "Hippokration", Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Giotakis
- First Department of Otolaryngology, Athens General Hospital "Hippokration", Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Manousos Konstantoulakis
- First Department of Propaedeutic Surgery, Athens General Hospital "Hippokration", Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Aliki Liakea
- First Department of Pathology, National and Kapodistrian University of Athens, Faculty of Medicine, Athens, Greece
| | - Evangelos P Misiakos
- Third Department of Surgery, University General Hospital "Attikon", Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Karousi P, Adamopoulos PG, Papageorgiou SG, Pappa V, Scorilas A, Kontos CK. A novel, mitochondrial, internal tRNA-derived RNA fragment possesses clinical utility as a molecular prognostic biomarker in chronic lymphocytic leukemia. Clin Biochem 2020; 85:20-26. [PMID: 32745483 DOI: 10.1016/j.clinbiochem.2020.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults. The prognosis of CLL patients varies considerably. Transfer RNA-derived RNA fragments (tRFs) constitute a class of small non-coding RNA fragments excised from mature tRNAs and pre-tRNAs located in nuclei as well as in mitochondria. In this study, the clinical utility of i-tRF-PheGAA, a novel mitochondrial tRF, was investigated in CLL. DESIGN AND METHODS Peripheral blood mononuclear cells (PBMCs) were isolated from 91 CLL patients and 43 non-leukemic controls. Total RNA was isolated from each sample, polyadenylated at the 3' end and reversely transcribed. An in-house developed real-time quantitative PCR assay was developed and applied, and the results were biostatistically analyzed. For the normalization of the i-tRF-PheGAA expression levels, the expression of a small nucleolar RNA (RNU48) was used as reference. RESULTS Mann-Whitney U test showed that i-tRF-PheGAA can distinguish between CLL samples and normal controls (p < 0.001). As determined by Kaplan-Meier survival analysis, overexpression of i-tRF-PheGAA was related to poor overall survival of the CLL patients (p < 0.001). Univariate bootstrap Cox regression analysis exhibited a higher hazard ratio of 7.95 (95% CI = 2.37-26.72, p < 0.001) for patients with positive i-tRF-PheGAA expression status. Multivariate bootstrap Cox regression analysis showed that the prognostic value of this tRF is independent of clinical stage, mutational status of the immunoglobulin heavy chain variable (IGHV) genetic locus, and CD38 expression status (p = 0.010). CONCLUSIONS Our results show that i-tRF-PheGAA can serve as a molecular biomarker of poor prognosis in CLL, alongside with the existing factors for CLL prognosis.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece
| | - Sotirios G Papageorgiou
- Second Department of Internal Medicine and Research Unit, University General Hospital "Attikon", 1 Rimini St., Haidari, GR 12462 Athens, Greece
| | - Vasiliki Pappa
- Second Department of Internal Medicine and Research Unit, University General Hospital "Attikon", 1 Rimini St., Haidari, GR 12462 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece.
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Xie Y, Yao L, Yu X, Ruan Y, Li Z, Guo J. Action mechanisms and research methods of tRNA-derived small RNAs. Signal Transduct Target Ther 2020; 5:109. [PMID: 32606362 PMCID: PMC7326991 DOI: 10.1038/s41392-020-00217-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023] Open
Abstract
tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.
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Affiliation(s)
- Yaoyao Xie
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Lipeng Yao
- Ningbo College of Health Sciences, Ningbo, 315000, Zhejiang, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Yao Ruan
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Zhe Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China.
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27
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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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28
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Identification of a novel, internal tRNA-derived RNA fragment as a new prognostic and screening biomarker in chronic lymphocytic leukemia, using an innovative quantitative real-time PCR assay. Leuk Res 2019; 87:106234. [PMID: 31669784 DOI: 10.1016/j.leukres.2019.106234] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/07/2019] [Accepted: 10/05/2019] [Indexed: 01/17/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is one of the most common types of leukemia in adults. Several studies have identified various prognostic biomarkers in CLL. In this study, we investigated the potential value of an internal fragment of the tRNAs bearing the Glycine anticodon CCC (i-tRF-GlyCCC), which is a small non-coding RNA, as a prognostic and screening biomarker in CLL. For this purpose, blood samples were collected from 90 CLL patients and 43 non-leukemic blood donors. Peripheral blood mononuclear cells (PBMCs) were isolated, total RNA was extracted and in-vitro polyadenylated, and first-strand cDNA was synthesized using an oligo-dT-adaptor primer. A real-time quantitative PCR assay was developed and applied for the quantification of i-tRF-GlyCCC in our samples. The biostatistical analysis revealed that i-tRF-GlyCCC levels are significantly lower in PBMCs of CLL patients, compared to PBMCs of non-leukemic controls, and that i-tRF-GlyCCC could be considered as a screening biomarker. Kaplan-Meier overall survival (OS) analysis revealed reduced OS for CLL patients with positive i-tRF-GlyCCC expression (P = 0.001). Multivariate Cox regression confirmed its independent unfavorable prognostic power with regard to OS. In conclusion, i-tRF-GlyCCC may constitute a promising molecular biomarker in CLL, for screening and prognostic purposes.
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