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Xi X, Wang B, Zhang R, Ling C. Serum exosome tRFs as a promising biomarker for active tuberculosis and latent tuberculosis infection. J Microbiol Methods 2024; 222:106944. [PMID: 38705210 DOI: 10.1016/j.mimet.2024.106944] [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: 12/05/2023] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To analyse the expression profiles of serum exosome tRFs/tiRNAs and to explore their diagnostic value in tuberculosis (TB) activity. METHODS The serum exosome tRF/tiRNA profile was analysed using high-throughput sequencing technology in 5 active tuberculosis (ATB) patients, 5 latent tuberculosis infection (LTBI) patients and 5 healthy controls (HCs). Then, serum exosome tRFs/tiRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR), and their diagnostic value was evaluated by receiver operating characteristic curve (ROC) and area under the curve (AUC). Finally, bioinformatics analysis was performed to explore and identify the potential biological pathways induced by tRFs/tiRNAs. RESULTS The sequencing results revealed that serum exosome tRF/tiRNA expression profiles were different among ATB patients, LTBI patients and HCs. Three tRFs (tRF-56:75-Trp-CCA-4, tRF-1:22-chrM.Ser-GCT and tRF-56:76-Val-TAC-1-M2) were selected for qRT-PCR validation. The results demonstrated that the expression level of tRF-1-22-chrM.Ser-GCT was upregulated in ATB patients, while tRF-56-75-Trp-CCA-4 was downregulated, which was consistent with the sequencing data. The AUCs of tRF-56:75-Trp-CCA-4 and tRF-1:22-chrM. Ser-GCT were 0.824 and 1.000, respectively, which have significant values in the diagnosis of ATB patients. Moreover, the expression levels of tRF-56:75-Trp-CCA-4 and tRF-1:22-chrM.Ser-GCT and tRF-56:76-Val-TAC-1-M2 in ATB patients and LTBI were different, which indicated that these three tRFs could effectively distinguish ATB patients and LTBI patients. CONCLUSION Our findings indicate that serum exosome tRFs can be used as potential markers for the diagnosis of ATB and LTBI.
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Affiliation(s)
- Xiangyu Xi
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; Xuzhou Infectious Disease Hospital, Xuzhou, Jiangsu, China
| | - Binghua Wang
- Department of Epidemiology, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ruimei Zhang
- Xuzhou Infectious Disease Hospital, Xuzhou, Jiangsu, China
| | - Chunhua Ling
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
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Wang K, Liu CY, Fang B, Li B, Li YH, Xia QQ, Zhao Y, Cheng XL, Yang SM, Zhang MH, Wang K. The function and therapeutic potential of transfer RNA-derived small RNAs in cardiovascular diseases: A review. Pharmacol Res 2024; 206:107279. [PMID: 38942340 DOI: 10.1016/j.phrs.2024.107279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are a class of small non-coding RNA (sncRNA) molecules derived from tRNA, including tRNA derived fragments (tRFs) and tRNA halfs (tiRNAs). tsRNAs can affect cell functions by participating in gene expression regulation, translation regulation, intercellular signal transduction, and immune response. They have been shown to play an important role in various human diseases, including cardiovascular diseases (CVDs). Targeted regulation of tsRNAs expression can affect the progression of CVDs. The tsRNAs induced by pathological conditions can be detected when released into the extracellular, giving them enormous potential as disease biomarkers. Here, we review the biogenesis, degradation process and related functional mechanisms of tsRNAs, and discuss the research progress and application prospects of tsRNAs in different CVDs, to provide a new perspective on the treatment of CVDs.
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Affiliation(s)
- Kai Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Ying-Hui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Qian-Qian Xia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xue-Li Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Su-Min Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| | - Mei-Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China.
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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3
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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. [PMID: 38867475 DOI: 10.1002/ijc.35041] [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: 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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4
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Shen Z, Naveed M, Bao J. Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1852. [PMID: 38715192 DOI: 10.1002/wrna.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 06/06/2024]
Abstract
Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Zhaokang Shen
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Muhammad Naveed
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianqiang Bao
- Department of Obstetrics and Gynecology, Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China (USTC), Hefei, Anhui, China
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Xu J, Wang Y, Li X, Zheng M, Li Y, Zhang W. Clinical value assessment for serum hsa_tsr013526 in the diagnosis of gastric carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:2753-2767. [PMID: 38251933 DOI: 10.1002/tox.24146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/29/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
Gastric carcinoma (GC) is a malignant tumor that is detrimental to human health. Transfer RNA-derived small RNAs are a newly identified class of noncoding small RNAs with specific biological functions that are aberrantly expressed in cancer. The aim of this study was to investigate the potential of hsa_tsr013526 as a biomarker for GC. Quantitative real-time fluorescence polymerase chain reaction was used to detect the expression level of hsa_tsr013526. The molecular characteristics of hsa_tsr013526 were verified by agarose gel electrophoresis, Sanger sequencing, and separation of nuclear and cytoplasmic RNA fractions. By testing the receiver operating characteristic (ROC) curves, the diagnostic efficiency of GC using hsa_tsr013526 was determined. Finally, we predicted the downstream of hsa_tsr013526 using functional assays and bioinformatics analysis. Serum expression of hsa_tsr013526 was higher in GC patients than in healthy donors. Serum expression showed differential changes in GC patients, gastritis patients, and healthy donors. Chi-squared tests showed that high expression of hsa_tsr013526 was significantly correlated with T stage, lymphatic metastasis, and tumor node metastasis stage. ROC curve analysis indicated that GC patients could be discriminated from healthy donors or gastritis patients based on their serum levels of hsa_tsr013526. Furthermore, hsa_tsr013526 expression was significantly reduced in postoperative GC patients (p = .0016). High expression of hsa_tsr013526 promotes gastric cancer cell proliferation, invasion, and migration. Serum hsa_tsr013526 was stable and specific, and could be used for dynamic monitoring of GC patients. Therefore, hsa_tsr013526 may be a new biomarker for the diagnosis and postoperative monitoring of GC patients.
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Affiliation(s)
- Jing Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Medical School, Nantong University, Nantong, China
| | - Yue Wang
- Basic Medicine School, Xuzhou Medical University, Xuzhou, China
| | - Xian Li
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Ming Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yang Li
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Medical School, Nantong University, Nantong, China
| | - Weiwei Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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Zhou M, He X, Zhang J, Mei C, Zhong B, Ou C. tRNA-derived small RNAs in human cancers: roles, mechanisms, and clinical application. Mol Cancer 2024; 23:76. [PMID: 38622694 PMCID: PMC11020452 DOI: 10.1186/s12943-024-01992-2] [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: 01/03/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are a new type of non-coding RNAs (ncRNAs) produced by the specific cleavage of precursor or mature tRNAs. tsRNAs are involved in various basic biological processes such as epigenetic, transcriptional, post-transcriptional, and translation regulation, thereby affecting the occurrence and development of various human diseases, including cancers. Recent studies have shown that tsRNAs play an important role in tumorigenesis by regulating biological behaviors such as malignant proliferation, invasion and metastasis, angiogenesis, immune response, tumor resistance, and tumor metabolism reprogramming. These may be new potential targets for tumor treatment. Furthermore, tsRNAs can exist abundantly and stably in various bodily fluids (e.g., blood, serum, and urine) in the form of free or encapsulated extracellular vesicles, thereby affecting intercellular communication in the tumor microenvironment (TME). Meanwhile, their abnormal expression is closely related to the clinicopathological features of tumor patients, such as tumor staging, lymph node metastasis, and poor prognosis of tumor patients; thus, tsRNAs can be served as a novel type of liquid biopsy biomarker. This review summarizes the discovery, production, and expression of tsRNAs and analyzes their molecular mechanisms in tumor development and potential applications in tumor therapy, which may provide new strategies for early diagnosis and targeted therapy of tumors.
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Affiliation(s)
- Manli Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jing Zhang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Cheng Mei
- Department of Blood Transfusion, Xiangya Hospital, Clinical Transfusion Research Center, Central South University, Changsha, Hunan, 410008, China.
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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Peng J, Zhang Y, Zhou G, Shao L, Li L, Zhang Z. Circulating serum exosomes i-tRF-AspGTC and tRF-1-SerCGA as diagnostic indicators for non-small cell lung cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03423-6. [PMID: 38502292 DOI: 10.1007/s12094-024-03423-6] [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: 12/10/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND tRF-RNA-a representative of non-coding RNA (ncRNA)-is a precursor or fragment of mature tRNA and plays a crucial regulatory role in the occurrence and development of cancer. There is currently little research on tRF-RNA as a diagnostic marker in cancer, especially for NSCLC from serum exosomes. METHOD Serum exosomes were successfully extracted from serum; their physical morphology was captured by transmission electron microscopy (TEM); appropriate particle size detection was performed using qNano; surface labeling was verified through western blotting. Serum exosomes i-tRF-AspGTC and tRF-1-SerCGA were selected through gene microarray, and qPCR was used to validate their significance in 242 patients and 201 healthy individuals. The area under the curve (AUC) was used to evaluate the diagnostic indicators of non-small cell lung cancer (NSCLC). RESULT Compared with 201 healthy individuals, i-tRF-AspGTC and tRF-1-SerCGA were significantly downregulated in 242 NSCLC patients and 95 early-stage patients. For tRF-AspGTC and tRF-1-SerCGA, the predictive diagnostic efficiency rates of AUC were 0.690 and 0.680, respectively, whereas the early diagnostic efficiency rates were 0.656 and 0.688, respectively. The result of combined diagnosis with CEA and CYFRA21-1 was 0.928, and the early diagnostic efficiency was 0.843, which is a very high biological predictive factor for NSCLC. CONCLUSION The expression of serum exosomes i-tRF-AspGTC and tRF-1-SerCGA was significantly downregulated in NSCLC patients. These exosomes could be used as predictive indicators for diagnosis or early diagnosis of NSCLC.
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Affiliation(s)
- Jiefei Peng
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-drug Resistant Drug Research, Taian City Central Hospital, Taian, 271000, China
| | - Yue Zhang
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Guangfei Zhou
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Luolin Shao
- Department of Dermatology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Lin Li
- Pharmacy Intravenous Admixture Services, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China.
| | - Zhijun Zhang
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China.
- Shandong Provincial Key Medical and Health Laboratory of Anti-drug Resistant Drug Research, Taian City Central Hospital, Taian, 271000, China.
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Xie L, Zhao Z, Xia H, Su S, He L, Huang Z, Li Y, Gao M, Chen J, Peng J, Ruan Y. A novel tsRNA-5008a promotes ferroptosis in cardiomyocytes that causes atrial structural remodeling predisposed to atrial fibrillation. Exp Cell Res 2024; 435:113923. [PMID: 38190870 DOI: 10.1016/j.yexcr.2024.113923] [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: 11/15/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/10/2024]
Abstract
Atrial fibrillation (AF) is an extremely common clinical arrhythmia disease, but whether its mechanism is associated with ferroptosis remains unclear. The tRNA-derived small RNAs (tsRNAs) are involved in a variety of cardiovascular diseases, however, their role and mechanism in atrial remodeling in AF have not been studied. We aimed to explore whether tsRNAs mediate ferroptosis in AF progression. The AF models were constructed to detect ferroptosis-related indicators, and Ferrostatin-1 (Fer-1) was introduced to clarify the relationship between ferroptosis and AF. Atrial myocardial tissue was used for small RNA sequencing to screen potential tsRNAs. tsRNA functioned on ferroptosis and AF was explored. Atrial fibrosis and changes in the cellular structures and arrangement were observed in AF mice model, and these alterations were accompanied by ferroptosis occurrence, exhibited by the accumulation of Fe2+ and MDA levels and the decrease of expression of FTH1, GPX4, and SLC7A11. Blocking above ferroptosis activation with Fer-1 resulted in a significant improvement for AF. A total of 7 tsRNAs were upregulated (including tsRNA-5008a) and 2 tsRNAs were downregulated in atrial myocardial tissue in the AF group compared with the sham group. We constructed a tsRNA-mRNA regulated network, which showed tsRNA-5008a targeted 16 ferroptosis-related genes. Knockdown of tsRNA-5008a significantly suppressed ferroptosis through targeting SLC7A11 and diminished myocardial fibrosis both in vitro and in vivo. On the contrary, tsRNA-5008a mimics promoted ferroptosis in cardiomyocytes. Collectively, tsRNA-5008a involved in AF through ferroptosis. Our study provides novel insights into the role of tsRNA-5008a mediated ferroptosis in AF progression.
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Affiliation(s)
- Liangzhen Xie
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zewei Zhao
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Hao Xia
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shuang Su
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Liwei He
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhaohui Huang
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yongchun Li
- Department of Traditional Chinese Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mingjian Gao
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun Chen
- Department of Cardiology, Southern University of Science and Technology Hospital, Shenzhen, Guangdong, China
| | - Jian Peng
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Yunjun Ruan
- Department of Geriatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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Wu F, Yang Q, Pan W, Meng W, Ma Z, Wang W. tRNA-derived fragments: mechanism of gene regulation and clinical application in lung cancer. Cell Oncol (Dordr) 2024; 47:37-54. [PMID: 37642916 DOI: 10.1007/s13402-023-00864-z] [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] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Lung cancer, being the most widespread and lethal form of cancer globally, has a high incidence and mortality rate primarily attributed to challenges associated with early detection, extensive metastasis, and frequent recurrence. In the context of lung cancer development, noncoding RNA molecules have a crucial role in governing gene expression and protein synthesis. Specifically, tRNA-derived fragments (tRFs), a subset of noncoding RNAs, exert significant biological influences on cancer progression, encompassing transcription and translation processes as well as epigenetic regulation. This article primarily examines the mechanisms by which tRFs modulate gene expression and contribute to tumorigenesis in lung cancer. Furthermore, we provide a comprehensive overview of the current bioinformatics analysis of tRFs in lung cancer, with the objective of offering a systematic and efficient approach for studying the expression profiling, functional enrichment, and molecular mechanisms of tRFs in this disease. Finally, we discuss the clinical significance and potential avenues for future research on tRFs in lung cancer. This paper presents a comprehensive systematic review of the existing research findings on tRFs in lung cancer, aiming to offer improved biomarkers and drug targets for clinical management of lung cancer.
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Affiliation(s)
- Fan Wu
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Qianqian Yang
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Wei Meng
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China
| | - Zhongliang Ma
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, 381 Nanchen Road, Shanghai, 200444, China.
| | - Weiwei Wang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Cancer Hospital, Yunnan Cancer Center, Kunming, 650118, China.
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Panstruga R, Spanu P. Transfer RNA and ribosomal RNA fragments - emerging players in plant-microbe interactions. THE NEW PHYTOLOGIST 2024; 241:567-577. [PMID: 37985402 DOI: 10.1111/nph.19409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
According to current textbooks, the principal task of transfer and ribosomal RNAs (tRNAs and rRNAs, respectively) is synthesizing proteins. During the last decade, additional cellular roles for precisely processed tRNA and rRNAs fragments have become evident in all kingdoms of life. These RNA fragments were originally overlooked in transcriptome datasets or regarded as unspecific degradation products. Upon closer inspection, they were found to engage in a variety of cellular processes, in particular the modulation of translation and the regulation of gene expression by sequence complementarity- and Argonaute protein-dependent gene silencing. More recently, the presence of tRNA and rRNA fragments has also been recognized in the context of plant-microbe interactions, both on the plant and the microbial side. While most of these fragments are likely to affect endogenous processes, there is increasing evidence for their transfer across kingdoms in the course of such interactions; these processes may involve mutual exchange in association with extracellular vesicles. Here, we summarize the state-of-the-art understanding of tRNA and rRNA fragment's roles in the context of plant-microbe interactions, their potential biogenesis, presumed delivery routes, and presumptive modes of action.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Worringerweg 1, Aachen, 52056, Germany
| | - Pietro Spanu
- Department of Life Sciences, Imperial College London, Imperial College Road, London, SW7 2AZ, UK
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11
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [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: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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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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13
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Du J, Huang T, Zheng Z, Fang S, Deng H, Liu K. Biological function and clinical application prospect of tsRNAs in digestive system biology and pathology. Cell Commun Signal 2023; 21:302. [PMID: 37904174 PMCID: PMC10614346 DOI: 10.1186/s12964-023-01341-8] [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: 06/24/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023] Open
Abstract
tsRNAs are small non-coding RNAs originating from tRNA that play important roles in a variety of physiological activities such as RNA silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, as well as involvement in cellular differentiation, proliferation, and apoptosis. tsRNA-related abnormalities have a significant influence on the onset, development, and progression of numerous human diseases, including malignant tumors through affecting the cell cycle and specific signaling molecules. This review introduced origins together with tsRNAs classification, providing a summary for regulatory mechanism and physiological function while dysfunctional effect of tsRNAs in digestive system diseases, focusing on the clinical prospects of tsRNAs for diagnostic and prognostic biomarkers. Video Abstract.
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Affiliation(s)
- Juan Du
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Tianyi Huang
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Zhen Zheng
- Department of Radiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Shuai Fang
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Hongxia Deng
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Kaitai Liu
- Department of Radiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
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Li H, Wang Z, Zhao B, Zhang H, Fan D, Ma H, Zhang Y, Wang Y. Sperm-borne lncRNA loc100847420 improves development of early bovine embryos. Anim Reprod Sci 2023; 257:107333. [PMID: 37729849 DOI: 10.1016/j.anireprosci.2023.107333] [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: 07/05/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
Long non-coding RNAs (lncRNAs) act as competing endogenous RNAs (ceRNAs) that play a significant role in bovine embryo development; but the influence of sperm-borne lncRNA on the preimplantation development of bovine embryos has not been reported in detail. In this study, we aimed to clarify how sperm-borne lncRNAs can act to regulate early development of bovine embryos. Utilizing high-throughput sequencing technology and quantitative real-time PCR (qPCR), we found that the lncRNA, loc100847420, was highly enriched in bovine sperm and was carried into the oocyte during fertilization. Introduction of wild-type loc100847420 had no effect on cleavage rate of parthenogenetic embryos compared with injection of mutant loc100847420 (70.58 ± 2.85% vs 70.46 ± 1.98%, p > 0.05), but significantly improved the blastocyst rate (33.67 ± 2.40% vs 28.35 ± 3.06%, p < 0.05), total numbers of cells (p < 0.05), numbers of inner cell mass (ICM) cells (p < 0.05) and numbers of trophoblast (TE) cells (p < 0.05). In summary, the sperm-borne lncRNA, loc100847420, can improve the developmental potential of early bovine embryos.
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Affiliation(s)
- Heqiang Li
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China
| | - Zheng Wang
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China
| | - Baobao Zhao
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China
| | - Han Zhang
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China
| | - Dexiang Fan
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China
| | - Huiming Ma
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Key Laboratory of Reproduction and Genetics in Ningxia, Department of Histology and Embryology, Ningxia Medical University, Yinchuan 750004, PR China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China.
| | - Yongsheng Wang
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Ministry of Agriculture and Rural Affairs, Northwest A&∼F University, Yangling, Shaanxi, 712100, PR China.
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15
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Gan L, Song H, Ding X. Transfer RNA-derived small RNAs (tsRNAs) in gastric cancer. Front Oncol 2023; 13:1184615. [PMID: 37503324 PMCID: PMC10369188 DOI: 10.3389/fonc.2023.1184615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are newly discovered noncoding RNAs (ncRNAs). According to the specific cleavage of nucleases at different sites of tRNAs, the produced tsRNAs are divided into tRNA-derived stress-inducible RNAs (tiRNAs) and tRNA-derived fragments (tRFs). tRFs and tiRNAs have essential biological functions, such as mRNA stability regulation, translation regulation and epigenetic regulation, and play significant roles in the occurrence and development of various tumors. Although the roles of tsRNAs in some tumors have been intensively studied, their roles in gastric cancer are still rarely reported. In this review, we focus on recent advances in the generation and classification of tsRNAs, their biological functions, and their roles in gastric cancer. Sixteen articles investigating dysregulated tsRNAs in gastric cancer are summarized. The roles of 17 tsRNAs are summarized, of which 9 were upregulated and 8 were downregulated compared with controls. Aberrant regulation of tsRNAs was closely related to the main clinicopathological factors of gastric cancer, such as lymph node metastasis, Tumor-Node-Metastasis (TNM) stage, tumor size, and vascular invasion. tsRNAs participate in the progression of gastric cancer by regulating the PTEN/PI3K/AKT, MAPK, Wnt, and p53 signaling pathways. The available literature suggests the potential of using tsRNAs as clinical biomarkers for gastric cancer diagnosis and prognosis and as therapeutic targets for gastric cancer treatment.
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Affiliation(s)
- Lu Gan
- Health Science Center, Ningbo University, Ningbo, China
| | - Haojun Song
- The Gastroenterology Department, The First Affiliated Hospital of Ningbo University, Ningbo, China
- The Biobank of The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Xiaoyun Ding
- The Gastroenterology Department, The First Affiliated Hospital of Ningbo University, Ningbo, China
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16
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Wang XY, Zhou YJ, Chen HY, Chen JN, Chen SS, Chen HM, Li XB. 5’tiRNA-Pro-TGG, a novel tRNA halve, promotes oncogenesis in sessile serrated lesions and serrated pathway of colorectal cancer. World J Gastrointest Oncol 2023; 15:1005-1018. [PMID: 37389118 PMCID: PMC10302996 DOI: 10.4251/wjgo.v15.i6.1005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are small fragments that form when tRNAs severe. tRNA halves (tiRNAs), a subcategory of tsRNA, are involved in the oncogenic processes of many tumors. However, their specific role in sessile serrated lesions (SSLs), a precancerous lesion often observed in the colon, has not yet been elucidated.
AIM To identify SSL-related tiRNAs and their potential role in the development of SSLs and serrated pathway of colorectal cancer (CRC).
METHODS Small-RNA sequencing was conducted in paired SSLs and their adjacent normal control (NC) tissues. The expression levels of five SSL-related tiRNAs were validated by q-polymerase chain reaction. Cell counting kit-8 and wound healing assays were performed to detect cell proliferation and migration. The target genes and sites of tiRNA-1:33-Pro-TGG-1 (5′tiRNA-Pro-TGG) were predicted by TargetScan and miRanda algorithms. Metabolism-associated and immune-related pathways were analyzed by single-sample gene set enrichment analysis. Functional analyses were performed to establish the roles of 5′tiRNA-Pro-TGG based on the target genes.
RESULTS In total, we found 52 upregulated tsRNAs and 28 downregulated tsRNAs in SSLs compared to NC. The expression levels of tiRNA-1:33-Gly-CCC-2, tiRNA-1:33-Pro-TGG-1, and tiRNA-1:34-Thr-TGT-4-M2 5′tiRNAs were higher in SSLs than those in NC, while that of 5′tiRNA-Pro-TGG was associated with the size of SSLs. It was demonstrated that 5′tiRNA-Pro-TGG promoted cell proliferation and migration of RKO cell in vitro. Then, heparanase 2 (HPSE2) was identified as a potential target gene of 5′tiRNA-Pro-TGG. Its lower expression was associated with a worse prognosis in CRC. Further, lower expression of HPSE2 was observed in SSLs compared to normal controls or conventional adenomas and in BRAF-mutant CRC compared to BRAF-wild CRC. Bioinformatics analyses revealed that its low expression was associated with a low interferon γ response and also with many metabolic pathways such as riboflavin, retinol, and cytochrome p450 drug metabolism pathways.
CONCLUSION tiRNAs may profoundly impact the development of SSLs. 5′tiRNA-Pro-TGG potentially promotes the progression of serrated pathway CRC through metabolic and immune pathways by interacting with HPSE2 and regulating its expression in SSLs and BRAF-mutant CRC. In the future, it may be possible to use tiRNAs as novel biomarkers for early diagnosis of SSLs and as potential therapeutic targets in serrated pathway of CRC.
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Affiliation(s)
- Xin-Yuan Wang
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Yu-Jie Zhou
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Hai-Ying Chen
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Jin-Nan Chen
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Shan-Shan Chen
- Department of Spleen and Stomach and Rheumatology, Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, Sichuan Province, China
| | - Hui-Min Chen
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
| | - Xiao-Bo Li
- Division of Gastroenterology and Hepatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200000, China
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Pan J, Liu Z, Shen B, Xu J, Dai G, Xu W, Wang J, Li L, Cheng L. tsRNA-04002 alleviates intervertebral disk degeneration by targeting PRKCA to inhibit apoptosis of nucleus pulposus cells. J Orthop Surg Res 2023; 18:413. [PMID: 37287061 PMCID: PMC10249188 DOI: 10.1186/s13018-023-03878-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Intervertebral disk degeneration (IDD) is a degenerative disease that underlies various musculoskeletal and spinal disorders and is positively correlated with age. tRNA-derived small RNAs (tsRNA), as a new small noncoding RNAs, its function in IDD is unclear. Herein, our goal was to find the key tsRNA that affects IDD independently of age and explore the underlying mechanisms. METHODS Small RNA sequencing was performed in nucleus pulposus (NP) tissues of traumatic lumbar fracture individuals, young IDD (IDDY) patients, and old IDD (IDDO) patients. The biological functions of tsRNA-04002 in NP cells (NPCs) were investigated by qRT-PCR, western blot, and flow cytometry analysis. The molecular mechanism of tsRNA-04002 was demonstrated by luciferase assays and rescue experiments. Furthermore, the therapeutic effects of tsRNA-04002 on IDD rat model were used and evaluated in vivo. RESULTS Compared with fresh traumatic lumbar fracture patients, a total of 695 disordered tsRNAs is obtained (398 down-regulated tsRNAs and 297 up-regulated tsRNAs). These disordered tsRNAs were mainly involved in Wnt signaling pathway and MAPK signaling pathway. tsRNA-04002 was an age-independent key target in IDD, which was both lower expressed in IDDY and IDDO groups than control group. Overexpression of tsRNA-04002 restrained inflammatory cytokines IL-1β and TNF-α expression, increased the COL2A1, and inhibited the NPCs apoptosis. Furthermore, we determined that PRKCA was the target gene of tsRNA-04002 and was negatively regulated by tsRNA-04002. The rescue experiment results suggested that the high expression of PRKCA reversed the inhibitory effect of tsRNA-04002 mimics on NPCs inflammation and apoptosis, and promotive effect of COL2A1. Moreover, tsRNA-04002 treatment dramatically ameliorated the IDD process in the puncture-induced rat model, together with the blockade of PRKCA in vivo. CONCLUSION Collectively, our results substantiated that tsRNA-04002 could alleviate IDD by targeting PRKCA to inhibit apoptosis of NPCs. tsRNA-04002 may be a novel therapeutic target of IDD progression.
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Affiliation(s)
- Jie Pan
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Zhonghan Liu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Bin Shen
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jin Xu
- Department of Anesthesiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Gonghua Dai
- Department of Medical Imaging, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Wen Xu
- Department of Medical Imaging, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jianjie Wang
- Department of Orthopedics, Tongji Hospital, School of Medicine, Tongji University, No.389 Xincun Road, Putuo Distrcit, Shanghai, 200092, China
| | - Lijun Li
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Liming Cheng
- Department of Orthopedics, Tongji Hospital, School of Medicine, Tongji University, No.389 Xincun Road, Putuo Distrcit, Shanghai, 200092, China.
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Di Fazio A, Gullerova M. An old friend with a new face: tRNA-derived small RNAs with big regulatory potential in cancer biology. Br J Cancer 2023; 128:1625-1635. [PMID: 36759729 PMCID: PMC10133234 DOI: 10.1038/s41416-023-02191-4] [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: 08/19/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs (sncRNAs) essential for protein translation. Emerging evidence suggests that tRNAs can also be processed into smaller fragments, tRNA-derived small RNAs (tsRNAs), a novel class of sncRNAs with powerful applications and high biological relevance to cancer. tsRNAs biogenesis is heterogeneous and involves different ribonucleases, such as Angiogenin and Dicer. For many years, tsRNAs were thought to be just degradation products. However, accumulating evidence shows their roles in gene expression: either directly via destabilising the mRNA or the ribosomal machinery, or indirectly via regulating the expression of ribosomal components. Furthermore, tsRNAs participate in various biological processes linked to cancer, including apoptosis, cell cycle, immune response, and retroviral insertion into the human genome. It is emerging that tsRNAs have significant therapeutic potential. Endogenous tsRNAs can be used as cancer biomarkers, while synthetic tsRNAs and antisense oligonucleotides can be employed to regulate gene expression. In this review, we are recapitulating the regulatory roles of tsRNAs, with a focus on cancer biology.
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Affiliation(s)
- Arianna Di Fazio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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19
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Gong M, Deng Y, Xiang Y, Ye D. The role and mechanism of action of tRNA-derived fragments in the diagnosis and treatment of malignant tumors. Cell Commun Signal 2023; 21:62. [PMID: 36964534 PMCID: PMC10036988 DOI: 10.1186/s12964-023-01079-3] [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: 07/09/2022] [Accepted: 02/13/2023] [Indexed: 03/26/2023] Open
Abstract
Cancer is a leading cause of morbidity and death worldwide. While various factors are established as causing malignant tumors, the mechanisms underlying cancer development remain poorly understood. Early diagnosis and the development of effective treatments for cancer are important research topics. Transfer RNA (tRNA), the most abundant class of RNA molecules in the human transcriptome, participates in both protein synthesis and cellular metabolic processes. tRNA-derived fragments (tRFs) are produced by specific cleavage of pre-tRNA and mature tRNA molecules, which are highly conserved and occur widely in various organisms. tRFs were initially thought to be random products with no physiological function, but have been redefined as novel functional small non-coding RNA molecules that help to regulate RNA stability, modulate translation, and influence target gene expression, as well as other biological processes. There is increasing evidence supporting roles for tRFs in tumorigenesis and cancer development, including the regulation of tumor cell proliferation, invasion, migration, and drug resistance. Understanding the regulatory mechanisms by which tRFs impact these processes has potential to inform malignant tumor diagnosis and treatment. Further, tRFs are expected to become new biological markers for early diagnosis and prognosis prediction in patients with tumors, as well as a targets for precision cancer therapies. Video abstract.
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Affiliation(s)
- Mengdan Gong
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yongqin Deng
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yizhen Xiang
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Dong Ye
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China.
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Yang M, Mo Y, Ren D, Liu S, Zeng Z, Xiong W. Transfer RNA-derived small RNAs in tumor microenvironment. Mol Cancer 2023; 22:32. [PMID: 36797764 PMCID: PMC9933334 DOI: 10.1186/s12943-023-01742-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Transfer RNAs (tRNAs) are a class of non-coding RNAs responsible for amino acid translocation during protein synthesis and are ubiquitously found in organisms. With certain modifications and under specific conditions, tRNAs can be sheared and fragmented into small non-coding RNAs, also known as tRNA-derived small RNAs (tDRs). With the development of high-throughput sequencing technologies and bioinformatic strategies, more and more tDRs have been identified and their functions in organisms have been characterized. tRNA and it derived tDRs, have been shown to be essential not only for transcription and translation, but also for regulating cell proliferation, apoptosis, metastasis, and immunity. Aberrant expression of tDRs is associated with a wide range of human diseases, especially with tumorigenesis and tumor progression. The tumor microenvironment (TME) is a complex ecosystem consisting of various cellular and cell-free components that are mutually compatible with the tumor. It has been shown that tDRs regulate the TME by regulating cancer stem cells, immunity, energy metabolism, epithelial mesenchymal transition, and extracellular matrix remodeling, playing a pro-tumor or tumor suppressor role. In this review, the biogenesis, classification, and function of tDRs, as well as their effects on the TME and the clinical application prospects will be summarized and discussed based on up to date available knowledge.
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Affiliation(s)
- Mei Yang
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yongzhen Mo
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Daixi Ren
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Shun Liu
- grid.452708.c0000 0004 1803 0208Department of Cardiovascular Medicine, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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21
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Chen S, Zhang X, Meng K, Sun Y, Shu R, Han Y, Feng Q, Li Z, Yang P, Liang J. Urinary exosome tsRNAs as novel markers for diagnosis and prediction of lupus nephritis. Front Immunol 2023; 14:1077645. [PMID: 36845141 PMCID: PMC9946979 DOI: 10.3389/fimmu.2023.1077645] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Objective Lupus nephritis (LN) is one of the most severe organ manifestations of systemic lupus erythematosus (SLE). Early identification of renal disease in SLE is important. Renal biopsy is currently recognized as the gold standard for diagnosing LN, however, it is invasive and inconvenient for dynamic monitoring. Urine has been considered more promising and valuable than blood in identifying inflamed kidney tissue. Here, we determine whether the signatures of tRNA-derived small noncoding RNA (tsRNA) in urinary exosomes can serve as novel biomarkers for the diagnosis of LN. Methods tsRNA sequencing was performed in exosome extracted from pooled urine of 20 LN patients and 20 SLE without LN, and the top 10 upregulated tsRNAs were screened as candidate markers of LN. The candidate urinary exosomal tsRNAs were primarily elected by TaqMan probe-based quantitative reverse transcription-PCR (RT-PCR) in 40 samples (20 LN and 20 SLE without LN) in the training phase. In the validation phase, selected tsRNAs from the training phase were further confirmed in a larger cohort (54 LN patients and 39 SLE without LN). Receiver operating characteristic curve (ROC) analysis was conducted to evaluate the diagnostic efficacy. Results Upregulated levels of tRF3-Ile-AAT-1 and tiRNA5-Lys-CTT-1 in the urinary exosomes were observed in LN compared with SLE without LN (P < 0.0001 and P < 0.001) and healthy controls (P < 0.01 and P < 0.01), with the area under the curve (AUC) of 0.777 (95% CI: 0.681-0.874, sensitivity 79.63%, specificity 66.69%) and 0.715 (95% CI: 0.610-0.820, sensitivity 66.96%, specificity 76.92%) for discriminating LN from SLE without LN patients. SLE patients with mild activity and moderate to severe activity had higher levels of urinary exosome derived tRF3-Ile AAT-1 (P = 0.035 and P < 0.001) and tiRNA5-Lys-CTT-1 (P = 0.021 and P < 0.001) compared with patients with no activity. Moreover, bioinformatics analysis revealed that both of the tsRNAs regulate the immune process by modulating metabolism and signal pathway. Conclusion In this study, we demonstrated that urinary exosome tsRNAs can be served as noninvasive biomarkers for the efficient diagnosis and prediction of nephritis in SLE.
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Affiliation(s)
- Shanshan Chen
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiaoshan Zhang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Kaifang Meng
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yifan Sun
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Ruilu Shu
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yan Han
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qingxiu Feng
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhiyang Li
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,*Correspondence: Jun Liang, ; Zhiyang Li, ; Ping Yang,
| | - Ping Yang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,*Correspondence: Jun Liang, ; Zhiyang Li, ; Ping Yang,
| | - Jun Liang
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China,*Correspondence: Jun Liang, ; Zhiyang Li, ; Ping Yang,
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Ziętara KJ, Lejman J, Wojciechowska K, Lejman M. The Importance of Selected Dysregulated microRNAs in Diagnosis and Prognosis of Childhood B-Cell Precursor Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020428. [PMID: 36672378 PMCID: PMC9856444 DOI: 10.3390/cancers15020428] [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: 12/08/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a frequent type of childhood hematological malignancy. The disease is classified into several subtypes according to genetic abnormalities. MicroRNAs (miRNAs) are involved in pathological processes (e.g., proliferation, apoptosis, differentiation). A miRNA is a group of short non-coding RNAs with relevant regulatory effects on gene expression achieved by suppression of the translation or degradation of messenger RNA (mRNA). These molecules act as tumor suppressors and/or oncogenes in the pathogenesis of pediatric leukemias. The characteristic features of miRNAs are their stable form and the possibility of secretion to the circulatory system. The role of miRNA in BCP-ALL pathogenesis is still emerging, but several studies have suggested using miRNA expression profiles as biomarkers for diagnosis, prognosis, and response to therapy in leukemia. The dysregulation of some miRNAs involved in childhood acute lymphoid leukemia, such as miR-155, miR-200c, miR-100, miR-181a, miR125b, and miR146a is discussed, showing their possible employment as therapeutic targets. In the current review, the capabilities of miRNAs in non-invasive diagnostics and their prognostic potential as biomarkers are presented.
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Affiliation(s)
- Karolina Joanna Ziętara
- Student Scientific Society, Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-093 Lublin, Poland
| | - Jan Lejman
- Independent Public Health Care Facility of The Ministry of Internal Affairs and Administration in Lublin, 20-331 Lublin, Poland
| | - Katarzyna Wojciechowska
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-059 Lublin, Poland
| | - Monika Lejman
- Independent Laboratory of Genetic Diagnostics, Medical University of Lublin, 20-059 Lublin, Poland
- Correspondence:
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23
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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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24
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George S, Rafi M, Aldarmaki M, ElSiddig M, Al Nuaimi M, Amiri KMA. tRNA derived small RNAs—Small players with big roles. Front Genet 2022; 13:997780. [PMID: 36199575 PMCID: PMC9527309 DOI: 10.3389/fgene.2022.997780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022] Open
Abstract
In the past 2 decades, small non-coding RNAs derived from tRNA (tsRNAs or tRNA derived fragments; tRFs) have emerged as new powerful players in the field of small RNA mediated regulation of gene expression, translation, and epigenetic control. tRFs have been identified from evolutionarily divergent organisms from Archaea, the higher plants, to humans. Recent studies have confirmed their roles in cancers and other metabolic disorders in humans and experimental models. They have been implicated in biotic and abiotic stress responses in plants as well. In this review, we summarize the current knowledge on tRFs including types of tRFs, their biogenesis, and mechanisms of action. The review also highlights recent studies involving differential expression profiling of tRFs and elucidation of specific functions of individual tRFs from various species. We also discuss potential considerations while designing experiments involving tRFs identification and characterization and list the available bioinformatics tools for this purpose.
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Affiliation(s)
- Suja George
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohamed ElSiddig
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mariam Al Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- *Correspondence: Khaled M. A. Amiri,
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25
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Zhang X, Yang P, Khan A, Xu D, Chen S, Zhai J, Zhang B, Xiong T, Wang Y, Li Z. Serum tsRNA as a novel molecular diagnostic biomarker for lupus nephritis. Clin Transl Med 2022; 12:e830. [PMID: 35593207 PMCID: PMC9121311 DOI: 10.1002/ctm2.830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/31/2022] [Accepted: 04/05/2021] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xiaoshan Zhang
- College of Life Science, Yangtze University, Jingzhou, China.,Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Ping Yang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Adeel Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Dongjie Xu
- College of Life Science, Yangtze University, Jingzhou, China.,Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Shanshan Chen
- Department of Rheumatic Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Junbin Zhai
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Bin Zhang
- College of Life Science, Yangtze University, Jingzhou, China.,Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Tao Xiong
- College of Life Science, Yangtze University, Jingzhou, China
| | - Yanbo Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Sciences, NJU Advanced Institute of Life Sciences (NAILS), Nanjing University, Nanjing, China
| | - Zhiyang Li
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
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26
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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: 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: 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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27
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Li J, Cao C, Fang L, Yu W. Serum transfer RNA-derived fragment tRF-31-79MP9P9NH57SD acts as a novel diagnostic biomarker for non-small cell lung cancer. J Clin Lab Anal 2022; 36. [PMID: 35576497 PMCID: PMC9279995 DOI: 10.1002/jcla.24492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background tRNA‐derived fragments (tRFs) have been found to have a crucial function in the pathophysiology of cancers. However, the function of tRFs in non‐small cell lung cancer (NSCLC) is yet unknown. The goal of this study was to assess the tRF‐31‐79MP9P9NH57SD serum expression from NSCLC patients and to determine its diagnostic usefulness. Methods By using stem‐loop quantitative real‐time PCR, we were able to detect various tRF‐31‐79MP9P9NH57SD expressions in 96 NSCLC serum samples, 96 healthy controls, and 20 pairs of NSCLC serum samples pre‐ and post‐surgery (qRT‐PCR). After that, we analyzed its diagnostic effectiveness using the receiver operating characteristic (ROC) curve. Results Serum tRF‐31‐79MP9P9NH57SD expression was higher in NSCLC patients, and levels of tRF‐31‐79MP9P9NH57SD were linked to the clinical stage (p = 0.002) and the malignancy of lymph node (p = 0.012). In addition, after the procedure, the serum tRF‐31‐79MP9P9NH57SD expression in NSCLC patients dropped. With 48.96 percent sensitivity and 90.62 percent specificity, the area under ROC curve (AUC) was 0.733. Conclusion serum tRF‐31‐79MP9P9NH57SD possibly is a new and groundbreaking biomarker for the NSCLC.
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Affiliation(s)
- Jipeng Li
- Department of Central Laboratory, The Affiliated People's Hospital, Ningbo University, Ningbo, China
| | - Chao Cao
- Department of Respiratory and Critical Medicine, Ningbo First Hospital, Ningbo, China
| | - Laifu Fang
- Department of Pathology, The Affiliated People's Hospital, Ningbo University, Ningbo, China
| | - Wanjun Yu
- Department of Respiratory and Critical Medicine, The Affiliated People's Hospital, Ningbo University, Ningbo, China
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28
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Crisóstomo L, Bourgery M, Rato L, Raposo JF, Batterham RL, Kotaja N, Alves MG. Testicular “Inherited Metabolic Memory” of Ancestral High-Fat Diet Is Associated with Sperm sncRNA Content. Biomedicines 2022; 10:biomedicines10040909. [PMID: 35453658 PMCID: PMC9027117 DOI: 10.3390/biomedicines10040909] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023] Open
Abstract
Excessive adiposity caused by high-fat diets (HFDs) is associated with testicular metabolic and functional abnormalities up to grand-offspring, but the mechanisms of this epigenetic inheritance are unclear. Here we describe an association of sperm small non-coding RNA (sncRNA) with testicular “inherited metabolic memory” of ancestral HFD, using a transgenerational rodent model. Male founders were fed a standard chow for 200 days (CTRL), HFD for 200 days (HFD), or standard chow for 60 days followed by HFD for 140 days (HFDt). The male offspring and grand-offspring were fed standard chow for 200 days. The sncRNA sequencing from epidydimal spermatozoa revealed signatures associated with testicular metabolic plasticity in HFD-exposed mice and in the unexposed progeny. Sperm tRNA-derived RNA (tsRNA) and repeat-derived small RNA (repRNA) content were specially affected by HFDt and in the offspring of HFD and HFDt mice. The grand-offspring of HFD and HFDt mice showed lower sperm counts than CTRL descendants, whereas the sperm miRNA content was affected. Although the causality between sperm sncRNAs content and transgenerational epigenetic inheritance of HFD-related traits remains elusive, our results suggest that sperm sncRNA content is influenced by ancestral exposure to HFD, contributing to the sperm epigenome up to the grand-offspring.
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Affiliation(s)
- Luís Crisóstomo
- Departamento de Anatomia, e UMIB—Unidade Multidisciplinar de Investigação em Biomedicina, ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal;
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, 4050-600 Porto, Portugal
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (M.B.); (N.K.)
| | - Matthieu Bourgery
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (M.B.); (N.K.)
| | - Luís Rato
- Polytechnic Institute of Guarda, School of Health, 6300-035 Guarda, Portugal;
- Faculty of Health Sciences, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - João F. Raposo
- NOVA Medical School, New University Lisbon, 1250-189 Lisbon, Portugal;
- Associação Protetora dos Diabéticos de Portugal (APDP), 1250-189 Lisbon, Portugal
| | - Rachel L. Batterham
- Centre for Obesity Research, Department of Medicine, University College London (UCL), London WC1E 6JF, UK;
- National Institute for Health Research, Biomedical Research Centre, University College London Hospital (UCLH), London W1T 7DN, UK
| | - Noora Kotaja
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (M.B.); (N.K.)
| | - Marco G. Alves
- Departamento de Anatomia, e UMIB—Unidade Multidisciplinar de Investigação em Biomedicina, ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal;
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, 4050-600 Porto, Portugal
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, 17003 Girona, Spain
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, 17003 Girona, Spain
- Correspondence: ; Tel.: +351-967245248
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Liang Y, Zhang J, Qiu W, Chen B, Zhou Y, Chen X, Shentu Y, Zhang H, Bai Y, Chen C. Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis. Lupus 2021; 30:2248-2255. [PMID: 34923866 DOI: 10.1177/09612033211061482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.
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Affiliation(s)
- Yan Liang
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Ji Zhang
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Wenxian Qiu
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Bo Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Ying Zhou
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Xiaoqian Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Yangping Shentu
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Yongheng Bai
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chaosheng Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
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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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Lin Y, Cai J, Huang D, Zhou B, Luo Z, Yu S, Lu J. Effects of dexmedetomidine on the expression profile of tsRNAs in LPS-induced acute lung injury. J Clin Lab Anal 2021; 36:e24115. [PMID: 34811808 PMCID: PMC8761442 DOI: 10.1002/jcla.24115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Acute lung injury (ALI) is characterized by impaired alveolar function and excessive inflammation, which is commonly seen in clinical anesthesia and intensive care units. tRNA-derived small RNA (tsRNA) is a non-coding RNA that can be used as a potential disease diagnostic biomarker. The connection between ALI and tsRNA remains unknown. We aimed to explore the possible regulatory functions and mechanisms of tsRNAs in ALI treated with DEX. METHODS Firstly, we established the ALI model by LPS injection and explored the effect of dexmedetomidine (DEX) treatment on lung damage. Then, the lung tissues were obtained from the LPS and LPS + DEX group for small RNA sequencing. RESULTS We proved that DEX could ameliorate pulmonary injury, and decreased inflammation, pulmonary edema, and ferroptosis (MDA down-regulation and GPX4 up-regulation) in ALI. Furthermore, in the tsRNA expression profile, the top 10 down-regulated tsRNAs were tsRNA-1018, tsRNA-3045b, tsRNA-5021a, tsRNA-1020, tsRNA-5002b, tsRNA-3045b, tsRNA-1026, tsRNA-5004a, tsRNA-5005b and tsRNA-1009, and the top 10 up-regulated tsRNAs were tsRNA-3025b, tsRNA-3025a, tsRNA-5016b, tsRNA-3042b, tsRNA-3029b, tsRNA-3028b, tsRNA-5006a, tsRNA-3027b, tsRNA-3027a, and tsRNA-5009b. The enrichment analysis of GO terms and KEGG pathways pointed that target genes of DE-tsRNAs were mainly enriched in regulation of transcription-associated GO terms, NF-kappa B signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway. The RT-qPCR results of tsRNA-1020 and tsRNA-1018 were in accordance with small RNA sequencing data. CONCLUSION DEX affected the abnormal expression of tsRNAs in ALI. These aberrantly expressed tsRNAs and enriched physiological processes provide a scientific basis for the diagnosis and treatment of ALI.
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Affiliation(s)
- Yue Lin
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Junying Cai
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Dan Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Bin Zhou
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Zhenzhong Luo
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Shuchun Yu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Jun Lu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
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Zhou Y, Hu J, Liu L, Yan M, Zhang Q, Song X, Lin Y, Zhu D, Wei Y, Fu Z, Hu L, Chen Y, Li X. Gly-tRF enhances LCSC-like properties and promotes HCC cells migration by targeting NDFIP2. Cancer Cell Int 2021; 21:502. [PMID: 34537070 PMCID: PMC8449465 DOI: 10.1186/s12935-021-02102-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Background Accumulating evidence demonstrates that tRFs (tRNA-derived small RNA fragments) and tiRNAs (tRNA-derived stress-induced RNA), an emerging category of regulatory RNA molecules derived from transfer RNAs (tRNAs), are dysregulated in in various human cancer types and play crucial roles. However, their roles and mechanisms in hepatocellular carcinoma (HCC) and liver cancer stem cells (LCSCs) are still unknown. Methods The expression of glycine tRNA-derived fragment (Gly-tRF) was measured by qRT-PCR. Flow cytometric analysis and sphere formation assays were used to determine the properties of LCSCs. Transwell assays and scratch wound assays were performed to detect HCC cell migration. Western blotting was conducted to evaluate the abundance change of Epithelial-mesenchymal transition (EMT)-related proteins. Dual luciferase reporter assays and signalling pathway analysis were performed to explore the underlying mechanism of Gly-tRF functions. Results Gly-tRF was highly expressed in HCC cell lines and tumour tissues. Gly-tRF mimic increased the LCSC subpopulation proportion and LCSC-like cell properties. Gly-tRF mimic promoted HCC cell migration and EMT. Loss of Gly-tRF inhibited HCC cell migration and EMT. Mechanistically, Gly-tRF decreased the level of NDFIP2 mRNA by binding to the NDFIP2 mRNA 3′ UTR. Importantly, overexpression of NDFIP2 weakened the promotive effects of Gly-tRF on LCSC-like cell sphere formation and HCC cell migration. Signalling pathway analysis showed that Gly-tRF increased the abundance of phosphorylated AKT. Conclusions Gly-tRF enhances LCSC-like cell properties and promotes EMT by targeting NDFIP2 and activating the AKT signalling pathway. Gly-tRF plays tumor-promoting role in HCC and may lead to a potential therapeutic target for HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02102-8.
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Affiliation(s)
- Yongqiang Zhou
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Jinjing Hu
- Gansu Province Key Laboratory of Biotherapy and Regenerative Medicine, Lanzhou, 730000, China.,School of Life Science of Lanzhou University, Lanzhou University, Lanzhou, 730000, China
| | - Lu Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Mengchao Yan
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Qiyu Zhang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China.,Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Xiaojing Song
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China.,Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yan Lin
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Dan Zhu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Yongjian Wei
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Zongli Fu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Liming Hu
- School of Life Science of Lanzhou University, Lanzhou University, Lanzhou, 730000, China
| | - Yue Chen
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Xun Li
- The First Clinical Medical College of Lanzhou University, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China. .,Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730000, China. .,Gansu Province Key Laboratory of Biotherapy and Regenerative Medicine, Lanzhou, 730000, China.
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Li HM, Tan X, Zhang S, Yao J, Li HG. Transfer- or 'transmission'-RNA fragments? The roles of tsRNAs in the reproductive system. Mol Hum Reprod 2021; 27:6218776. [PMID: 33837423 DOI: 10.1093/molehr/gaab026] [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: 01/11/2021] [Revised: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
Transfer-RNAs (tRNAs) help ribosomes decode mRNAs and synthesize proteins; however, tRNA fragments produced under certain conditions, known as tRNA-derived small RNAs (tsRNAs), have been found to play important roles in pathophysiological processes. In the reproductive system, tsRNAs are abundant in gametes and embryos and at the maternal-fetal interface, as well as in microvesicles like epididymosomes, seminal plasma exosomes, and syncytiotrophoblast-derived extracellular vesicles. tsRNAs can affect gamete cell maturation, zygote activation, and early embryonic development. tsRNAs can transmit epigenetic information to later generations. In particular, exposure to environmental factors such as nutrition, isoproterenol, and poly(I:C) may allow tsRNAs to transfer information to the gametes or placenta to alter offspring phenotype. The underlying mechanisms of tsRNAs action include transposon silencing, translation regulation, and target mRNA degradation. Herein, we review the currently reported tsRNAs in the reproductive system, their validated functions, and potential roles. A better understanding of this field may help to provide useful recommendations or develop strategies to increase fertility and conception of healthy babies.
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Affiliation(s)
- Hui-Min Li
- Guilin Medical University, Guilin, P.R. China
| | - Xia Tan
- Center of Reproductive Medicine, Wuhan Union Hospital, Wuhan, P.R. China
| | - Shun Zhang
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Jun Yao
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Hong-Gang Li
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,Genetic Laboratory, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, P.R. China
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Kumar S, Gonzalez EA, Rameshwar P, Etchegaray JP. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12:E3657. [PMID: 33291485 PMCID: PMC7762117 DOI: 10.3390/cancers12123657] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that regulate gene expressions. NcRNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), circular RNAs (cRNAs) and piwi-interacting RNAs (piRNAs). This review focuses on two types of ncRNAs: microRNAs (miRNAs) or short interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs). We highlight the mechanisms by which miRNAs and lncRNAs impact the epigenome in the context of cancer. Both miRNAs and lncRNAs have the ability to interact with numerous epigenetic modifiers and transcription factors to influence gene expression. The aberrant expression of these ncRNAs is associated with the development and progression of tumors. The primary reason for their deregulated expression can be attributed to epigenetic alterations. Epigenetic alterations can cause the misregulation of ncRNAs. The experimental evidence indicated that most abnormally expressed ncRNAs impact cellular proliferation and apoptotic pathways, and such changes are cancer-dependent. In vitro and in vivo experiments show that, depending on the cancer type, either the upregulation or downregulation of ncRNAs can prevent the proliferation and progression of cancer. Therefore, a better understanding on how ncRNAs impact tumorigenesis could serve to develop new therapeutic treatments. Here, we review the involvement of ncRNAs in cancer epigenetics and highlight their use in clinical therapy.
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Affiliation(s)
- Subhasree Kumar
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Hematology/Oncology, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
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