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Zhu J, Tang W, Wu X, Mu M, Zhang Q, Zhao X. Tectorigenin improves metabolic dysfunction-associated steatohepatitis by down-regulating tRF-3040b and promoting mitophagy to inhibit pyroptosis pathway. Biochem Biophys Res Commun 2024; 720:150118. [PMID: 38776757 DOI: 10.1016/j.bbrc.2024.150118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/26/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Tectorigenin (TEC) as a plant extract has the advantage of low side effects on metabolic dysfunction-associated steatohepatitis (MASH) treatment. Our previous study have shown that tRNA-derived RNA fragments (tRFs) associated with autophagy and pyroptosis in MASH, but whether TEC can mitigate MASH through tRFs-mediated mitophagy is not fully understood. This study aims to investigate whether TEC relies on tRFs to adjust the crosstalk of hepatocyte mitophagy with pyroptosis in MASH. Immunofluorescence results of PINK1 and PRKN with MitoTracker Green-labeled mitochondria verified that TEC enhanced mitophagy. Additionally, TEC inhibited pyroptosis, as reflected by the level of GSDME, NLRP3, IL-1β, and IL-18 decreased after TEC treatment, while the effect of pyroptosis inhibition by TEC was abrogated by Pink1 silencing. We found that the upregulation expression of tRF-3040b caused by MASH was suppressed by TEC. The promotion of mitophagy and the suppression of pyroptosis induced by TEC were abrogated by tRF-3040b mimics. TEC reduced lipid deposition, inflammation, and pyroptosis, and promoted mitophagy in mice, but tRF-3040b agomir inhibited these effects. In summary, our findings provided that TEC significantly reduced the expression of tRF-3040b to enhance mitophagy, thereby inhibiting pyroptosis in MASH. We elucidated a powerful theoretical basis and provided safe and effective potential drugs for MASH with the prevention and treatment.
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Affiliation(s)
- Juanjuan Zhu
- Department of Infectious Diseases, The Affiliated Hospital of Guizhou Medical University, Guizhou, China.
| | | | - Xian Wu
- Department of Infectious Diseases, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Mao Mu
- Department of Infectious Diseases, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Quan Zhang
- Department of Infectious Diseases, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
| | - Xueke Zhao
- Department of Infectious Diseases, The Affiliated Hospital of Guizhou Medical University, Guizhou, China
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2
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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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3
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Lin H, Deng H, Jiang Z, Hua P, Hu S, Ao H, Zhong M, Liu M, Guo G. Microarray analysis of tRNA-derived small RNA (tsRNA) in LPS-challenged macrophages treated with metformin. Gene 2024; 913:148399. [PMID: 38518902 DOI: 10.1016/j.gene.2024.148399] [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: 10/19/2023] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Metformin, a widely used anti-diabetic drug, has demonstrated its efficacy in addressing various inflammatory conditions. tRNA-derived small RNA (tsRNA), a novel type of small non-coding RNA, exhibits diverse regulatory functions and holds promise as both a diagnostic biomarker and a therapeutic target for various diseases. The purpose of this study is to investigate whether the abundance of tsRNAs changed in LPS versus LPS + metformin-treated cells, utilizing microarray technology. Firstly, we established an in vitro lipopolysaccharide (LPS)-induced inflammation model using RAW264.7 macrophages and assessed the protective effects of metformin against inflammatory damage. Subsequently, we extracted total RNA from both LPS-treated and metformin + LPS-treated cell samples for microarray analysis to identify differentially abundant tsRNAs (DA-tsRNAs). Furthermore, we conducted bioinformatics analysis to predict target genes for validated DA-tsRNAs and explore the biological functions and signaling pathways associated with DA-tsRNAs. Notably, metformin was found to inhibit the inflammatory response in RAW264.7 macrophages. The microarray results revealed a total of 247 DA-tsRNAs, with 58 upregulated and 189 downregulated tsRNAs in the Met + LPS group compared to the LPS group. The tsRNA-mRNA network was visualized, shedding light on potential interactions. The results of bioinformatics analysis suggested that these potential targets of specific tsRNAs were mainly related to inflammation and immunity. Our study provides compelling evidence that metformin exerts anti-inflammatory effects and modulates the abundance of tsRNAs in LPS-treated RAW264.7 macrophages. These findings establish a valuable foundation for using tsRNAs as potential biomarkers for metformin in the treatment of inflammatory conditions.
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Affiliation(s)
- Huan Lin
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Hongao Deng
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhengying Jiang
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Peng Hua
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Shiqiang Hu
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Haiyong Ao
- Jiangxi Key Laboratory of Nanobiomaterials & School of Materials Science and Engineering, East China Jiaotong University, Nanchang, China
| | - Meiling Zhong
- School of Materials Science and Engineering, East China Jiaotong University, Nanchang, China
| | - Mingzhuo Liu
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
| | - Guanghua Guo
- Medical center of Burn plastic and wound repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
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4
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Lan S, Liu S, Wang K, Chen W, Zheng D, Zhuang Y, Zhang S. tRNA-derived RNA fragment, tRF-18-8R6546D2, promotes pancreatic adenocarcinoma progression by directly targeting ASCL2. Gene 2024:148739. [PMID: 38955307 DOI: 10.1016/j.gene.2024.148739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/11/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
Pancreatic adenocarcinoma (PAAD) is a life-threatening cancer. Exploring new diagnosis and treatment targets helps improve its prognosis. tRNA-derived small non-coding RNAs (tsRNAs) are a novel type of gene expression regulators and their dysregulation is closely related to many human cancers. Yet the expression and functions of tsRNAs in PAAD are not well understood. Our study used RNA sequencing to identify tsRNA expression profiles in PAAD cells cultured in no or high glucose media and found tRF-18-8R6546D2 was an uncharacterized tsRNA, which has significantly high expression in PAAD cells and tissues. Clinically, tRF-18-8R6546D2 is linked to poor prognosis in PAAD patients and can be used to distinguish them from healthy populations. Functionally, in vitro and vivo, tRF-18-8R6546D2 over-expression promoted PAAD cell proliferation, migration and invasion, inhibited apoptosis, whereas tRF-18-8R6546D2 knock-down showed opposite effects. Mechanistically, tRF-18-8R6546D2 promoted PAAD malignancy partly by directly silencing ASCL2 and further regulating its downstream genes such as MYC and CASP3. These findings show that tRF-18-8R6546D2 is a novel oncogenic factor and can be a promising diagnostic or prognostic biomarker and therapeutic target for PAAD.
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Affiliation(s)
- Sihua Lan
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China; Guangdong Provincial Key Laboratory of Epigenetics and Gene Regulation of Malignant Tumors, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510000, China
| | - Sixue Liu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Ke Wang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Wenying Chen
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Dandan Zheng
- Doctor of excellence program, First Affiliated Hospital of Jilin University, Changchun 130000, China
| | - Yanyan Zhuang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China; Guangdong Provincial Key Laboratory of Epigenetics and Gene Regulation of Malignant Tumors, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510000, China.
| | - Shineng Zhang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China; Guangdong Provincial Key Laboratory of Epigenetics and Gene Regulation of Malignant Tumors, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510000, China.
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5
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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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6
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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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7
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Ying X, Hu W, Huang Y, Lv Y, Ji D, Chen C, Yang B, Zhang C, Liang Y, Zhang H, Liu M, Yuan G, Wu W, Ji W. A Novel tsRNA, m 7G-3' tiRNA Lys TTT, Promotes Bladder Cancer Malignancy Via Regulating ANXA2 Phosphorylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400115. [PMID: 38894581 DOI: 10.1002/advs.202400115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/29/2024] [Indexed: 06/21/2024]
Abstract
Emerging evidence indicates that transfer RNA (tRNA)-derived small RNAs (tsRNAs), originated from tRNA with high abundance RNA modifications, play an important role in many complex physiological and pathological processes. However, the biological functions and regulatory mechanisms of modified tsRNAs in cancer remain poorly understood. Here, it is screened for and confirmed the presence of a novel m7G-modified tsRNA, m7G-3'-tiRNA LysTTT (mtiRL), in a variety of chemical carcinogenesis models by combining small RNA sequencing with an m7G small RNA-modified chip. Moreover, it is found that mtiRL, catalyzed by the tRNA m7G-modifying enzyme mettl1, promotes bladder cancer (BC) malignancy in vitro and in vivo. Mechanistically, mtiRL is found to specifically bind the oncoprotein Annexin A2 (ANXA2) to promote its Tyr24 phosphorylation by enhancing the interactions between ANXA2 and Yes proto-oncogene 1 (Yes1), leading to ANXA2 activation and increased p-ANXA2-Y24 nuclear localization in BC cells. Together, these findings define a critical role for mtiRL and suggest that targeting this novel m7G-modified tsRNA can be an efficient way for to treat BC.
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Affiliation(s)
- Xiaoling Ying
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510220, China
- Guangdong Provincial Key Laboratory of Urology, Guangzhou, 510230, China
| | - Wenyu Hu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yapeng Huang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yifan Lv
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Ding Ji
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, Guangzhou, 510080, China
| | - Cong Chen
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Baotong Yang
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510220, China
| | - Chengcheng Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yaomin Liang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Haiqing Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Mingrui Liu
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Gang Yuan
- Private Medical Service & Healthcare Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wenqi Wu
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510220, China
- Guangdong Provincial Key Laboratory of Urology, Guangzhou, 510230, China
| | - Weidong Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
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8
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Noble M, Chatterjee A, Sekaran T, Schwarzl T, Hentze MW. Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase. RNA (NEW YORK, N.Y.) 2024; 30:839-853. [PMID: 38609156 PMCID: PMC11182015 DOI: 10.1261/rna.079925.123] [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: 12/11/2023] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Several enzymes of intermediary metabolism have been identified to bind RNA in cells, with potential consequences for the bound RNAs and/or the enzyme. In this study, we investigate the RNA-binding activity of the mitochondrial enzyme malate dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and the malate-aspartate shuttle. We confirmed in cellulo RNA binding of MDH2 using orthogonal biochemical assays and performed enhanced cross-linking and immunoprecipitation (eCLIP) to identify the cellular RNAs associated with endogenous MDH2. Surprisingly, MDH2 preferentially binds cytosolic over mitochondrial RNAs, although the latter are abundant in the milieu of the mature protein. Subcellular fractionation followed by RNA-binding assays revealed that MDH2-RNA interactions occur predominantly outside of mitochondria. We also found that a cytosolically retained N-terminal deletion mutant of MDH2 is competent to bind RNA, indicating that mitochondrial targeting is dispensable for MDH2-RNA interactions. MDH2 RNA binding increased when cellular NAD+ levels (MDH2's cofactor) were pharmacologically diminished, suggesting that the metabolic state of cells affects RNA binding. Taken together, our data implicate an as yet unidentified function of MDH2-binding RNA in the cytosol.
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Affiliation(s)
- Michelle Noble
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | | | - Thileepan Sekaran
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
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Han XY, Kong LJ, Li D, Tong M, Li XM, Zhao C, Jiang Q, Yan B. Targeting endothelial glycolytic reprogramming by tsRNA-1599 for ocular anti-angiogenesis therapy. Theranostics 2024; 14:3509-3525. [PMID: 38948065 PMCID: PMC11209708 DOI: 10.7150/thno.96946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Rationale: Current treatments for ocular angiogenesis primarily focus on blocking the activity of vascular endothelial growth factor (VEGF), but unfavorable side effects and unsatisfactory efficacy remain issues. The identification of novel targets for anti-angiogenic treatment is still needed. Methods: We investigated the role of tsRNA-1599 in ocular angiogenesis using endothelial cells, a streptozotocin (STZ)-induced diabetic model, a laser-induced choroidal neovascularization model, and an oxygen-induced retinopathy model. CCK-8 assays, EdU assays, transwell assays, and matrigel assays were performed to assess the role of tsRNA-1599 in endothelial cells. Retinal digestion assays, Isolectin B4 (IB4) staining, and choroidal sprouting assays were conducted to evaluate the role of tsRNA-1599 in ocular angiogenesis. Transcriptomic analysis, metabolic analysis, RNA pull-down assays, and mass spectrometry were utilized to elucidate the mechanism underlying angiogenic effects mediated by tsRNA-1599. Results: tsRNA-1599 expression was up-regulated in experimental ocular angiogenesis models and endothelial cells in response to angiogenic stress. Silencing of tsRNA-1599 suppressed angiogenic effects in endothelial cells in vitro and inhibited pathological ocular angiogenesis in vivo. Mechanistically, tsRNA-1599 exhibited little effect on VEGF signaling but could cause reduced glycolysis and NAD+/NADH production in endothelial cells by regulating the expression of HK2 gene through interacting with YBX1, thus affecting endothelial effects. Conclusions: Targeting glycolytic reprogramming of endothelial cells by a tRNA-derived small RNA represents an exploitable therapeutic approach for ocular neovascular diseases.
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Affiliation(s)
- Xiao-yan Han
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Ling-jie Kong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Duo Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing 210000, China
| | - Ming Tong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Xiu-miao Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing 210000, China
| | - Chen Zhao
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Qin Jiang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing 210000, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing 210000, China
| | - Biao Yan
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
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10
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Zhang S, Gu Y, Ge J, Xie Y, Yu X, Wu X, Sun D, Zhang X, Guo J, Guo J. tRF-33-P4R8YP9LON4VDP inhibits gastric cancer progression via modulating STAT3 signaling pathway in an AGO2-dependent manner. Oncogene 2024:10.1038/s41388-024-03062-9. [PMID: 38783100 DOI: 10.1038/s41388-024-03062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
It has been demonstrated that tRNA-derived small RNAs (tsRNAs) perform essential functions in the pathophysiology of cancer. In this study, we focused on the possible mechanisms of tRF-33-P4R8YP9LON4VDP (tRF-33) underlying the development of gastric malignancy. In total, 454 tissue samples with different gastric mucosal lesions were collected. The tRF-33 expression level in different cohorts was determined, and its value for diagnostic efficiency and prognosis evaluation were assessed. Cell proliferation assays, Transwell assay, flow cytometry, and xenotransplantation model were used to evaluate its effect on gastric cancer cells. The molecular mechanism was verified by fluorescence in situ hybridization, dual luciferase assay, Western blot, and RNA binding protein immunoprecipitation. The results showed that the expression of tRF-33 exhibited a gradual modification from normal control samples to gastritis tissues, early and latent stage of gastric cancer tissues. Consequently, tRF-33 holds significant potential as a predictive and diagnostic biomarker for gastric malignancy. Over-expression of tRF-33 inhibited gastric cancer cell progression and metastatic viability, and induced cell apoptosis. Tumorigenicity in nude mice showed the suppressive characteristics of tRF-33. Mechanistic investigation revealed that tRF-33 exerted silencing on STAT3 mRNA via binding to AGO2. In conclusion, tRF-33 exhibited values in diagnosing gastric cancer and evaluating its prognosis, and suppressed tumor cell viability by inhibiting STAT3 signaling pathway. The schematic mechanisms underlying tRF-33 regulating gastric cancer occurrence. tRF-33 binds to AGO2 proteins and then negatively regulates STAT3 expression through targeting its 3'UTR. The downregulated expression of STAT3 results in the decrease of STAT3 and p-STAT3 and further blocks the transcription of the downstream genes and finally inhibits the gastric cancer occurrence. MMP-9, matrix metalloproteinase-9; Bcl-2, B-cell lymphoma-2; STAT3, signal transducer and activator of transcription 3; UTR, untranslated region.
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Affiliation(s)
- Shuangshuang Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Yeqi Gu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jiaxin Ge
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, China.
- Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
| | - Yaoyao Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Xiuchong Yu
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Xinxin Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Desen Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Xinjun Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, China
- Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China
| | - Jie Guo
- School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Junming Guo
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, 315211, China.
- Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
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Li X, Li Y, Yuan J, Zhang W, Xu T, Jing R, Ju S. Serum tRF-33-RZYQHQ9M739P0J as a novel biomarker for auxiliary diagnosis and disease course monitoring of hepatocellular carcinoma. Heliyon 2024; 10:e30084. [PMID: 38707447 PMCID: PMC11068615 DOI: 10.1016/j.heliyon.2024.e30084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
Objective In most cases, patients with hepatocellular carcinoma (HCC) develop advanced disease when diagnosed. Finding new molecules to combine with traditional biomarkers is crucial for HCC early diagnosis. In cancer development, tRNA-derived small RNAs (tsRNA) play a crucial role. Here, we aimed to identify a novel biomarker among tsRNAs that can facilitate HCC diagnosis and monitor its prognosis. Methods We screened candidate tsRNAs in 3 pairs of HCC and adjacent tissues through high-throughput sequencing. tRF-33-RZYQQ9M739P0J was screened in tissues, sera, and cells through quantitative real-time polymerase chain reaction (qRT-PCR) for further analysis. tRF-33-RZYQHQ9M739P0J was characterized using agarose gel electrophoresis, Sanger sequencing, and nuclear and cytoplasmic RNA isolation. Experiments at room temperature and repeated freeze-thaw cycles were conducted to evaluate the detection performance of tRF-33-RZYQHQ9M739P0J. We measured the levels of differential expression of tRF-33-RZYQHQ9M739P0J in sera using qRT-PCR. We applied the chi-square test to evaluate the correlation between tRF-33-RZYQHQ9M739P0J expression levels and clinicopathological features, and assessed its prognostic value by plotting Kaplan-Meier curves. The diagnostic efficacy of tRF-33-RZYQHQ9M739P0J was evaluated using the receiver operating characteristic (ROC) curve. Finally, the downstream genes related to tRF-33-RZYQHQ9M739P0J were explored through bioinformatics prediction. Results tRF-33-RZYQHQ9M739P0J was highly expressed in HCC tissues and sera, and its expression was correlated with metastasis, TNM stage, BCLC stage, and vein invasion. Expression of tRF-33-RZYQHQ9M739P0J were decreased after surgery in patients with HCC. High serum tRF-33-RZYQHQ9M739P0J levels are associated with low survival rates, and they can predict survival times in patients with HCC according to the Kaplan-Meier analysis. Combining tRF-33-RZYQHQ9M739P0J with serum alpha-fetoprotein and prothrombin induced by vitamin K absence II can improve the diagnostic efficiency of HCC, suggesting its potential as a biomarker for HCC. Conclusion tRF-33-RZYQHQ9M739P0J may not only be a promising non-invasive marker for early diagnosis, but also a predictor of liver cancer progression.
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Affiliation(s)
- Xian Li
- Medical School of Nantong University, Nantong, Jiangsu, 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong, Jiangsu, 226001, China
| | - Jie Yuan
- Medical School of Nantong University, Nantong, Jiangsu, 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, China
| | - Weiwei Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, China
| | - Tianxin Xu
- Medical School of Nantong University, Nantong, Jiangsu, 226001, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226001, China
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Huang L, Bai D, Su X. Altered expression of transfer RNAs and their possible roles in brain white matter injury. Neuroreport 2024; 35:536-541. [PMID: 38597261 DOI: 10.1097/wnr.0000000000002036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Transfer RNAs (tRNAs) can regulate cell behavior and are associated with neurological disorders. Here, we aimed to investigate the expression levels of tRNAs in oligodendrocyte precursor cells (OPCs) and their possible roles in the regulation of brain white matter injury (WMI). Newborn Sprague-Dawley rats (postnatal day 5) were used to establish a model that mimicked neonatal brain WMI. RNA-array analysis was performed to examine the expression of tRNAs in OPCs. psRNAtarget software was used to predict target mRNAs of significantly altered tRNAs. Gene ontology (GO) and KEGG were used to analyze the pathways for target mRNAs. Eighty-nine tRNAs were changed after WMI (fold change absolute ≥1.5, P < 0.01), with 31 downregulated and 58 upregulated. Among them, three significantly changed tRNAs were identified, with two being significantly increased (chr10.trna1314-ProTGG and chr2.trna2771-ProAGG) and one significantly decreased (chr10.trna11264-GlyTCC). Further, target mRNA prediction and GO/KEGG pathway analysis indicated that the target mRNAs of these tRNAs are mainly involved in G-protein coupled receptor signaling pathways and beta-alanine metabolism, which are both related to myelin formation. In summary, the expression of tRNAs in OPCs was significantly altered after brain WMI, suggesting that tRNAs may play important roles in regulating WMI. This improves the knowledge about WMI pathophysiology and may provide novel treatment targets for WMI.
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Affiliation(s)
- Lingyi Huang
- Department of Orthodontics, West China College of Stomatology/State Key Laboratory of Oral Diseases, Sichuan University
| | - Ding Bai
- Department of Orthodontics, West China College of Stomatology/State Key Laboratory of Oral Diseases, Sichuan University
| | - Xiaojuan Su
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
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13
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Wan X, Shi W, Ma L, Wang L, Zheng R, He J, Wang Y, Li X, Zha X, Wang J, Xu L. A 3'-pre-tRNA-derived small RNA tRF-1-Ser regulated by 25(OH)D promotes proliferation and stemness by inhibiting the function of MBNL1 in breast cancer. Clin Transl Med 2024; 14:e1681. [PMID: 38725048 PMCID: PMC11082093 DOI: 10.1002/ctm2.1681] [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: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND We explored the potential novel anticancer mechanisms of 25-hydroxyvitamin D (25(OH)D), a vitamin D metabolite with antitumour effects in breast cancer. It is stable in serum and is used to assess vitamin D levels in clinical practice. Transfer RNA-derived small RNAs are small noncoding RNAs that generate various distinct biological functions, but more research is needed on their role in breast cancer. METHODS Small RNA microarrays were used to explore the novel regulatory mechanism of 25(OH)D. High-throughput RNA-sequencing technology was used to detect transcriptome changes after 25(OH)D treatment and tRF-1-Ser knockdown. RNA pull-down and high-performance liquid chromatography-mass spectrometry/mass spectrometry were used to explore the proteins bound to tRF-1-Ser. In vitro and in vivo functional experiments were conducted to assess the influence of 25(OH)D and tRF-1-Ser on breast cancer. Semi-quantitative PCR was performed to detect alternative splicing events. Western blot assay and qPCR were used to assess protein and mRNA expression. RESULTS The expression of tRF-1-Ser is negatively regulated by 25(OH)D. In our breast cancer (BRCA) clinical samples, we found that the expression of tRF-1-Ser was higher in cancer tissues than in paired normal tissues, and was significantly associated with tumour invasion. Moreover, tRF-1-Ser inhibits the function of MBNL1 by hindering its nuclear translocation. Functional experiments and transcriptome data revealed that the downregulation of tRF-1-Ser plays a vital role in the anticancer effect of 25(OH)D. CONCLUSIONS In brief, our research revealed a novel anticancer mechanism of 25(OH)D, unveiled the vital function of tRF-1-Ser in BRCA progression, and suggested that tRF-1-Ser could emerge as a new therapeutic target for BRCA.
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Affiliation(s)
- Xinyu Wan
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Wenjie Shi
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lingjun Ma
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lexin Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ran Zheng
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinzhi He
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ye Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xuan Li
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaoming Zha
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jue Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lu Xu
- Department of NutritionThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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Qiao YY, Ji JL, Hou WL, Qu GT, Li SW, Li XY, Jin R, Li YF, Shi HM, Zhang AQ. tRF3-IleAAT reduced extracellular matrix synthesis in diabetic kidney disease mice by targeting ZNF281 and inhibiting ferroptosis. Acta Pharmacol Sin 2024; 45:1032-1043. [PMID: 38286833 PMCID: PMC11053026 DOI: 10.1038/s41401-024-01228-5] [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: 08/26/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
It is well established that the synthesis of extracellular matrix (ECM) in mesangial cells is a major determinant of diabetic kidney disease (DKD). Elucidating the major players in ECM synthesis may be helpful to provide promising candidates for protecting against DKD progression. tRF3-IleAAT is a tRNA-derived fragment (tRF) produced by nucleases at tRNA-specific sites, which is differentially expressed in the sera of patients with diabetes mellitus and DKD. In this study we investigated the potential roles of tRFs in DKD. Db/db mice at 12 weeks were adapted as a DKD model. The mice displayed marked renal dysfunction accompanied by significantly reduced expression of tRF3-IleAAT and increased ferroptosis and ECM synthesis in the kidney tissues. The reduced expression of tRF3-IleAAT was also observed in high glucose-treated mouse glomerular mesangial cells. We administered ferrostatin-1 (1 mg/kg, once every two days, i.p.) to the mice from the age of 12 weeks for 8 weeks, and found that inhibition of the onset of ferroptosis significantly improved renal function, attenuated renal fibrosis and reduced collagen deposition. Overexpression of tRF3-IleAAT by a single injection of AAV carrying tRF3-IleAAT via caudal vein significantly inhibited ferroptosis and ECM synthesis in DKD model mice. Furthermore, we found that the expression of zinc finger protein 281 (ZNF281), a downstream target gene of tRF3-IleAAT, was significantly elevated in DKD models but negatively regulated by tRF3-IleAAT. In high glucose-treated mesangial cells, knockdown of ZNF281 exerted an inhibitory effect on ferroptosis and ECM synthesis. We demonstrated the targeted binding of tRF3-IleAAT to the 3'UTR of ZNF281. In conclusion, tRF3-IleAAT inhibits ferroptosis by targeting ZNF281, resulting in the mitigation of ECM synthesis in DKD models, suggesting that tRF3-IleAAT may be an attractive therapeutic target for DKD.
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Affiliation(s)
- Yun-Yang Qiao
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China
| | - Jia-Ling Ji
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China
| | - Wei-Ling Hou
- Department of Science and Education, the Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211199, China
| | - Gao-Ting Qu
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Shan-Wen Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Xing-Yue Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Ran Jin
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Yin-Fang Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Hui-Min Shi
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China.
| | - Ai-Qing Zhang
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, 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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16
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Strømme O, Heck KA, Brede G, Lindholm HT, Otterlei M, Arum CJ. tRNA-Derived Fragments as Biomarkers in Bladder Cancer. Cancers (Basel) 2024; 16:1588. [PMID: 38672670 PMCID: PMC11049458 DOI: 10.3390/cancers16081588] [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: 03/29/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Bladder cancer (BC) diagnosis is reliant on cystoscopy, an invasive procedure associated with urinary tract infections. This has sparked interest in identifying noninvasive biomarkers in body fluids such as blood and urine. A source of biomarkers in these biofluids are extracellular vesicles (EVs), nanosized vesicles that contain a wide array of molecular cargo, including small noncoding RNA such as transfer RNA-derived fragments (tRF) and microRNA. Here, we performed small-RNA next-generation sequencing from EVs from urine and serum, as well as from serum supernatant. RNA was extracted from 15 non-cancer patients (NCPs) with benign findings in cystoscopy and 41 patients with non-muscle invasive BC. Urine and serum were collected before transurethral resection of bladder tumors (TUR-b) and at routine post-surgery check-ups. We compared levels of tRFs in pre-surgery samples to samples from NCPs and post-surgery check-ups. To further verify our findings, samples from 10 patients with stage T1 disease were resequenced. When comparing tRF expression in urine EVs between T1 stage BC patients and NCPs, 14 differentially expressed tRFs (DEtRFs) were identified. In serum supernatant, six DEtRFs were identified among stage T1 patients when comparing pre-surgery to post-surgery samples and four DEtRFs were found when comparing pre-surgery samples to NCPs. By performing a blast search, we found that sequences of DEtRFs aligned with genomic sequences pertaining to processes relevant to cancer development, such as enhancers, regulatory elements and CpG islands. Our findings display a number of tRFs that may hold potential as biomarkers for the diagnosis and recurrence-free survival of BC.
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Affiliation(s)
- Olaf Strømme
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Kathleen A. Heck
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Gaute Brede
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Håvard T. Lindholm
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
| | - Carl-Jørgen Arum
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7034 Trondheim, Norway; (K.A.H.); (G.B.); (H.T.L.); (M.O.); (C.-J.A.)
- Department of Urology, St. Olav’s University Hospital, 7030 Trondheim, Norway
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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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Čáp M, Palková Z. Non-Coding RNAs: Regulators of Stress, Ageing, and Developmental Decisions in Yeast? Cells 2024; 13:599. [PMID: 38607038 PMCID: PMC11012152 DOI: 10.3390/cells13070599] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must change their properties in order to adapt to a constantly changing environment. Most of the cellular sensing and regulatory mechanisms described so far are based on proteins that serve as sensors, signal transducers, and effectors of signalling pathways, resulting in altered cell physiology. In recent years, however, remarkable examples of the critical role of non-coding RNAs in some of these regulatory pathways have been described in various organisms. In this review, we focus on all classes of non-coding RNAs that play regulatory roles during stress response, starvation, and ageing in different yeast species as well as in structured yeast populations. Such regulation can occur, for example, by modulating the amount and functional state of tRNAs, rRNAs, or snRNAs that are directly involved in the processes of translation and splicing. In addition, long non-coding RNAs and microRNA-like molecules are bona fide regulators of the expression of their target genes. Non-coding RNAs thus represent an additional level of cellular regulation that is gradually being uncovered.
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Affiliation(s)
- Michal Čáp
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 128 00 Prague, Czech Republic
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Yu X, Bu C, Yang X, Jiang W, He X, Sun R, Guo H, Shang L, Ou C. Exosomal non-coding RNAs in colorectal cancer metastasis. Clin Chim Acta 2024; 556:117849. [PMID: 38417779 DOI: 10.1016/j.cca.2024.117849] [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: 06/08/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.
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Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chiwen Bu
- Department of General Surgery, People's Hospital of Guanyun County, Lianyungang 222200, Jiangsu, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wenying Jiang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of Blood Transfusion, Affiliated Hospital of North Sichuan Medical College, Xichang 637000, Sichuan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Li Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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20
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Zhao Y, Wang K, Zhao C, Liu N, Wang Z, Yang W, Cheng Z, Zhou L, Wang K. The function of tRNA-derived small RNAs in cardiovascular diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102114. [PMID: 38314096 PMCID: PMC10835008 DOI: 10.1016/j.omtn.2024.102114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
tRNA-derived small RNAs (tsRNAs) constitute a subgroup of small noncoding RNAs (ncRNAs) originating from tRNA molecules. Their rich content, evolutionary conservatism, high stability, and widespread existence makes them significant in disease research. These characteristics have positioned tsRNAs as key players in various physiological and pathological processes. tsRNA actively participates in regulating many cellular processes, such as cell death, proliferation, and metabolism. tsRNAs could be promising diagnostic markers for cardiovascular diseases (CVDs). tsRNAs have been identified in serums, suggesting their utility as early indicators for the diagnosis of CVDs. Moreover, the regulatory roles of tsRNAs in CVDs make them promising targets for therapeutic intervention. This review provides a succinct overview of the characteristics, classification, and regulatory functions of tsRNAs in the context of CVDs. By shedding light on the intricate roles of tsRNAs, this knowledge could pave the way for the development of innovative diagnostic tools and therapeutic strategies for CVDs.
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Affiliation(s)
- Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Chun Zhao
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Ning Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zhihong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Wenting Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zewei Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Luyu Zhou
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
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21
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Huang T, Zhao Y, Jiang G, Yang Z. tsRNA: A Promising Biomarker in Breast Cancer. J Cancer 2024; 15:2613-2626. [PMID: 38577588 PMCID: PMC10988313 DOI: 10.7150/jca.93531] [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: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are a novel class of non-coding small RNAs, generated from specific cleavage sites of tRNA or pre-tRNA. tsRNAs can directly participate in RNA silencing, transcription, translation, and other processes. Their dysregulation is closely related to the occurrence and development of various cancers. Breast cancer is one of the most common and fastest-growing malignant tumors in humans. tsRNAs have been found to be dysregulated in breast cancer, serving as a new target for exploring the pathogenesis of breast cancer. They are also considered new tumor markers, providing a basis for diagnosis and treatment. This article reviews the generation, classification, mechanism of action, function of tsRNAs, and their biological effects and related mechanisms in breast cancer, in the hope of providing a new direction for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Ting Huang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yuexin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Guoqin Jiang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zhixue Yang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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22
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Cabrelle C, Giorgi FM, Mercatelli D. Quantitative and qualitative detection of tRNAs, tRNA halves and tRFs in human cancer samples: Molecular grounds for biomarker development and clinical perspectives. Gene 2024; 898:148097. [PMID: 38128792 DOI: 10.1016/j.gene.2023.148097] [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: 07/29/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs playing a central role during protein synthesis. Besides translation, growing evidence suggests that in many contexts, precursor or mature tRNAs can also be processed into smaller fragments playing many non-canonical regulatory roles in different biological pathways with oncogenic relevance. Depending on the source, these molecules can be classified as tRNA halves (also known as tiRNAs) or tRNA-derived fragments (tRFs), and furtherly divided into 5'-tRNA and 3'-tRNA halves, or tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, respectively. Unlike DNA and mRNA, high-throughput sequencing of tRNAs is challenging, because of technical limitations of currently developed sequencing methods. In recent years, different sequencing approaches have been proposed allowing the quantification and identification of an increasing number of tRNA fragments with critical functions in distinct physiological and pathophysiological processes. In the present review, we discussed pros and cons of recent advances in different sequencing methods, also introducing the expanding repertoire of bioinformatics tool and resources specifically focused on tRNA research and discussing current issues in the study of these small RNA molecules. Furthermore, we discussed the potential value of tRNA fragments as diagnostic and prognostic biomarkers for different types of cancers.
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Affiliation(s)
- Chiara Cabrelle
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
| | | | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.
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23
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Tan L, Wu X, Tang Z, Chen H, Cao W, Wen C, Zou G, Zou H. The tsRNAs (tRFdb-3013a/b) serve as novel biomarkers for colon adenocarcinomas. Aging (Albany NY) 2024; 16:4299-4326. [PMID: 38451187 PMCID: PMC10968714 DOI: 10.18632/aging.205590] [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: 07/13/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024]
Abstract
The tsRNAs (tRNA-derived small RNAs) are a novel class of small non-coding RNAs derived from transfer-RNAs. Colon adenocarcinoma (COAD) is the most malignant intestinal tumor. This study focused on the identification and characterization of tsRNA biomarkers in colon adenocarcinomas. Data processing and bioinformatic analyses were performed with the packages of R and Python software. The cell proliferation, migration and invasion abilities were determined by CCK-8 and transwell assays. Luciferase reporter assay was used to test the binding of tsRNA with its target genes. With computational methods, we identified the tRNA fragments profiles within COAD datasets, and discriminated forty-two differentially expressed tsRNAs between paired colon adenocarcinomas and non-tumor controls. Among the fragments derived from the 3' end of tRNA-His-GUG (a histidyl-transfer-RNA), tRFdb-3013a and tRFdb-3013b (tRFdb-3013a/b) were notably decreased in colon and rectum adenocarcinomas, especially, tRFdb-3013a/b might tend to be down-regulated in patients with lymphatic or vascular invasion present. The clinical survival of colorectal adenocarcinoma patients with low tRFdb-3013a/b expression was significantly worse than that of high expression patients. In colon adenocarcinoma cells, tRFdb-3013a could have inhibited cell proliferations, and reduced cell migration and invasion abilities. The enrichment analyses showed that most of tRFdb-3013a correlated-genes were enriched in the extracellular matrix associated GO terms, phagosome pathway, and a GSEA molecular signature pathway. Additionally, the 3'UTR of ST3GAL1 mRNA was predicted to contain the binding site of tRFdb-3013a/b, tRFdb-3013a/b might directly target and regulate ST3GAL1 expression in colon adenocarcinomas. These results suggested that tRFdb-3013a/b might serve as novel biomarkers for diagnosis and prognosis of colon adenocarcinomas, and act a key player in the progression of colon adenocarcinomas.
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Affiliation(s)
- Lihong Tan
- Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Xiaoling Wu
- Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Zhurong Tang
- Chongqing Medical University, Chongqing 400016, China
| | - Huan Chen
- Yueyang Hospital of Traditional Chinese Medicine, Yueyang 414000, China
- Chongqing Medical University, Chongqing 400016, China
| | - Weiguo Cao
- Chongqing Medical University, Chongqing 400016, China
| | - Chunjie Wen
- Chongqing Medical University, Chongqing 400016, China
| | - Guojun Zou
- Yueyang Hospital of Traditional Chinese Medicine, Yueyang 414000, China
| | - Hecun Zou
- Chongqing Medical University, Chongqing 400016, China
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24
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Fu B, Lou Y, Lu X, Wu Z, Ni J, Jin C, Wu P, Xu C. tRF-1:30-Gly-CCC-3 inhibits thyroid cancer via binding to PC and modulating metabolic reprogramming. Life Sci Alliance 2024; 7:e202302285. [PMID: 38081642 PMCID: PMC10713435 DOI: 10.26508/lsa.202302285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
tRFs and tiRNAs (tRNA-derived fragments) are an emerging class of small noncoding RNAs produced by the precise shearing of tRNAs in response to specific stimuli. They have been reported to regulate the pathological processes of numerous human cancers. However, the biofunction of tRFs and tiRNAs in the development and progression of papillary thyroid cancer (PTC) has not been reported yet. In this study, we aimed to explore the biological roles of tRFs and tiRNAs in PTC and discovered that a novel 5'tRNA-derived fragment called tRF-1:30-Gly-CCC-3 (tRF-30) was markedly down-regulated in PTC tissues and cell lines. Functionally, tRF-30 inhibited the proliferation and invasion of PTC cells. Mechanistically, tRF-30 directly bound to the biotin-dependent enzyme pyruvate carboxylase (PC), downregulated its protein level, interfered with the TCA cycle intermediate anaplerosis, and thus affected metabolic reprogramming and PTC progression. These findings revealed a novel regulatory mechanism for tRFs and a potential therapeutic target for PTC.
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Affiliation(s)
- Bifei Fu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - YuMing Lou
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaofeng Lu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Zhaolin Wu
- Department of Anaesthesiology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Junjie Ni
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Cong Jin
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Pu Wu
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Chaoyang Xu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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25
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La Ferlita A, Alaimo S, Nigita G, Distefano R, Beane JD, Tsichlis PN, Ferro A, Croce CM, Pulvirenti A. tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer. iScience 2024; 27:108810. [PMID: 38303722 PMCID: PMC10831894 DOI: 10.1016/j.isci.2024.108810] [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: 04/28/2023] [Revised: 08/02/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
tRNA-derived ncRNAs are a heterogeneous class of non-coding RNAs recently proposed to be active regulators of gene expression and be involved in many diseases, including cancer. Consequently, several online resources on tRNA-derived ncRNAs have been released. Although interesting, such resources present only basic features and do not adequately exploit the wealth of knowledge available about tRNA-derived ncRNAs. Therefore, we introduce tRFUniverse, a novel online resource for the analysis of tRNA-derived ncRNAs in human cancer. tRFUniverse presents an extensive collection of classes of tRNA-derived ncRNAs analyzed across all the TCGA and TARGET tumor cohorts, NCI-60 cell lines, and biological fluids. Moreover, public AGO CLASH/CLIP-Seq data were analyzed to identify the molecular interactions between tRNA-derived ncRNAs and other transcripts. Importantly, tRFUniverse combines in a single resource a comprehensive set of features that we believe may be helpful to investigate the involvement of tRNA-derived ncRNAs in cancer biology.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Joal D. Beane
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
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26
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Ng N, Gibriel HAY, Halang L, Jirström E, Ioana JA, Burke M, Byrne MM, Prehn JHM. tRNA-derived fragments are altered in diabetes. Diabet Med 2024; 41:e15258. [PMID: 37935454 DOI: 10.1111/dme.15258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023]
Abstract
AIMS Maternally inherited diabetes and deafness (MIDD) is a rare form of adult-onset diabetes that can be difficult to diagnose due to its variable clinical phenotype. Transfer RNA-derived small fragments are a novel, emerging class of small non-coding RNAs (sncRNAs) that have significant potential as serum biomarkers due to their stress-induced generation, abundance, stability and ease of detection. METHODS We investigated the levels of tiRNA 5'ValCAC (alone and in combination with miR-23b-3p) identified from small RNA sequencing studies in serum samples from healthy controls, type 1 diabetes, type 2 diabetes and MIDD subjects. RESULTS Serum levels of 5'ValCAC were reduced in MIDD and type 2 diabetes subjects compared to controls. Type 2 diabetes subjects had higher serum levels of miR-23b-3p compared to all other subjects. Receiver Operating Characteristic analysis showed the potential of 5'ValCAC and miR-23b-3p as MIDD biomarkers, with the combination showing excellent separation from type 2 diabetes subjects. CONCLUSIONS This is the first report showing altered serum levels of tiRNAs in diabetes subjects. The combined use of 5'ValCAC and miR-23b-3p as serum biomarkers could potentially differentiate between MIDD subjects and type 2 diabetes subjects.
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Affiliation(s)
- N Ng
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - H A Y Gibriel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - L Halang
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - E Jirström
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - J A Ioana
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - M Burke
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - M M Byrne
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - J H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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27
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Li D, Xie X, Yin N, Wu X, Yi B, Zhang H, Zhang W. tRNA-Derived Small RNAs: A Novel Regulatory Small Noncoding RNA in Renal Diseases. KIDNEY DISEASES (BASEL, SWITZERLAND) 2024; 10:1-11. [PMID: 38322624 PMCID: PMC10843216 DOI: 10.1159/000533811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/23/2023] [Indexed: 02/08/2024]
Abstract
Background tRNA-derived small RNAs (tsRNAs) are an emerging class of small noncoding RNAs derived from tRNA cleavage. Summary With the development of high-throughput sequencing, various biological roles of tsRNAs have been gradually revealed, including regulation of mRNA stability, transcription, translation, direct interaction with proteins and as epigenetic factors, etc. Recent studies have shown that tsRNAs are also closely related to renal disease. In clinical acute kidney injury (AKI) patients and preclinical AKI models, the production and differential expression of tsRNAs in renal tissue and plasma were observed. Decreased expression of tsRNAs was also found in urine exosomes from chronic kidney disease patients. Dysregulation of tsRNAs also appears in models of nephrotic syndrome and patients with lupus nephritis. And specific tsRNAs were found in high glucose model in vitro and in serum of diabetic nephropathy patients. In addition, tsRNAs were also differentially expressed in patients with kidney cancer and transplantation. Key Messages In the present review, we have summarized up-to-date works and reviewed the relationship and possible mechanisms between tsRNAs and kidney diseases.
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Affiliation(s)
- Dan Li
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Xian Xie
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Ni Yin
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Xueqin Wu
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Bin Yi
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Wei Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
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28
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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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29
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Yang N, Li R, Liu R, Yang S, Zhao Y, Xiong W, Qiu L. The Emerging Function and Promise of tRNA-Derived Small RNAs in Cancer. J Cancer 2024; 15:1642-1656. [PMID: 38370372 PMCID: PMC10869971 DOI: 10.7150/jca.89219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/20/2024] Open
Abstract
Fragments derived from tRNA, called tRNA-derived small RNAs (tsRNAs), have attracted widespread attention in the past decade. tsRNAs are widespread in prokaryotic and eukaryotic transcriptome, which contains two main types, tRNA-derived fragments (tRFs) and tRNA-derived stress-inducing RNA (tiRNAs), derived from the precursor tRNAs or mature tRNAs. According to differences in the cleavage position, tRFs can be divided into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, whereas tiRNAs can be divided into 5'-tiRNA and 3'-tiRNA. Studies have found that tRFs and tiRNAs are abnormally expressed in a variety of human malignant tumors, promote or inhibit the proliferation and apoptosis of cancer cells by regulating the expression of oncogene, and play an important role in the aggressive metastasis and progression of tumors. This article reviews the biological origins of various tsRNAs, introduces their functions and new concepts of related mechanisms, and focuses on the molecular mechanisms of tsRNAs in cancer, including breast cancer, prostate cancer, colorectal cancer, lung cancer, b-cell lymphoma, and chronic lymphoma cell leukemia. Lastly, this article puts forward some unresolved problems and future research prospects.
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Affiliation(s)
- Na Yang
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Ruijun Li
- College of Foreign Languages, Chuxiong Normal University, Chuxiong 675000, China
| | - Ruai Liu
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Shengjie Yang
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Yi Zhao
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Wei Xiong
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Lu Qiu
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
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Liang Y, Kong L, Zhang Y, Zhang Y, Shi M, Huang J, Kong H, Qi S, Yang Y, Hong J, Zhu M, Zhu X, Sun X, Zhang S, Wu L, Zhao C. Transfer RNA derived fragment, tRF-Glu-CTC, aggravates the development of neovascular age-related macular degeneration. Theranostics 2024; 14:1500-1516. [PMID: 38389841 PMCID: PMC10879880 DOI: 10.7150/thno.92943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Rationale: Angiogenesis expedites tissue impairment in many diseases, including age-related macular degeneration (AMD), a leading cause of irreversible blindness in elderly. A substantial proportion of neovascular AMD patients, characterized by aberrant choroidal neovascularization (CNV), exhibit poor responses or adverse reactions to anti-VEGF therapy. Herein, we aimed to unveil the function of newly identified transfer RNA-derived small RNA, tRF-Glu-CTC, in the pathology of CNV and determine its potential in inhibiting angiogenesis. Methods: Small non-coding RNA sequencing and quantitative polymerase chain reaction were conducted to detect expression pattern of tRF-Glu-CTC in CNV development. Immunofluorescence staining, fundus fluorescein angiography and ex vivo choroidal sprouting assays were employed for the evaluation of tRF-Glu-CTC's function in CNV development. The role of tRF-Glu-CTC in endothelial cells were determined by in vitro endothelial cell proliferation, migration and tube formation assays. Transcriptome sequencing, dual-luciferase reporter assay and in vitro experiments were conducted to investigate downstream mechanism of tRF-Glu-CTC mediated pathology. Results: tRF-Glu-CTC exhibited substantial up-regulation in AMD patients, laser-induced CNV model, and endothelial cells under hypoxia condition, which is a hallmark of CNV. Inhibiting tRF-Glu-CTC reduced angiogenesis and hypoxia stress in the neovascular region without neuroretina toxicity in laser-induced CNV model, showing an anti-angiogenic effect comparable to bevacizumab, while overexpression of tRF-Glu-CTC significantly augmented CNV. Mechanically, under hypoxia condition, angiogenin was involved in the production of tRF-Glu-CTC, which in turn triggered endothelial cell tubulogenesis, migration and promoted the secretion of inflammatory factors via the suppression of vasohibin 1 (VASH1). When downregulating VASH1 expression, the inhibition of tRF-Glu-CTC showed minimal suppression on angiogenesis. Conclusions: This study demonstrated the important role of tRF-Glu-CTC in the progression of angiogenesis. Targeting of tRF-Glu-CTC may be an alternative to current anti-VEGF therapy for CNV in AMD and other conditions with angiogenesis.
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Affiliation(s)
- Yu Liang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Lingjie Kong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yuelu Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yihan Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Mingsu Shi
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Jiaqiu Huang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Hongyu Kong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Siyi Qi
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yunlong Yang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiaxu Hong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Meidong Zhu
- Save Sight Institute, Discipline of Clinical Ophthalmology and Eye Health, University of Sydney, Camperdown, NSW 2000, Australia
- New South Weals Tissue Bank, New South Weals Organ and Tissue Donation Service, Sydney Eye Hospital, 8 Macquarie Street, Sydney 2000, Australia
| | - Xiangjia Zhu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Xinghuai Sun
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Shujie Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Lianqun Wu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Chen Zhao
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
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Wang L, Peng B, Yan Y, Liu G, Yang D, Wang Q, Li Y, Mao Q, Chen Q. The tRF-3024b hijacks miR-192-5p to increase BCL-2-mediated resistance to cytotoxic T lymphocytes in Esophageal Squamous Cell Carcinoma. Int Immunopharmacol 2024; 126:111135. [PMID: 37977065 DOI: 10.1016/j.intimp.2023.111135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023]
Abstract
The limited efficacy of immune checkpoint inhibitors (ICIs) in the treatment of advanced Esophageal Squamous Cell Carcinoma (ESCC) poses a challenge. Recent evidence suggests that tumor cells' insensitivity to cytotoxic T lymphocytes (CTLs) contributes to drug resistance against ICIs. Here, a particular tRNA-derived fragment called tRF-3024b has been identified as playing a significant role in tumor cell resistance to CTLs. Through tRF sequencing (tRF-seq), we observed a high expression of tRF-3024b in ESCC cells that survived co-culture with CTLs. Further in vitro studies demonstrated that tRF-3024b reduced the apoptosis of tumor cells when co-cultured with CTLs. The mechanism behind this resistance involves tRF-3024b promoting the expression of B-cell lymphoma-2 (BCL-2) by sequestering miR-192-5p, a microRNA that would normally inhibit BCL-2 expression. This means that tRF-3024b indirectly enhances the protective effects of BCL-2, reducing apoptosis in tumor cells. Rescue assays confirmed that the suppressive function of tRF-3024b relies on BCL-2. In summary, the tRF-3024b/miR-192-5p/BCL-2 axis sheds light on the crucial role of tRF-3024b in regulating BCL-2 expression. These findings offer valuable insights into strategies to enhance the response of ESCC to CTLs and improve the effectiveness of immunotherapy approaches in treating ESCC.
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Affiliation(s)
- Lin Wang
- Department of Oncology, Department of Geriatric Lung Cancer Laboratory, The Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Bo Peng
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Yan
- Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guangjun Liu
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Dunpeng Yang
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qibin Wang
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yongcheng Li
- Department of Oncology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Qixing Mao
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Qiang Chen
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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Li N, Yao S, Yu G, Lu L, Wang Z. tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. Nucleic Acids Res 2024; 52:D345-D350. [PMID: 37811890 PMCID: PMC10767876 DOI: 10.1093/nar/gkad815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/22/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
tRFtarget 1.0 (http://trftarget.net/) is a platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments (tRFs) and target genes (or transcripts) across multiple organisms. Here, we introduce a newly released version of tRFtarget 2.0, in which we integrated 6 additional tRF sources, resulting in a comprehensive collection of 2614 high-quality tRF sequences spanning across 9 species, including 1944 Homo sapiens tRFs and one newly incorporated species Rattus norvegicus. We also expanded target genes by including ribosomal RNAs, long non-coding RNAs, and coding genes >50 kb in length. The predicted binding sites have surged up to approximately 6 billion, a 20.5-fold increase than that in tRFtarget 1.0. The manually curated publications relevant to tRF targets have increased to 400 and the gene-level experimental evidence has risen to 232. tRFtarget 2.0 introduces several new features, including a web-based tool that identifies potential binding sites of tRFs in user's own datasets, integration of standardized tRF IDs, and inclusion of external links to contents within the database. Additionally, we enhanced website framework and user interface. With these improvements, tRFtarget 2.0 is more user-friendly, providing researchers a streamlined and comprehensive platform to accelerate their research progress.
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Affiliation(s)
- Ningshan Li
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong 518172, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Siqiong Yao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangjun Yu
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong 518172, China
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
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Tzur Y, Winek K, Madrer N, Dubnov S, Bennett ER, Greenberg DS, Hanin G, Gammal A, Tam J, Arkin IT, Paldor I, Soreq H. Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via β-Klotho and perilipin 2. Mol Metab 2024; 79:101856. [PMID: 38141848 PMCID: PMC10805669 DOI: 10.1016/j.molmet.2023.101856] [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: 08/31/2023] [Revised: 11/20/2023] [Accepted: 12/17/2023] [Indexed: 12/25/2023] Open
Abstract
OBJECTIVE Non-alcoholic fatty liver disease (NAFLD) involves hepatic accumulation of intracellular lipid droplets via incompletely understood processes. Here, we report distinct and cooperative NAFLD roles of LysTTT-5'tRF transfer RNA fragments and microRNA miR-194-5p. METHODS Combined use of diet induced obese mice with human-derived oleic acid-exposed Hep G2 cells revealed new NAFLD roles of LysTTT-5'tRF and miR-194-5p. RESULTS Unlike lean animals, dietary-induced NAFLD mice showed concurrent hepatic decrease of both LysTTT-5'tRF and miR-194-5p levels, which were restored following miR-132 antisense oligonucleotide treatment which suppresses hepatic steatosis. Moreover, exposing human-derived Hep G2 cells to oleic acid for 7 days co-suppressed miR-194-5p and LysTTT-5'tRF levels while increasing lipid accumulation. Inversely, transfecting fattened cells with a synthetic LysTTT-5'tRF mimic elevated mRNA levels of the metabolic regulator β-Klotho while decreasing triglyceride amounts by 30% within 24 h. In contradistinction, antisense suppression of miR-194-5p induced accumulation of its novel target, the NAFLD-implicated lipid droplet-coating PLIN2 protein. Further, two out of 15 steatosis-alleviating screened drug-repurposing compounds, Danazol and Latanoprost, elevated miR-194-5p or LysTTT-5'tRF levels. CONCLUSION Our findings highlight the different yet complementary roles of miR-194-5p and LysTTT-5'tRF and offer new insights into the complex roles of small non-coding RNAs and the multiple pathways involved in NAFLD pathogenesis.
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Affiliation(s)
- Yonat Tzur
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Katarzyna Winek
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel; The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Nimrod Madrer
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Serafima Dubnov
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel; The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Estelle R Bennett
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - David S Greenberg
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Geula Hanin
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Asaad Gammal
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joseph Tam
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isaiah T Arkin
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Iddo Paldor
- Shaare Zedek Medical Center, The Neurosurgery Department, Main Building, 10th Floor, 12 Shmu'el Bait Street, Jerusalem, 9103102 Israel
| | - Hermona Soreq
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel; The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel.
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Odogwu NM, Hagen C, Nelson TJ. Transcriptome studies of congenital heart diseases: identifying current gaps and therapeutic frontiers. Front Genet 2023; 14:1278747. [PMID: 38152655 PMCID: PMC10751320 DOI: 10.3389/fgene.2023.1278747] [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: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
Congenital heart disease (CHD) are genetically complex and comprise a wide range of structural defects that often predispose to - early heart failure, a common cause of neonatal morbidity and mortality. Transcriptome studies of CHD in human pediatric patients indicated a broad spectrum of diverse molecular signatures across various types of CHD. In order to advance research on congenital heart diseases (CHDs), we conducted a detailed review of transcriptome studies on this topic. Our analysis identified gaps in the literature, with a particular focus on the cardiac transcriptome signatures found in various biological specimens across different types of CHDs. In addition to translational studies involving human subjects, we also examined transcriptomic analyses of CHDs in a range of model systems, including iPSCs and animal models. We concluded that RNA-seq technology has revolutionized medical research and many of the discoveries from CHD transcriptome studies draw attention to biological pathways that concurrently open the door to a better understanding of cardiac development and related therapeutic avenue. While some crucial impediments to perfectly studying CHDs in this context remain obtaining pediatric cardiac tissue samples, phenotypic variation, and the lack of anatomical/spatial context with model systems. Combining model systems, RNA-seq technology, and integrating algorithms for analyzing transcriptomic data at both single-cell and high throughput spatial resolution is expected to continue uncovering unique biological pathways that are perturbed in CHDs, thus facilitating the development of novel therapy for congenital heart disease.
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Affiliation(s)
- Nkechi Martina Odogwu
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Clinton Hagen
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
| | - Timothy J. Nelson
- Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States
- Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States
- Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
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Ohsaka F, Yamaguchi M, Teshigahara Y, Yasui M, Kato E, Sonoyama K. Murine fecal microRNAs alter the composition of cultured gut microbiota. Biochem Biophys Res Commun 2023; 685:149184. [PMID: 37922787 DOI: 10.1016/j.bbrc.2023.149184] [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: 10/17/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Fecal microRNAs (miRNAs) derived from intestinal epithelial cells have been suggested to influence gut microbiota homeostasis. The present study examined whether fecal miRNAs alter the structure of cultured gut microbiota. Fecal bacteria isolated from murine cecal contents were cultured for 24 h under anaerobic conditions. Supplementation with fecal small RNAs isolated from cecal contents altered the structure of cultured fecal microbiota as assessed by 16S rRNA gene sequence analysis. In particular, fecal small RNAs increased Enterococcus spp. Fractionation of fecal small RNAs by ultrafiltration showed that small RNAs smaller than 10 kDa significantly increased enterococci compared to those larger than 10 kDa, as assessed by quantitative PCR, suggesting that the increase in enterococci by fecal small RNAs can mainly be attributed to miRNAs. Negative control miRNA that has low homology to miRNA sequences of human, mouse, and rat, failed to increase enterococci. Therefore, the findings from the present study employing cultured fecal bacteria suggest that fecal small RNAs, most likely host-derived miRNAs, alter gut microbiota structure by expanding enterococci in a sequence-dependent manner.
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Affiliation(s)
- Fumina Ohsaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Mayuko Yamaguchi
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yuka Teshigahara
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Moeka Yasui
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Eisuke Kato
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kei Sonoyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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Jianfeng M, Mailin G, Yitang Y, Lei C, Ye Z, Lili N, Yan W, Shunhua Z, Jingyong W, Li Z, Linyuan S. tRNA-derived small RNA dataset in multiple organs of intrauterine growth-restricted pig. Sci Data 2023; 10:793. [PMID: 37949905 PMCID: PMC10638418 DOI: 10.1038/s41597-023-02715-w] [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: 05/29/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Intrauterine growth restriction (IUGR) impairs neonatal weight and causes multiple organ dysplasia. IUGR not only threatens human health but is also a significant constraint to the development of animal husbandry. However, the molecular mechanism underlying IUGR remains to be further elucidated. tRNA-derived small RNA (tsRNAs) is a regulative non-coding RNA, which has recently been reported to correlate with the onset and progression of several diseases. In this study, we investigated the tsRNAs expression profiles of IUGR pigs. A tsRNAs dataset for multiple organs in normal and IUGR pigs was generated, including muscle, liver, spleen and intestine. We further analyzed the characteristics of tsRNAs in different organs of pigs, and KEGG pathway analysis was performed to investigate possible pathways involved. This dataset will provide valuable information for further exploring the molecular mechanism of IUGR formation.
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Affiliation(s)
- Ma Jianfeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gan Mailin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yang Yitang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chen Lei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhao Ye
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Niu Lili
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wang Yan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhang Shunhua
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wang Jingyong
- Chongqing Academy of Animal Science, Chongqing, China
| | - Zhu Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China.
| | - Shen Linyuan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China.
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Aquino-Jarquin G. tRNA Thr-miR-720 mimicry in glioma cells. Hum Cell 2023; 36:2276-2277. [PMID: 37578573 DOI: 10.1007/s13577-023-00968-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Affiliation(s)
- Guillermo Aquino-Jarquin
- RNA Biology and Genome Editing Section, Genomics, Genetics, and Bioinformatics Research Laboratory, 'Federico Gómez' Children's Hospital of Mexico, Dr. Márquez 162, Doctores, Cuauhtémoc, C.P. 06720, Ciudad de México, Mexico.
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Anastassiadis T, Köhrer C. Ushering in the era of tRNA medicines. J Biol Chem 2023; 299:105246. [PMID: 37703991 PMCID: PMC10583094 DOI: 10.1016/j.jbc.2023.105246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
Long viewed as an intermediary in protein translation, there is a growing awareness that tRNAs are capable of myriad other biological functions linked to human health and disease. These emerging roles could be tapped to leverage tRNAs as diagnostic biomarkers, therapeutic targets, or even as novel medicines. Furthermore, the growing array of tRNA-derived fragments, which modulate an increasingly broad spectrum of cellular pathways, is expanding this opportunity. Together, these molecules offer drug developers the chance to modulate the impact of mutations and to alter cell homeostasis. Moreover, because a single therapeutic tRNA can facilitate readthrough of a genetic mutation shared across multiple genes, such medicines afford the opportunity to define patient populations not based on their clinical presentation or mutated gene but rather on the mutation itself. This approach could potentially transform the treatment of patients with rare and ultrarare diseases. In this review, we explore the diverse biology of tRNA and its fragments, examining the past and present challenges to provide a comprehensive understanding of the molecules and their therapeutic potential.
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Li X, Zhang Y, Li Y, Gu X, Ju S. A comprehensive evaluation of serum tRF-29-R9J8909NF5JP as a novel diagnostic and prognostic biomarker for gastric cancer. Mol Carcinog 2023; 62:1504-1517. [PMID: 37314123 DOI: 10.1002/mc.23592] [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: 03/19/2023] [Revised: 05/09/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
Gastric cancer (GC) is a common malignant digestive system tumor. Since the early symptoms of GC are usually vague and the positive rate of common biomarkers of GC is low, it is of urgent need to find new biomarkers with good sensitivity and specificity to screen and diagnose GC patients. The tRNA-derived small RNAs (tsRNAs) are emerging small noncoding RNAs that play an essential role in cancer progression. In this study, we explored whether novel tsRNAs have the potential to serve as biomarkers for GC. Three tsRNAs significantly upregulated in GC were screened by the tsRFun database. The expression level of tRF-29-R9J8909NF5JP was detected by real-time fluorescence quantitative polymerase chain reaction. Agarose gel electrophoresis and Sanger sequencing were used to verify the characteristics of tRF-29-R9J8909NF5JP. The receiver operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of tRF-29-R9J8909NF5JP. The χ2 test was used to analyze the correlation between tRF-29-R9J8909NF5JP expression level and clinicopathological parameters. Kaplan-Meier survival curves were used to analyze the correlation between tRF-29-R9J8909NF5JP expression levels and survival time of GC patients. In this study, the expression level of tRF-29-R9J8909NF5JP was significantly increased in GC tissues. The expression level of tRF-29-R9J8909NF5JP was considerably higher in the serum of GC patients than in the serum of gastritis patients and in the serum of healthy donors, and the expression level of tRF-29-R9J8909NF5JP was significantly decreased in the serum of GC patients after surgery. In addition, the χ2 test showed that the expression level of tRF-29-R9J8909NF5JP in GC serum was correlated with differentiation grade, T-stage, lymph node metastasis, tumor node metastasis stage, and neurological/vascular invasion. The results of the survival curve showed that the high expression of serum tRF-29-R9J8909NF5JP was associated with a low survival rate. ROC analysis showed that serum tRF-29-R9J8909NF5JP had higher diagnostic efficiency than common GC biomarkers, and the diagnostic efficiency was further improved by combining them. At the end of the study, we predicted the downstream of tRF-29-R9J8909NF5JP. The expression level of tRF-29-R9J8909NF5JP in the serum of GC patients can effectively identify GC patients and has higher efficacy than conventional biomarkers. In addition, serum tRF-29-R9J8909NF5JP can monitor the postoperative condition of GC patients, suggesting that it has the potential to become a biomarker for GC.
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Affiliation(s)
- Xun Li
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yu Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Yang Li
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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Chen Q, Shen L, Liao T, Qiu Y, Lei Y, Wang X, Chen L, Zhao Y, Niu L, Wang Y, Zhang S, Zhu L, Gan M. A Novel tRNA-Derived Fragment, tRF GlnCTG, Regulates Angiogenesis by Targeting Antxr1 mRNA. Int J Mol Sci 2023; 24:14552. [PMID: 37833999 PMCID: PMC10572189 DOI: 10.3390/ijms241914552] [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: 09/08/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
As a novel non-coding RNA with important functions corresponding to various cellular stresses, the function of tRFs in angiogenesis remains unclear. Firstly, small RNA sequencing was performed on normal and post-muscle injury mouse tibialis anterior muscle to identify and analyse differentially expressed tRF/tiRNA. tRNA GlnCTG-derived fragments (tRFGlnCTG) were found to be overexpressed in high abundance in the damaged muscle. Subsequent in vitro experiments revealed that the overexpression of tRFGlnCTG suppressed the vascular endothelial cells' viability, cell cycle G1/S transition, proliferation, migration, and tube-formation capacity. Similarly, in vivo experiments showed that the tRFGlnCTG decreased the relative mRNA levels of vascular endothelial cell markers and pro-angiogenic factors and reduced the proportion of CD31-positive cells. Finally, luciferase activity analysis confirmed that the tRFGlnCTG directly targeted the 3'UTR of Antxr1, leading to a significant reduction in the mRNA expression of the target gene. These results suggest that tRFGlnCTG is a key regulator of vascular endothelial cell function. The results provide a new idea for further exploration of the molecular mechanisms that regulate angiogenesis.
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Affiliation(s)
- Qiuyang Chen
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianci Liao
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanhao Qiu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Lei
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xingyu Wang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (Q.C.); (L.S.); (T.L.); (Y.Q.); (Y.L.); (X.W.)
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Zhou S, Van Bortle K. The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1782. [PMID: 36754845 PMCID: PMC10498592 DOI: 10.1002/wrna.1782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023]
Abstract
The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Wu Q, Zou S, Liu W, Liang M, Chen Y, Chang J, Liu Y, Yu X. A novel onco-cardiological mouse model of lung cancer-induced cardiac dysfunction and its application in identifying potential roles of tRNA-derived small RNAs. Biomed Pharmacother 2023; 165:115117. [PMID: 37406509 DOI: 10.1016/j.biopha.2023.115117] [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: 05/20/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023] Open
Abstract
An increasing body of research suggests cancer-induced cardiovascular diseases, leading to the appearance of an interdisciplinary study known as onco-cardiology. Lung cancer has the highest incidence and mortality. Cardiac dysfunction constitutes a major cause of death in lung cancer patients. However, its mechanism has not been elucidated because suitable animal models that adequately mimic clinical features are lacking. Here, we established a novel chemically induced lung cancer mouse model using benzo[a]pyrene and urethane to recapitulate the general characteristics of cardiac dysfunction caused by lung cancer, the cardiac disorders in the context of the progression of lung cancer were evaluated using echocardiographic and histological approaches. The pathological changes included myocardial ischaemia, pericarditis, cardiac pre-cachexia, and pulmonary artery hypertension. We performed sequencing to detect the tRNA-derived fragments and tRNA-derived stress-induced RNAs (tRFs/tiRNAs) expressions in mouse heart tissue. 22 upregulated and 16 downregulated tRFs/tiRNAs were identified. Subsequently, the top 10 significant results of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were presented. The in vitro model was established by exposing neonatal rat cardiomyocytes and myocardial fibroblasts to lung tumour cell-conditioned medium, respectively. Western blotting revealed significant changes in cardiac failure markers (atrial natriuretic peptide and α-myosin heavy chain) and cardiac fibrosis markers (Collagen-1 and Collagen-3). Our model adequately reflects the pathological features of lung cancer-induced cardiac dysfunction. Furthermore, the altered tRF/tiRNA profiles showed great promise as novel targets for therapies. These results might pave the way for research on therapeutic targets in onco-cardiology.
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Affiliation(s)
- Qian Wu
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China
| | - Shiting Zou
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China
| | - Wanjie Liu
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China
| | - Miao Liang
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China
| | - Yuling Chen
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China
| | - Jishuo Chang
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China
| | - Yinghua Liu
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China.
| | - Xiyong Yu
- Department of Pharmacology, the Municipal & Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, National Medical Products Administration & State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, PR China.
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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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Chen Y, Tang Y, Hou S, Luo J, Chen J, Qiu H, Chen W, Li K, He J, Li J. Differential expression spectrum and targeted gene prediction of tRNA-derived small RNAs in idiopathic pulmonary arterial hypertension. Front Mol Biosci 2023; 10:1204740. [PMID: 37496778 PMCID: PMC10367008 DOI: 10.3389/fmolb.2023.1204740] [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: 04/12/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023] Open
Abstract
Background: Idiopathic pulmonary arterial hypertension (PAH) is a potentially fatal pulmonary vascular disease with an extremely poor natural course. The limitations of current treatment and the unclear etiology and pathogenesis of idiopathic PAH require new targets and avenues of exploration involved in the pathogenesis of PAH. tRNA-derived small RNAs (tsRNAs), a new type of small non-coding RNAs, have a significant part in the progress of diverse diseases. However, the potential functions behind tsRNAs in idiopathic PAH remain unknown. Methods: Small RNA microarray was implemented on three pairs of plasma of idiopathic PAH patients and healthy controls to investigate and compare tsRNAs expression profiles. Validation samples were used for real-time polymerase chain reaction (Real-time PCR) to verify several dysregulated tsRNAs. Bioinformatic analysis was adopted to determine potential target genes and mechanisms of the validated tsRNAs in PAH. Results: Microarray detected 816 statistically significantly dysregulated tsRNAs, of which 243 tsRNAs were upregulated and 573 were downregulated in PAH. Eight validated tsRNAs in the results of Real-time PCR were concordant with the small RNA microarray: four upregulated (tRF3a-AspGTC-9, 5'tiRNA-31-GluCTC-16, i-tRF-31:54-Val-CAC-1 and tRF3b-TyrGTA-4) and four downregulated (5'tiRNA-33-LysTTT-4, i-tRF-8:32-Val-AAC-2, i-tRF-2:30-His-GTG-1, and i-tRF-15:31-Lys-CTT-1). The Gene Ontology analysis has shown that the verified tsRNAs are related to cellular macromolecule metabolic process, regulation of cellular process, and regulation of cellular metabolic process. It is disclosed that potential target genes of verified tsRNAs are widely involved in PAH pathways by Kyoto Encyclopedia of Genes and Genomes. Conclusion: This study investigated tsRNA profiles in idiopathic PAH and found that the dysregulated tsRNAs may become a novel type of biomarkers and possible targets for PAH.
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Affiliation(s)
- Yusi Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yi Tang
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Department of Cardiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, China
| | - Sitong Hou
- Clinical Medicine, Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Jun Luo
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jingyuan Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haihua Qiu
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wenjie Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Kexing Li
- Department of Pharmacology, Hebei University, Baoding, Hebei, China
| | - Jin He
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Department of Cardiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, China
| | - Jiang Li
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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Xie Y, Zhang S, Yu X, Ye G, Guo J. Transfer RNA-derived fragments as novel biomarkers of the onset and progression of gastric cancer. Exp Biol Med (Maywood) 2023; 248:1095-1102. [PMID: 37387464 PMCID: PMC10583753 DOI: 10.1177/15353702231179415] [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: 12/14/2022] [Accepted: 02/27/2023] [Indexed: 07/01/2023] Open
Abstract
Gastric cancer (GC) is a particularly malignant disease; thus, early diagnosis and treatment are especially important. Transfer RNA-derived small RNAs (tsRNAs) have been implicated in the onset and progression of various cancers. Therefore, the aim of this study was to explore the role of tRF-18-79MP9P04 (previously named tRF-5026a) in the onset and progression of GC. Expression levels of tRF-18-79MP9P04 were quantified in gastric mucosa specimens of healthy controls and plasma samples of patients with different stages of GC. The results showed that plasma levels of tRF-18-79MP9P04 were significantly decreased in the early and advanced stages of GC. The results of the nucleocytoplasmic separation assay found that tRF-18-79MP9P04 was localized in the nuclei of GC cells. High-throughput transcriptome sequencing identified genes regulated by tRF-18-79MP9P04 in GC cells, and the function of tRF-18-79MP9P04 was predicted by bioinformatics. Collectively, the findings of this study suggest that tRF-18-79MP9P04 would be useful as non-invasive biomarker for early diagnosis of GC and is related to cornification, the type I interferon signaling pathway, RNA polymerase II activities, and DNA binding.
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Affiliation(s)
- Yaoyao Xie
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo 315211, China
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Shuangshuang Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Xiuchong Yu
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Guoliang Ye
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo 315211, China
- Institute of Digestive Diseases, Ningbo University, Ningbo 315020, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo 315211, China
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
- Institute of Digestive Diseases, Ningbo University, Ningbo 315020, China
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Scacchetti A, Shields EJ, Trigg NA, Wilusz JE, Conine CC, Bonasio R. A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543899. [PMID: 37333231 PMCID: PMC10274639 DOI: 10.1101/2023.06.06.543899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Despite the numerous sequencing methods available, the vast diversity in size and chemical modifications of RNA molecules makes the capture of the full spectrum of cellular RNAs a difficult task. By combining quasi-random hexamer priming with a custom template switching strategy, we developed a method to construct sequencing libraries from RNA molecules of any length and with any type of 3' terminal modification, allowing the sequencing and analysis of virtually all RNA species. Ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to comprehensively characterize changes in small non-coding RNAs and mRNAs simultaneously, with performance comparable to separate dedicated methods. With LIDAR, we comprehensively characterized the coding and non-coding transcriptome of mouse embryonic stem cells, neural progenitor cells, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared to traditional ligation-dependent sequencing methods, and uncovered the presence of tDRs with blocked 3' ends that had previously escaped detection. Our findings highlight the potential of LIDAR to systematically detect all RNAs in a sample and uncover new RNA species with potential regulatory functions.
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Affiliation(s)
- Alessandro Scacchetti
- Epigenetics Institute and Department of Cell and Developmental Biology; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emily J. Shields
- Epigenetics Institute and Department of Cell and Developmental Biology; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Urology and Institute of Neuropathology, Medical Center–University of Freiburg, 79106 Freiburg, Germany
| | - Natalie A. Trigg
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women’s Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jeremy E. Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Colin C. Conine
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women’s Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Hernandez R, Shi J, Liu J, Li X, Wu J, Zhao L, Zhou T, Chen Q, Zhou C. PANDORA-Seq unveils the hidden small noncoding RNA landscape in atherosclerosis of LDL receptor-deficient mice. J Lipid Res 2023; 64:100352. [PMID: 36871792 PMCID: PMC10119612 DOI: 10.1016/j.jlr.2023.100352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/08/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Small noncoding RNAs (sncRNAs) play diverse roles in numerous biological processes. While the widely used RNA sequencing (RNA-Seq) method has advanced sncRNA discovery, RNA modifications can interfere with the complementary DNA library construction process, preventing the discovery of highly modified sncRNAs including transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) that may have important functions in disease development. To address this technical obstacle, we recently developed a novel PANDORA-Seq (Panoramic RNA Display by Overcoming RNA Modification Aborted Sequencing) method to overcome RNA modification-elicited sequence interferences. To identify novel sncRNAs associated with atherosclerosis development, LDL receptor-deficient (LDLR-/-) mice were fed a low-cholesterol diet or high-cholesterol diet (HCD) for 9 weeks. Total RNAs isolated from the intima were subjected to PANDORA-Seq and traditional RNA-Seq. By overcoming RNA modification-elicited limitations, PANDORA-Seq unveiled an rsRNA/tsRNA-enriched sncRNA landscape in the atherosclerotic intima of LDLR-/- mice, which was strikingly different from that detected by traditional RNA-Seq. While microRNAs were the dominant sncRNAs detected by traditional RNA-Seq, PANDORA-Seq substantially increased the reads of rsRNAs and tsRNAs. PANDORA-Seq also detected 1,383 differentially expressed sncRNAs induced by HCD feeding, including 1,160 rsRNAs and 195 tsRNAs. One of HCD-induced intimal tsRNAs, tsRNA-Arg-CCG, may contribute to atherosclerosis development by regulating the proatherogenic gene expression in endothelial cells. Overall, PANDORA-Seq revealed a hidden rsRNA and tsRNA population associated with atherosclerosis development. These understudied tsRNAs and rsRNAs, which are much more abundant than microRNAs in the atherosclerotic intima of LDLR-/- mice, warrant further investigations.
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Affiliation(s)
- Rebecca Hernandez
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Jingwei Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Xiuchun Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Jake Wu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA; Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
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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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Suresh PS, Thankachan S, Venkatesh T. Landscape of Clinically Relevant Exosomal tRNA-Derived Non-coding RNAs. Mol Biotechnol 2023; 65:300-310. [PMID: 35997930 DOI: 10.1007/s12033-022-00546-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022]
Abstract
Exosomes are extra-cellular vesicles that are < 150 nm that is formed by invagination of the plasma membrane and are released as vesicles. These contain proteins, RNA, and DNA as their cargo. In recent times, the non-coding RNA (ncRNA) present within exosomes has been studied extensively in the context of sorting, localization, and their potential as biomarkers. For example, miR-1246, miR-1290, miR-21, and miR-23a are exosomal biomarkers of cancer, and YBX1 (Y-Box Binding Protein 1) is attributed to exosomal RNA sorting. Transfer RNA-derived fragments are a class of small ncRNAs that were discovered in 2009. They are classified as tRFs (tRNA-derived fragments) and tsRNAs (tRNA halves). Interestingly, these tRNA-derived ncRNAs are emerging as biomarkers in various diseases, and these are found in exosomes. To date, the literature has covered only the biomarker potential of plasma/serum tRNA-derived ncRNAs. Hence, in the current review, we discuss the exosomal tRNA-derived fragments that are clinically relevant in pathological conditions.
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Affiliation(s)
- Padmanaban S Suresh
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, 673601, India
| | - Sanu Thankachan
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, 673601, India
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kerala, 671316, Periye, Kasaragod, India.
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