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Meng F, Bai H, Ke K, Fang L, Huang H, Liang X, Li W, Chen X, Chen C. tRF5-22-SerGCT-1 protects the heart against myocardial injury by targeting MSK1. Epigenomics 2025; 17:439-451. [PMID: 40269521 PMCID: PMC12026222 DOI: 10.1080/17501911.2025.2495544] [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: 12/01/2024] [Accepted: 04/14/2025] [Indexed: 04/25/2025] Open
Abstract
AIM This study aims to explore the expression profiles and potential functions of tsRNAs in MI. METHODS Using a mouse model of MI induced by coronary artery ligation, we used smallRNA array to obtain tsRNAs expression profiles. Reverse transcription quantitative polymerase chain reaction(RT-qPCR), Western Blot, tRF5-22-SerGCT-1 mimics and inhibitors, cell proliferation and apoptosis detection, luciferase reporter assay, and bioinformatics analysis were employed to screen differentially expressed tsRNAs and identify the functions of tsRNAs after MI. RESULTS A total of 175 significantly different tsRNAs (FC > 1.5, p < 0.05) were identified in MI mice, including 98 upregulated and 77 downregulated tsRNAs. Bioinformatics and target gene prediction revealed that two differentially expressed tsRNAs (5'tiRNA-34-GlnCTG-4, tRF5-22-SerGCT-1) may be involved in processes like autophagy and apoptosis, as well as in key signaling pathways such as MAPK and autophagy. Further investigation of tRF5-22-SerGCT-1 revealed that its overexpression or inhibition in vitro affected MSK1 levels and cardiomyocytes apoptosis following oxygen-glucose deprivation, providing a protective effect. Dual-luciferase assays confirmed that tRF5-22-SerGCT-1 targets MSK1. CONCLUSION We found differentially expressed tsRNAs in MI. In addition, our research showed first that tRF5-22-SerGCT-1 might be involved in the MAPK pathways by targeting the MSK1, modulating apoptosis.
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Affiliation(s)
- Fanji Meng
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, China
- Department of Biopharmaceutical Sciences, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics and School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hemanyun Bai
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Kangling Ke
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Lingyan Fang
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Haitao Huang
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Xiao Liang
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Weiyan Li
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
| | - Xiongwen Chen
- Department of Biopharmaceutical Sciences, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics and School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Can Chen
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
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2
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Jouravleva K, Zamore PD. A guide to the biogenesis and functions of endogenous small non-coding RNAs in animals. Nat Rev Mol Cell Biol 2025; 26:347-370. [PMID: 39856370 DOI: 10.1038/s41580-024-00818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2024] [Indexed: 01/27/2025]
Abstract
Small non-coding RNAs can be categorized into two main classes: structural RNAs and regulatory RNAs. Structural RNAs, which are abundant and ubiquitously expressed, have essential roles in the maturation of pre-mRNAs, modification of rRNAs and the translation of coding transcripts. By contrast, regulatory RNAs are often expressed in a developmental-specific, tissue-specific or cell-type-specific manner and exert precise control over gene expression. Reductions in cost and improvements in the accuracy of high-throughput RNA sequencing have led to the identification of many new small RNA species. In this Review, we provide a broad discussion of the genomic origins, biogenesis and functions of structural small RNAs, including tRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vtRNAs) and Y RNAs as well as their derived RNA fragments, and of regulatory small RNAs, such as microRNAs (miRNAs), endogenous small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs), in animals.
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Affiliation(s)
- Karina Jouravleva
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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3
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Orang A, Warnock NI, Migault M, Dredge BK, Bert AG, Bracken JM, Gregory PA, Pillman KA, Goodall GJ, Bracken CP. Chasing non-existent "microRNAs" in cancer. Oncogenesis 2025; 14:10. [PMID: 40251190 PMCID: PMC12008284 DOI: 10.1038/s41389-025-00550-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 02/23/2025] [Accepted: 03/20/2025] [Indexed: 04/20/2025] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression whose dysregulation is widely linked to tumourigenesis, tumour progression and Epithelial-Mesenchymal Transition (EMT), a developmental process that promotes metastasis when inappropriately activated. However, controversy has emerged regarding how many functional miRNAs are encoded in the genome, and to what extent non-regulatory products of RNA degradation have been mis-identified as miRNAs. Central to miRNA function is their capacity to associate with an Argonaute (AGO) protein and form an RNA-Induced Silencing Complex (RISC), which mediates target mRNA suppression. We report that numerous "miRNAs" previously reported in EMT and cancer contexts, are not incorporated into RISC and are not capable of endogenously silencing target genes, despite the fact that hundreds of publications in the cancer field describe their roles. Apparent function can be driven through the expression of artificial miRNA mimics which is not necessarily reflective of any endogenous gene regulatory function. We present biochemical and bioinformatic criteria that can be used to distinguish functional miRNAs from mistakenly annotated RNA fragments.
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Affiliation(s)
- Ayla Orang
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Nicholas I Warnock
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Melodie Migault
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Julie M Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia
- School of Medicine, Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia.
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia.
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia.
- School of Medicine, Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, South Australia, Australia.
- School of Medicine, Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia.
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4
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Dong H, Ye C, Ye X, Yan J, Ye G, Shao Y. The biological role and molecular mechanism of transfer RNA-derived small RNAs in tumor metastasis. Front Oncol 2025; 15:1560943. [PMID: 40265011 PMCID: PMC12011605 DOI: 10.3389/fonc.2025.1560943] [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: 01/15/2025] [Accepted: 03/24/2025] [Indexed: 04/24/2025] Open
Abstract
Tumor metastasis is a significant contributor to increased cancer mortality. Transfer RNA-derived small RNAs (tsRNAs), a class of endogenous non-coding RNA molecules, play crucial functional roles in various physiological processes, including the regulation of transcription and reverse transcription, the modulation of translation processes, the modification of epigenetic inheritance, the regulation of the cell cycle, etc. Dysregulated tsRNAs are closely related to the occurrence and progression of human malignancies. Accumulating evidence indicates that the abnormal expression of tsRNAs is associated with tumor metastasis through a variety of mechanisms. Hence, we summarize the fundamental structure and biological functions of tsRNAs, with a focus on how tsRNAs influence the tumor metastasis process through downstream targets or the regulation of interactions between upstream and downstream molecules, thereby providing a novel perspective for targeted therapy for tumor metastasis.
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Affiliation(s)
- Haotian Dong
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, China
| | - Chengyuan Ye
- Health Science Center, Ningbo University, Ningbo, China
| | - Xiaohan Ye
- Health Science Center, Ningbo University, Ningbo, China
| | - Jianing Yan
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Guoliang Ye
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yongfu Shao
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, China
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5
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Ding R, Li Y, Zhang Y, Li X, Song Y, Gu X, Shen X, Ju S. Comprehensive assessment of serum 3'-tRF Arg as a novel diagnostic biomarker for gastric cancer. Transl Oncol 2025; 54:102338. [PMID: 40058233 PMCID: PMC11929888 DOI: 10.1016/j.tranon.2025.102338] [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: 08/15/2024] [Revised: 01/15/2025] [Accepted: 02/27/2025] [Indexed: 03/18/2025] Open
Abstract
Gastric cancer is one of the malignant tumors with the highest morbidity and mortality rates worldwide. Yet, there is a lack of diagnostic markers with high sensitivity in the clinic. tRNA-derived small RNAs are a novel type of non-coding small RNAs, which are abundant in tumor cells and body fluids. In this study, we explored the potential of 3'-tRFArg as a tumor marker for the diagnosis of GC. Differential expression of 3'-tRFArg was screened by high-throughput sequencing, and Quantitative real-time PCR confirmed its low expression in GC serum with good stability. Differential expression of serum 3'-tRFArg could distinguish between GC patients, gastritis patients, and healthy donors and was significantly correlated with clinical pathological features such as tumor differentiation, lymph node metastasis, and TNM staging. The receiver operating characteristic curve showed that 3'-tRFArg had a higher diagnostic value compared with conventional biomarkers, especially in the diagnosis of early gastric cancer. In conclusion, our results suggest that 3'-tRFArg can serve as a highly sensitive biomarker with a certain value for monitoring tumor development and prognosis.
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Affiliation(s)
- Rui Ding
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yang Li
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yu Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xun Li
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yunjian Song
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Xinliang Gu
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xianjuan Shen
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
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6
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Vaidhyanathan S, Durbin M, Adetowubo AA, Do LH, Kavehmoghaddam S, Jonnalagadda SA, Aguilar BR, Ortiz-Gomez T, Lin YX, Dave A, Kiliç F, Karp AR, Rahmah MI, Riaz NF, Mandava N, Siner A, Grigoriev A. Mapping Current Studies of tRNA Fragments onto Disease Landscape. Biomolecules 2025; 15:512. [PMID: 40305238 PMCID: PMC12025293 DOI: 10.3390/biom15040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2025] [Revised: 03/27/2025] [Accepted: 03/27/2025] [Indexed: 05/02/2025] Open
Abstract
Transfer-RNA-derived fragments (tRFs) are a relatively recently discovered class of non-coding RNAs derived from both precursor and mature transfer RNAs (tRNAs). Research on these molecules has been expanding rapidly, revealing their diverse roles in cellular processes, both in normal physiology and in disease states, often via post-transcriptional regulation of target genes. Altered tRFs abundances have been implicated in various conditions, where they may act as either drivers of disease progression or as protective agents. For instance, specific tRFs are associated with increased risk for cancer metastasis, while others may suppress tumor cell proliferation. Despite the growing recognition of tRFs as functional RNAs rather than sequencing noise, this field of study faces numerous challenges. Inconsistent naming conventions and variability in experimental approaches hinder the comparison of findings across studies, limiting our understanding of the common roles and mechanisms of tRFs. This review provides a comprehensive analysis of current literature on the various roles of tRFs in different diseases, particularly focusing on four broad areas: cancer, neurological, cardiovascular, and musculoskeletal disorders. We analyze studies that link specific tRFs to various aspects of human diseases and provide a convenient classification of these studies regarding the depth of the provided evidence. Further, we note gaps in current investigations and consider strategies to address methodological inconsistencies, including validation experiments and unified nomenclature. By consolidating research in this manner, we aim to facilitate comparisons across diverse studies, enhancing our ability to identify functional commonalities and furthering our understanding of the mechanisms by which tRFs act.
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Affiliation(s)
- Sathyanarayanan Vaidhyanathan
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; (Y.X.L.); (A.D.); (M.I.R.)
| | - MacKenna Durbin
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Adesupo A. Adetowubo
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Lisa H. Do
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Sheida Kavehmoghaddam
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Sai Anusha Jonnalagadda
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Bryan Ramirez Aguilar
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Tamin Ortiz-Gomez
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; (Y.X.L.); (A.D.); (M.I.R.)
| | - Yan X. Lin
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; (Y.X.L.); (A.D.); (M.I.R.)
| | - Asim Dave
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; (Y.X.L.); (A.D.); (M.I.R.)
| | - Fatmanur Kiliç
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Alexa R. Karp
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Mohammed Imthiyas Rahmah
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; (Y.X.L.); (A.D.); (M.I.R.)
| | - Noor F. Riaz
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Nikhila Mandava
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Aleece Siner
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
| | - Andrey Grigoriev
- Department of Biology, Rutgers University, Camden, NJ 08102, USA; (S.V.); (M.D.); (A.A.A.); (L.H.D.); (S.K.); (S.A.J.); (B.R.A.); (T.O.-G.); (F.K.); (A.R.K.); (N.F.R.); (N.M.); (A.S.)
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; (Y.X.L.); (A.D.); (M.I.R.)
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7
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Kim SI, Lyu H, Pujara DS, Bordiya Y, Bhatt PS, Mayorga J, Zogli PK, Kundu P, Chung H, Yan X, Zhang X, Kim J, Louis J, Yu Q, Kang HG. A nuclear tRNA-derived fragment triggers immunity in Arabidopsis. Commun Biol 2025; 8:533. [PMID: 40169869 PMCID: PMC11962134 DOI: 10.1038/s42003-025-07737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 02/13/2025] [Indexed: 04/03/2025] Open
Abstract
In Arabidopsis, effector-triggered immunity (ETI) against avirulent Pseudomonas syringae pv. tomato (Pst) correlates with the rapid, Dicer-Like 1 (DCL1)-dependent nuclear accumulation of a 31-nt 5'-tRNA fragment derived from Asp-tRNA (tRF31Asp2). Several tRFs, including tRF31Asp2, are induced at early stages of infection and associate with AGO2 in the nucleus. Infiltrating Arabidopsis leaves with synthetic tRF31Asp2 induces over 500 defense-associated genes, conferring immunity against virulent and avirulent Pst as well as aphids, while tRF31Asp2 depletion compromises resistance to avirulent Pst. The biological activity of tRF31Asp2 requires its 5' sequence and predicted stem-loop structure, and its loading into AGO2 or related clade members may contribute to activating defense responses. Chromatin affinity precipitation-sequencing revealed that tRF31Asp2 binds specific sequences in defense genes and the Gypsy superfamily of LTR retrotransposons, particularly at their primer binding sites (PBS). tRF31Asp2 binding appears to modulate transcriptional reprogramming, inducing neighboring tRF-responsive defense genes while suppressing active retrotransposons. Since Gypsy retrotransposon proliferation is primed by tRNA binding at PBS, tRF31Asp2 may exploit a similar mechanism to coordinate defense responses. Together, these findings reveal a role for DCL1 and tRF31Asp2 in regulating plant immunity and transcriptional dynamics at defense-associated loci and retrotransposons.
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Affiliation(s)
- Sung-Il Kim
- Department of Biology, Texas State University, San Marcos, USA
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Haomin Lyu
- Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA
- Huazhi Biotechnology, Changsha, Hunan, China
| | - Dinesh S Pujara
- Department of Biology, Texas State University, San Marcos, USA
- School of Integrated Plant Science, Cornell University, Ithaca, NY, USA
| | - Yogendra Bordiya
- Department of Biology, Texas State University, San Marcos, USA
- Biosciences Division, Thermo Fisher Scientific, Austin, TX, USA
| | - Padam S Bhatt
- Department of Biology, Texas State University, San Marcos, USA
| | - José Mayorga
- Department of Biology, Texas State University, San Marcos, USA
| | - Prince K Zogli
- Department of Entomology & Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
- GALY.CO, Boston, MA, USA
| | - Pritha Kundu
- Department of Entomology & Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - Haewon Chung
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
- Synthetic biology, Asimov, Boston, MA, USA
| | - Xingxing Yan
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Xiuren Zhang
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Joe Louis
- Department of Entomology & Department of Biochemistry, University of Nebraska, Lincoln, NE, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA Agricultural Research Service, Hilo, HI, USA
| | - Hong-Gu Kang
- Department of Biology, Texas State University, San Marcos, USA.
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8
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Wei D, Zhai B, Zeng H, Liu L, Gao H, Xiang S, Liu X, Ma J, Lin Y, Yao Y, Wang P. TRMT10A regulates tRNA-ArgCCT m 1G9 modification to generate tRNA-derived fragments influencing vasculogenic mimicry formation in glioblastoma. Cell Death Dis 2025; 16:209. [PMID: 40140670 PMCID: PMC11947273 DOI: 10.1038/s41419-025-07548-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 02/23/2025] [Accepted: 03/17/2025] [Indexed: 03/28/2025]
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary central nervous system tumor. The formation of vasculogenic mimicry (VM) in GBM is closely related to poor patient prognosis. Therefore, it is urgently necessary to explore the mechanisms that promote VM formation in GBM and identify therapeutic targets. CGGA data analysis revealed that TRMT10A expression is significantly downregulated in WHO grade IV primary glioma samples compared to grade II samples, consistent with the protein expression levels. Additionally, GBM patients with low TRMT10A expression have poorer prognoses. In human glioma cells, TRMT10A expression is significantly lower than in human astrocytes. Knockdown of TRMT10A reduces m1G9 modification of tRNA-ArgCCT, upregulates tRF-22 expression, and promotes glioma cell proliferation, migration, invasion, and tube formation. Overexpression of tRF-22 in glioma cells significantly downregulates MXD1 expression. tRF-22 negatively regulates MXD1 expression by binding to its 3'UTR, reducing MXD1's transcriptional inhibition of HIF1A, thereby promoting glioma cell proliferation, migration, invasion, and tube formation. Overexpression of TRMT10A combined with tRF-22 inhibition significantly reduces the number of VM channels and inhibits tumor growth in xenograft models in nude mice. This study elucidates the mechanism by which TRMT10A affects VM formation in glioma and provides a novel therapeutic target for GBM.
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Affiliation(s)
- Deng Wei
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Bei Zhai
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Hui Zeng
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Long Liu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Han Gao
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Shiqi Xiang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jun Ma
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Yang Lin
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China
| | - Yilong Yao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, China.
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9
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Swain SP, Bisht N, Kumar S. Comprehensive study of tRNA-derived fragments in plants for biotic stress responses. Funct Integr Genomics 2025; 25:70. [PMID: 40131555 DOI: 10.1007/s10142-025-01576-3] [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: 01/12/2025] [Revised: 02/28/2025] [Accepted: 03/11/2025] [Indexed: 03/27/2025]
Abstract
Plant growth and development are often disrupted by biological stressors as they interfere with the regulatory pathways. Among the key regulators, transfer-RNA-derived fragments (tRFs) have emerged as key players in plant defense mechanisms. While tRF-mediated responses to abiotic stress have been well studied, their role in biotic stress remains less understood, as various stressors may elicit different regulatory systems. In this study, tRF-mediated biotic responses in three species, viz. Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum are investigated using in-silico approaches. Analysis of predicted tRFs across various biotic stress conditions reveals specific interactions with mRNA targets, microRNAs (miRNAs), and transposable elements (TEs), highlighting their regulatory significance in plant adaptation mechanisms. These findings provide new insights into tRF-mediated stress responses and establish a computational framework for further functional studies. The study's database is publicly available at http://www.nipgr.ac.in/PbtRFdb .
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Affiliation(s)
- Supriya P Swain
- Bioinformatics Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niyati Bisht
- Bioinformatics Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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10
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Yin N, Xie X, Li D, Yang S, Liu Y, Tang Y, Zhang H, Zhang W. tRF-Val-TAC-004 protects against renal ischemia-reperfusion injury via attenuating Apaf1-mediated apoptosis. iScience 2025; 28:111954. [PMID: 40104049 PMCID: PMC11914182 DOI: 10.1016/j.isci.2025.111954] [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: 08/29/2024] [Revised: 10/22/2024] [Accepted: 01/31/2025] [Indexed: 03/20/2025] Open
Abstract
tRNA-derived fragments (tRFs) play critical roles in cellular process, and we have previously reported that tRFs are involved in ischemia reperfusion injury induced acute kidney injury (IRI-AKI). However, the precise involvement of tRFs in IRI-AKI remains obscure. This study aims to elucidate the impact of tRF-Val-TAC-004 (tRF-Val) on IRI-AKI and uncover the underlying mechanisms. Our observations reveal a significant downregulation of tRF-Val in IRI-AKI mice and its overexpression mitigated renal dysfunction, morphological damage, and apoptosis in IRI-AKI mice, while its inhibition exacerbated these effects. Similar outcomes were replicated in CoCl2-treated BUMPT cells upon transfection with tRF-Val mimic or inhibitor. Mechanistically, dual-luciferase reporter assay and AGO-RIP qPCR analyses demonstrated that tRF-Val suppresses Apaf1 expression by targeting the 3'-UTR of Apaf1 mRNA. Furthermore, the protective efficacy of tRF-Val was notably weakened by Apaf1-overexpressing plasmids. In summary, these novel findings unveil the protective role of tRF-Val against IRI-AKI through inhibition of Apaf1-mediated apoptosis.
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Affiliation(s)
- Ni Yin
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
| | - Xian Xie
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
| | - Dan Li
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
| | - Shikun Yang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
| | - Yan Liu
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
| | - Yongzhong Tang
- Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
| | - Wei Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Clinical Research Center for Critical Kidney Disease in Hunan Province, Changsha, Hunan 410013, China
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11
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Guan L, Vaidhyanathan S, Grigoriev A. rRFtargetDB: a database of Ago1-mediated targets of ribosomal RNA fragments. RNA (NEW YORK, N.Y.) 2025; 31:486-496. [PMID: 39788736 PMCID: PMC11912905 DOI: 10.1261/rna.080285.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 12/17/2024] [Indexed: 01/12/2025]
Abstract
rRNA-derived fragments (rRFs) are a class of emerging posttranscriptional regulators of gene expression likely binding to the transcripts of target genes. However, the lack of knowledge about such targets hinders our understanding of rRF functions or binding mechanisms. The paucity of resources supporting the identification of the targets of rRFs creates a bottleneck in the fast-developing field. We have previously analyzed chimeric reads in cross-linked Argonaute1-RNA complexes to help infer the guide-target pairs and binding mechanisms of multiple rRFs based on experimental data in human HEK293 cells. To efficiently disseminate these results to the research community, we designed a web-based database rRFtargetDB that preserves most of the experimental results after the removal of noise and has a user-friendly interface with flexible query options and filters allowing users to obtain comprehensive information on rRFs (or targets) of interest. rRFtargetDB is populated by ∼163,000 experimentally determined unique rRF-mRNA pairs (∼60,000 supported by ≥2 reads). Almost 30,000 rRF isoforms produced >385,000 (>156,000 with ≥2 reads) chimeras with all types of RNA targets (mRNAs and noncoding RNAs). Further analyses suggested hypothetical modes of interactions, supported by secondary structures of potential guide-target hybrids and binding motifs, essential for understanding the targeting mechanisms of rRFs. All these results (ranging from the weakest to the strongest experimental support) are presented in rRFtargetDB, whose goal is to provide a resource for building users' hypotheses on the potential roles of rRFs for experimental validation. Further, we illustrate the value/application of the database in several examples.rRFtargetDB is freely accessible at https://grigoriev-lab.camden.rutgers.edu/tardb.
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Affiliation(s)
- Lingyu Guan
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Sathyanarayanan Vaidhyanathan
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
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12
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Saad AAA, Zhang K, Deng Q, Zhou J, Ge L, Wang H. The functions and modifications of tRNA-derived small RNAs in cancer biology. Cancer Metastasis Rev 2025; 44:38. [PMID: 40072687 DOI: 10.1007/s10555-025-10254-6] [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: 07/01/2024] [Accepted: 02/19/2025] [Indexed: 03/14/2025]
Abstract
Recent progress in noncoding RNA research has highlighted transfer RNA-derived small RNAs (tsRNAs) as key regulators of gene expression, linking them to numerous cellular functions. tsRNAs, which are produced by ribonucleases such as angiogenin and Dicer, are classified based on their size and cleavage positions. They play diverse regulatory roles at the transcriptional, post-transcriptional, and translational levels. Furthermore, tRNAs undergo various modifications that influence their biogenesis, stability, functionality, biochemical characteristics, and protein-binding affinity. tsRNAs, with their aberrant expression patterns and modifications, act as both oncogenes and tumor suppressors. This review explores the biogenetic pathways of tsRNAs and their complex roles in gene regulation. We then focus on the importance of RNA modifications in tsRNAs, evaluating their impact on the biogenesis and biological functions on tsRNAs. Furthermore, we summarize recent data indicating that tsRNAs exhibit varied expression profiles across different cancer types, highlighting their potential as innovative biomarkers and therapeutic targets. This discussion integrates both existing and new knowledge about tsRNAs, emphasizing their importance in cancer biology and clinical advancement.
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Affiliation(s)
- Abdulaziz Ahmed A Saad
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, The State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Kun Zhang
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Nanbu People'S Hospital; Affiliated Cancer Hospital of Chengdu Medical College, School of Biological Sciences and Technology, Chengdu Medical College, Chengdu, 610500, China
| | - Qianqian Deng
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, The State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Jiawang Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, The State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Lichen Ge
- Department of Laboratory Medicine, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Hongsheng Wang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, The State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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13
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Bakowska-Zywicka K, Rzepczak A, Plawgo K, Sobanska D, Tyczewska A. tRNA-Derived Fragments in Age-Related Diseases: A Systematic Review. WILEY INTERDISCIPLINARY REVIEWS. RNA 2025; 16:e70013. [PMID: 40263934 DOI: 10.1002/wrna.70013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 03/27/2025] [Accepted: 03/31/2025] [Indexed: 04/24/2025]
Abstract
Aging is a progressive weakening of numerous functions of organisms resulting in diminished abilities to safeguard against environmental damage and augment physiological harmony. It is not a disease in itself; however, it is a main cause of debilitating and life-threatening chronic aging-related diseases (ARDs). tRNA-derived fragments (tDRs) are stable forms of tRNAs of 14-35 nt in length that function as regulatory small-RNA molecules. Here we aimed to perform a systematic review of original articles on the involvement of tDRs in the etiology of ARDs: their identification and characterization. The systematic review was conducted according to the Cochrane Handbook guidelines and the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement. Based on the eligibility criteria defined for the study, 21 original articles were included in this systematic review, covering 11 ARDs. The preferred research method used to study tDRs was high-throughput sequencing combined with RT-qPCR, and as a result, a number of tDRs were implicated in ARDs. Importantly, an in-depth analysis of the articles allowed us to identify several shortcomings: (i) the tDRs nomenclature varies between studies and articles, making it often difficult to precisely identify molecules differentiating in a given disease; (ii) the chosen tDRs have all been studied for a miRNA-like mechanism of action; however, tDRs also function in RNAi-independent ways, which need to be studied as well; (iii) to precisely identify tDRs, the sequencing techniques that overcome the issues of modifications harbored by tRNAs must be used.
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Affiliation(s)
| | - Alicja Rzepczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Kinga Plawgo
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Daria Sobanska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - Agata Tyczewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
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14
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Zhao S, Wang Y, Zhou L, Li Z, Weng Q. Exploring the Potential of tsRNA as Biomarkers for Diagnosis and Treatment of Neurogenetic Disorders. Mol Neurobiol 2025:10.1007/s12035-025-04760-5. [PMID: 40009263 DOI: 10.1007/s12035-025-04760-5] [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: 06/04/2024] [Accepted: 02/08/2025] [Indexed: 02/27/2025]
Abstract
tRNA-derived small RNA (tsRNA) is a recently discovered small non-coding RNA (ncRNA) molecule that widely exists in prokaryotic and eukaryotic transcriptomes and is produced by specific cleavage of mature tRNA or precursor tRNA. In recent years, with the development of high-throughput sequencing technology, tsRNA has been found to have a variety of biological functions, including gene expression regulation, stress signal activation, etc. In addition, it has been found that these molecules are abnormally expressed in various diseases and participate in various pathological processes, which play an important role. At present, more and more studies have shown that the expression level of tsRNA changes significantly during the development of neurogenetic diseases. This review provides an overview of the classification and biological functions of tsRNAs, with a particular emphasis on their roles in neurogenetic disorders and their potential as diagnostic biomarkers and therapeutic targets. Despite the nascent stage of tsRNA research, their relevance to the diagnosis and treatment of neurogenetic diseases warrants further investigation.
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Affiliation(s)
- Shiqi Zhao
- Department of Neurology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yujia Wang
- Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Liqun Zhou
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Zhe Li
- Department of Neurology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China.
| | - Qiuyan Weng
- Department of Neurology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China.
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15
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Chen Y, Shao Z, Wu S. Research progress on the tsRNA biogenesis, function, and application in lung cancer. Noncoding RNA Res 2025; 10:63-69. [PMID: 39309197 PMCID: PMC11414277 DOI: 10.1016/j.ncrna.2024.09.004] [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: 06/25/2024] [Revised: 08/18/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
In recent years, there has been a mounting occurrence of lung cancer, which stands as one of the most prevalent malignancies globally. This rise in incidence poses a significant hazard to human health, making lung cancer a matter of grave concern. It has been shown that tRNA-derived small non-coding RNA (tsRNA) is involved in the development of tumors, especially lung cancer, through mechanisms such as regulating mRNA stability, influencing protein translation, and acting as epigenetic regulators. Recent studies have shown that tsRNA is abnormally expressed in the plasma and tissues of lung cancer patients, and its expression level is closely related to the malignancy degree and postoperative recurrence of lung cancer. Therefore, for lung cancer patients, tsRNA represents a promising non-invasive biomarker, exhibiting significant potential for facilitating early diagnosis and prognostic evaluation, and for achieving precision treatment of lung cancer by regulating its expression. This article focuses on the biogenesis of tsRNA and its ability to promote lung cancer cell proliferation and invasion. In addition, the specific clinical significance of tsRNA in lung cancer was discussed. Finally, we discuss the need for further improvement of small RNA sequencing technology, and the future research directions and strategies of tsRNA in lung cancer and tumor diseases were summarized.
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Affiliation(s)
- Yu Chen
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Zhuowei Shao
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Shibo Wu
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
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16
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Esmaeili F, Banerjee K, Su Z, Dutta A. A general framework to over-express tRNA-derived fragments from their parental tRNAs in mammalian cells. Methods Enzymol 2025; 711:241-259. [PMID: 39952708 PMCID: PMC12020451 DOI: 10.1016/bs.mie.2024.11.008] [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] [Indexed: 02/17/2025]
Abstract
tRNA-derived fragments (tRFs), generated from the cleavage of mature or precursor tRNAs are a category of regulatory noncoding RNAs with diverse functions in physiological or pathophysiological conditions. Here we describe a framework for the over-expression of tRFs from their parental tRNAs in mammalian cells. The process involves bioinformatics analysis to identify specific tRNAs that produce the tRF, PCR amplification of corresponding tRNA genes, and insertion into expression vectors. Transfection is carried out in HEK293T cells and detection of tRFs is achieved through northern blotting and dual luciferase reporter assays. In the latter, a complementary sequence to the tRF of interest is inserted into the luciferase reporter. By observing the reduction in luciferase activity, we can validate the expression of tRFs. This method enables precise study of tRF functions and their roles in cellular processes.
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Affiliation(s)
- Fatemeh Esmaeili
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kumarjeet Banerjee
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zhangli Su
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Anindya Dutta
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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17
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Akhatova A, Jones C, Coward K, Yeste M. How do lifestyle and environmental factors influence the sperm epigenome? Effects on sperm fertilising ability, embryo development, and offspring health. Clin Epigenetics 2025; 17:7. [PMID: 39819375 PMCID: PMC11740528 DOI: 10.1186/s13148-025-01815-1] [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: 09/05/2024] [Accepted: 01/08/2025] [Indexed: 01/19/2025] Open
Abstract
Recent studies support the influence of paternal lifestyle and diet before conception on the health of the offspring via epigenetic inheritance through sperm DNA methylation, histone modification, and small non-coding RNA (sncRNA) expression and regulation. Smoking may induce DNA hypermethylation in genes related to anti-oxidation and insulin resistance. Paternal diet and obesity are associated with greater risks of metabolic dysfunction in offspring via epigenetic alterations in the sperm. Metabolic changes, such as high blood glucose levels and increased body weight, are commonly observed in the offspring of fathers subjected to chronic stress, in addition to an enhanced risk of depressive-like behaviour and increased sensitivity to stress in both the F0 and F1 generations. DNA methylation is correlated with alterations in sperm quality and the ability to fertilise oocytes, possibly via a differentially regulated MAKP81IP3 signalling pathway. Paternal exposure to toxic endocrine-disrupting chemicals (EDCs) is also linked to the transgenerational transmission of increased predisposition to disease, infertility, testicular disorders, obesity, and polycystic ovarian syndrome (PCOS) in females through epigenetic changes during gametogenesis. As the success of assisted reproductive technology (ART) is also affected by paternal diet, BMI, and alcohol consumption, its outcomes could be improved by modifying factors that are dependent on male lifestyle choices and environmental factors. This review discusses the importance of epigenetic signatures in sperm-including DNA methylation, histone retention, and sncRNA-for sperm functionality, early embryo development, and offspring health. We also discuss the mechanisms by which paternal lifestyle and environmental factors (obesity, smoking, EDCs, and stress) may impact the sperm epigenome.
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Affiliation(s)
- Ayazhan Akhatova
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
- School of Medicine, Nazarbayev University, Zhanybek-Kerey Khan Street 5/1, 010000, Astana, Kazakhstan
| | - Celine Jones
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin Coward
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, 17003, Girona, Spain.
- Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, 17003, Girona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.
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18
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Jia H, Zhang L. tRNA-derived small RNAs in disease immunity. Theranostics 2025; 15:245-257. [PMID: 39744232 PMCID: PMC11667222 DOI: 10.7150/thno.102650] [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: 08/22/2024] [Accepted: 11/08/2024] [Indexed: 01/11/2025] Open
Abstract
Recently, members of a unique species of non-coding RNA, known as transfer RNA-derived small RNAs (tsRNAs) have been reported to serve multiple molecular functions, including in cells that mediate immunity. Because of their low molecular weights, tsRNAs were previously difficult to detect and were thus overlooked, until now. In this review, we delve into the biogenesis of tsRNAs and their diverse biological functions, ranging from transcriptional regulation to modulation of mRNA translation. We highlight the current evidence demonstrating their involvement in the immune response, as well as how tsRNAs modulate immunity to influence tumor growth and spread, autoimmune disease pathology and infection by pathogens. We surmise that tsRNAs are likely informative as diagnostic markers of cellular homeostasis and disease, and that therapeutic targeting of tsRNAs could be beneficial for a range of human diseases. Improved knowledge on the functions for tsRNAs in the mammalian immune system will enable us to leverage tsRNAs for their effective clinical use as treatments for human health challenges.
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Affiliation(s)
- Hongyuan Jia
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Linling Zhang
- Department of Respiratory and Critical Care, Chengdu Third People's Hospital, Chengdu, China
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19
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Oberbauer V, Drino A, Schaefer MR. Determining small RNA-interacting proteomes using endogenously modified tRNA-derived RNAs. Methods Enzymol 2024; 711:356-380. [PMID: 39952715 DOI: 10.1016/bs.mie.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2025]
Abstract
tRNA-derived RNAs (tDRs), resulting from enzyme-mediated hydrolysis of tRNAs, have been implicated as active small RNAs in various molecular processes. While the molecular modes of action for these small RNAs remain unclear, attempts to decipher the mechanistic details of tDR functionality have mostly used synthetic tDR sequences. Since parental tRNAs are extensively post-transcriptionally modified, tDR functionality is likely affected by chemical modifications. To help approach the biological function of endogenously modified tDRs, this contribution details a protocol that allows purifying specific tDRs carrying post-transcriptional modifications from both in vivo and in vitro sources. Purified tDRs can be used for various downstream applications including differential affinity capture of tDR-binding proteins, the details of which are also described in this contribution.
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Affiliation(s)
- Vera Oberbauer
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse, Vienna, Austria
| | - Aleksej Drino
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse, Vienna, Austria
| | - Matthias R Schaefer
- Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse, Vienna, Austria.
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20
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Li G, Das S. Self-quenched tRNA reporters for imaging tRNA-derived RNA biogenesis. Methods Enzymol 2024; 711:324-335. [PMID: 39952713 PMCID: PMC11995413 DOI: 10.1016/bs.mie.2024.11.025] [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] [Indexed: 02/17/2025]
Abstract
tRNA-derived small RNAs (tDRs) are an emerging class of small non-coding RNAs that play crucial roles in various cellular processes. However, there is a paucity of data on their sub-cellular localization due to a lack of tools and reagents to image tDRs. Imaging tDRs remains challenging due to the similar sequences between tDR and its parent tRNA. Here, we describe an innovative tool for studying the formation and localization of tDRs in various biological processes using a self-quenched tDR biogenesis reporter. This method utilizes a full-length tRNA molecule conjugated with both fluorescence and quencher groups at 5'- and 3'- ends. In its intact state, the fluorescence is quenched. Upon cleavage by specific ribonucleases and strand separation, the fluorescence becomes detectable, allowing real-time imaging of tDR biogenesis. This protocol details the design, synthesis, and application of this reporter, including transfection procedures and imaging techniques. The method offers a powerful approach for investigating tDR dynamics in living cells, providing insights into their roles in cellular processes and stress responses.
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Affiliation(s)
- Guoping Li
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States; Department of Anesthesia, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
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21
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He M, Yin S, Huang X, Li Y, Li B, Gong T, Liu Q. Insights into the regulatory role of bacterial sncRNA and its extracellular delivery via OMVs. Appl Microbiol Biotechnol 2024; 108:29. [PMID: 38159117 DOI: 10.1007/s00253-023-12855-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] [Received: 05/23/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
Small noncoding RNAs (sncRNAs) play important regulatory roles in bacterial physiological processes and host-pathogen interactions. Meanwhile, bacterial outer membrane vesicles (OMVs), as naturally secreted outer membrane structures, play a vital role in the interaction between bacteria and their living environment, including the host environment. However, most current studies focus on the biological functions of sncRNAs in bacteria or hosts, while neglecting the roles and regulatory mechanisms of the OMVs that encapsulate these sncRNAs. Therefore, this review aims to summarize the intracellular regulatory roles of bacterial sncRNAs in promoting pathogen survival by regulating virulence, modulating bacterial drug resistance, and regulating iron metabolism, and their extracellular regulatory function for influencing host immunity through host-pathogen interactions. Additionally, we introduce the key role played by OMVs, which serve as important cargoes in bacterial sncRNA-host interactions. We propose emerging pathways of sncRNA action to further discuss the mode of host-pathogen interactions, highlighting that the inhibition of sncRNA delivery by OMVs may prevent the occurrence of infection to some extent. Hence, this review lays the foundation for future prophylactic treatments against bacterial infections and strategies for addressing bacterial drug resistance. KEY POINTS: •sncRNAs have intracellular and extracellular regulatory functions in bacterial physiological processes and host-pathogen interactions. •OMVs are potential mediators between bacterial sncRNAs and host cells. •OMVs encapsulating sncRNAs have more potential biological functions.
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Affiliation(s)
- Mengdan He
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Shuanshuan Yin
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Xinlei Huang
- Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Yi Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Biaoxian Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| | - Qiong Liu
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China.
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22
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Yuan J, Song Z, Liu J, Rahman KU, Zhou Q, Liu G, Deng Y, Wen H, Fan X, Fang N, Zhou Z, Song Q, Zhang G, Li P, Song Y. Transfer RNAs and transfer RNA-derived small RNAs in cerebrovascular diseases. Exp Neurol 2024; 382:114971. [PMID: 39326819 DOI: 10.1016/j.expneurol.2024.114971] [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: 06/23/2024] [Revised: 08/30/2024] [Accepted: 09/21/2024] [Indexed: 09/28/2024]
Abstract
This article explores the important functions of transfer RNA and - transfer RNA derived small RNAs (tsRNAs) in cellular processes and disease pathogenesis, with a particular emphasis on their involvement in cerebrovascular disorders. It discusses the biogenesis and structure of tsRNAs, including types such as tRNA halves and tRNA-derived fragments, and their functional significance in gene regulation, stress response, and cell signaling pathways. The importance of tsRNAs in neurodegenerative diseases, cancer, and cardiovascular diseases has already been highlighted, while their role in cerebrovascular diseases is in early phase of exploration. This paper presents the latest advancements in the field of tsRNAs in cerebrovascular conditions, such as ischemic stroke, intracerebral hemorrhage, and moyamoya disease. Furthermore, revealing the aptitude of tsRNAs as biomarkers for the prediction of cerebrovascular diseases and as targets for therapeutic intervention. It provides insights into the role of tsRNAs in these conditions and proposes directions for future research.
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Affiliation(s)
- Jiajie Yuan
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Zibin Song
- Neurosurgery Center, Department of Functional Neurosurgery, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Jun Liu
- Department of Neurosurgery, the 2nd affiliated hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Khalil Ur Rahman
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Qixiong Zhou
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Guangjie Liu
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Yifeng Deng
- First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Haotian Wen
- First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xiaonan Fan
- First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Nanqi Fang
- First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhaojun Zhou
- First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Qiancheng Song
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China
| | - Guozhong Zhang
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China.
| | - Peng Li
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China.
| | - Ye Song
- Department of Neurosurgery, Institute of Brain Diseases, Nanfang Hospital of Southern Medical University, Guangzhou 510515, China; Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China.
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23
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Li T, Zhen H, Wu W, Yang F, Cao Z. tsRNAs: A Prospective, Effective Therapeutic Intervention for Neurodegenerative Diseases. CNS Neurosci Ther 2024; 30:e70177. [PMID: 39690867 DOI: 10.1111/cns.70177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 11/11/2024] [Accepted: 12/03/2024] [Indexed: 12/19/2024] Open
Abstract
BACKGROUND Neurological disorders known as neurodegenerative diseases (NDDs) result in the slow loss of neurons in the central nervous system (CNS) or peripheral nervous system (PNS), as well as the collapse of neural networks in terms of structure and function. NDDs are expected to surpass cancer as the second biggest cause of mortality by 2040, according to World Health Organization (WHO) estimations. Neurons cannot effectively regenerate themselves because they are terminally differentiated. Accordingly, it is challenging to find medications that could stop or slow neurodegeneration. MAIN BODY The tsRNAs are a type of small non-coding RNAs derived from mature tRNAs or tRNA precursors. tsRNAs control gene expression and have a role in many physiological and pathological processes, including neurological illnesses. Antisense oligonucleotides are effective therapeutic agents for neurological diseases, and they may be the treatment of choice for neurodegenerative diseases in the future. Here, we review the biogenesis of tsRNA, its physiological and pathological functions in the central nervous system and neurological disorders, and its prospective use as a nucleic acid medication to treat NDDs, providing theoretical support and guidance for further exploration of tsRNAs in therapeutic intervention. CONCLUSION tsRNAs are emerging as important regulatory molecules in neurodegenerative diseases. Understanding the functions of tsRNAs in neurodegenerative diseases may provide new insights into disease mechanisms and lead to the development of novel treatment strategies.
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Affiliation(s)
- Tianqi Li
- School of Life Science and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Hui Zhen
- School of Life Science and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Weiwei Wu
- School of Life Science and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Fengtang Yang
- School of Life Science and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Zhonghong Cao
- School of Life Science and Medicine, Shandong University of Technology, Zibo, Shandong, China
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24
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Gong L, Hu Y, Pan L, Cheng Y. tRNA-derived small RNAs (tsRNAs): establishing their dominance in the regulation of human cancer. Front Genet 2024; 15:1466213. [PMID: 39659673 PMCID: PMC11628509 DOI: 10.3389/fgene.2024.1466213] [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: 07/17/2024] [Accepted: 11/11/2024] [Indexed: 12/12/2024] Open
Abstract
The main function of transfer RNAs (tRNAs) is to carry amino acids into the ribosome and synthesize proteins under the guidance of messenger RNAs (mRNAs). In addition to this, it has been observed that tRNAs undergo precise cleavage at specific loci, giving rise to an extensive array of distinct small RNAs, termed tRNA-derived small RNAs (tsRNAs). Existing studies have shown that tsRNAs are widely present across various organisms and comprehensively regulate gene expression, aberrant expression of tsRNAs is inextricably linked to tumorigenesis and development, thus, a systematic understanding of tsRNAs is necessary. This review aims to comprehensively delineate the genesis and expression patterns of tsRNAs, elucidate their diverse functions and emphasize their prospective clinical application as biomarkers and targets for therapy. It is noteworthy that we innovatively address the roles played by tsRNAs in human cancers at the level of the hallmarks of tumorigenesis proposed by Hanahan in anticipation of a broad understanding of tsRNAs and to guide the treatment of tumors.
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Affiliation(s)
- Li Gong
- Department of Radiation Oncology, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong, China
| | - Yajie Hu
- Department of Radiation Oncology, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong, China
| | - Ling Pan
- Department of Radiation Oncology, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong, China
- Research Center for Basic Medical Sciences, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yufeng Cheng
- Department of Radiation Oncology, Cheeloo College of Medicine, Qilu Hospital of Shandong University, Shandong University, Jinan, Shandong, China
- Research Center for Basic Medical Sciences, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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25
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Goldkamp AK, Atchison RG, Falkenberg SM, Dassanayake RP, Neill JD, Casas E. Transfer RNA-derived fragment production in calves challenged with Mycoplasma bovis or co-infected with bovine viral diarrhea virus and Mycoplasma bovis in several tissues and blood. Front Vet Sci 2024; 11:1463431. [PMID: 39582886 PMCID: PMC11583443 DOI: 10.3389/fvets.2024.1463431] [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: 07/12/2024] [Accepted: 10/28/2024] [Indexed: 11/26/2024] Open
Abstract
Understanding the molecular mechanisms underlying immune response can allow informed decisions in drug or vaccine development, and aid in the identification of biomarkers to predict exposure or evaluate treatment efficacy. The objective of this study was to identify differentially expressed transfer RNA-derived fragments (tRFs) in calves challenged with Mycoplasma bovis (M. bovis) or co-infected with M. bovis and bovine viral diarrhea virus (BVDV). Serum, white blood cells (WBC), liver, mesenteric lymph node (MLN), tracheal-bronchial lymph node (TBLN), spleen, and thymus were collected from Control (n = 2), M. bovis (MB; n = 3), and co-infected (Dual; n = 3) animals, and small RNAs extracted for sequencing. An average of 94% of reads were derived from 5` halves and/or 5` tRFs in serum, liver, WBC, TBLN, spleen, MLN, and thymus. The expression of tRFs in lymphatic tissues (MLN, TBLN, Thymus, Spleen) were highly correlated with each other (r ≥ 0.82), but not with serum and WBC. A total of 25 and 65 differentially expressed tRFs were observed in liver and thymus, respectively. There were no differentially expressed tRFs found in other tissues analyzed. Nineteen thymus tRFs were differentially expressed in Dual compared to Control and MB, and the predicted targets of these tRFs were associated with MAPK signaling pathways and ERK1 and ERK2 cascades. The differentially expressed tRFs found in thymus and liver may underlie mechanisms of thymic depletion or liver inflammation previously observed in BVDV. Additional studies should be pursued to investigate differential expression of the predicted tRF targets.
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Affiliation(s)
| | | | | | | | | | - Eduardo Casas
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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26
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Buck AH, Nolte-'t Hoen ENM. The Nature and Nurture of Extracellular Vesicle-Mediated Signaling. Annu Rev Genet 2024; 58:409-432. [PMID: 39231450 DOI: 10.1146/annurev-genet-111523-102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
In the last decade, it has become clear that extracellular vesicles (EVs) are a ubiquitous component of living systems. These small membrane-enclosed particles can confer diverse functions to the cells that release, capture, or coexist with them in an environment. We use examples across living systems to produce a conceptual framework that classifies three modes by which EVs exert functions: (a) EV release that serves a function for producing cells, (b) EV modification of the extracellular environment, and (c) EV interactions with, and alteration of, receiving cells. We provide an overview of the inherent properties of EVs (i.e., their nature) as well as factors in the environment and receiving cell (i.e., nurture) that determine whether transmission of EV cargo leads to functional cellular responses. This review broadens the context for ruminating on EV functions and highlights the emergent properties of EVs that define their role in biology and will shape their applications in medicine.
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Affiliation(s)
- Amy H Buck
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom;
| | - Esther N M Nolte-'t Hoen
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands;
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27
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Baindoor S, Gibriel HAY, Venø MT, Su J, Morrissey EP, Jirström E, Woods I, Kenny A, Alves M, Halang L, Fabbrizio P, Bilen M, Engel T, Hogg MC, Bendotti C, Nardo G, Slack RS, Kjems J, Prehn JHM. Distinct fingerprints of tRNA-derived small non-coding RNA in animal models of neurodegeneration. Dis Model Mech 2024; 17:dmm050870. [PMID: 39552337 PMCID: PMC11603119 DOI: 10.1242/dmm.050870] [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: 04/30/2024] [Accepted: 10/17/2024] [Indexed: 11/19/2024] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) - categorized as tRNA-derived fragments (tRFs), tRNA-derived stress-induced RNAs (tiRNAs) and internal tRF (itRF) - are small non-coding RNAs that participate in various cellular processes such as translation inhibition and responses to cellular stress. We here identified tsRNA profiles within susceptible tissues in animal models of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Parkinson's disease (PD) to pinpoint disease-specific tsRNAs and those shared across neurodegenerative diseases. We performed small RNA sequencing in the SOD1G93A and TDP43A315T mouse models of ALS (spinal cord), the TauP301S model of FTD (hippocampus), and the parkin/POLG model of PD (substantia nigra). Bioinformatic analysis showed higher expression of 5' tiRNAs selectively in the two ALS models, lower expression of 3' tRFs in both the ALS and FTD mouse models, and lower expression of itRF Arg in the PD model. Experimental validation confirmed the expression of tsRNAs. Gene Ontology analysis of targets associated with validated 3' tRFs indicated functions in the regulation of synaptic and neuronal pathways. Our profiling of tsRNAs indicates disease-specific fingerprints in animal models of neurodegeneration, which require validation in human disease.
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Affiliation(s)
- Sharada Baindoor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Hesham A. Y. Gibriel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | | | - Junyi Su
- Omiics ApS, DK-8200 Aarhus N, Denmark
- Interdisciplinary Nanoscience Centre, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Elena Perez Morrissey
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Elisabeth Jirström
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Ina Woods
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Aidan Kenny
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Mariana Alves
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Luise Halang
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Paola Fabbrizio
- Laboratory of Neurobiology and Preclinical Therapeutics, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via Mario Negri, 2, 20156 Milan, Italy
| | - Maria Bilen
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Tobias Engel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
| | - Marion C. Hogg
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
- Department of Biosciences, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Caterina Bendotti
- Laboratory of Neurobiology and Preclinical Therapeutics, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via Mario Negri, 2, 20156 Milan, Italy
| | - Giovanni Nardo
- Laboratory of Neurobiology and Preclinical Therapeutics, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via Mario Negri, 2, 20156 Milan, Italy
| | - Ruth S. Slack
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Centre, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jochen H. M. Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases, Royal College of Surgeons in Ireland, Dublin D02 YN77, Ireland
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28
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Chang X, Du M, Wei J, Zhang Y, Feng X, Deng B, Liu P, Wang Y. Serum tsncRNAs reveals novel potential therapeutic targets of Salvianolic Acid B on atherosclerosis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 134:155994. [PMID: 39243751 DOI: 10.1016/j.phymed.2024.155994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 07/17/2024] [Accepted: 08/26/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Salvianolic Acid B (SalB) has been proven to delay the progression of atherosclerosis. The therapeutic mechanisms of this compound are unclear. A novel class of short non-coding RNAs, pre-transfer RNA and mature transfer RNA (tsncRNAs) may regulate gene expression. TsncRNAs-sequencing revealed novel therapeutic targets for SalB. This is the first study focusing on tsncRNAs to treat atherosclerosis using SalB. PURPOSE To explore the potential mechanism of SalB treating atherosclerosis through tsncRNAs. METHODS Five groups of mice were created at random: control group (CON), atherosclerosis model group (MOD), SalB with high dose-treated group (SABH), SalB with low dose-treated group (SABL), and Simvastatin-treated group (ST). Aortic sinus plaque, body weight and inflammatory cytokines were evaluated. The Illumina NextSeq equipment was used to do expression profiling of tsncRNAs from serum. The targets of tsncRNAs were then predicted using tRNAscan and TargetScan. The KEGG pathway and GO analysis were utilized to forecast the bioinformatics analysis. Potential tsncRNAs and associated mRNAs were validated using quantitative real-time PCR. RESULTS tRF-Glu-CTC-014 and tRF-Gly-GCC-074 were markedly increased by SalB with high dose treatment and validated with quantitative real-time PCR. Two mRNAs SRF and Arrb related to tRF-Glu-CTC-014 changed consistently. GO analysis revealed that the altered target genes of the selected tsncRNAs were most enriched in protein binding and cellular process. Moreover, KEGG pathway analysis demonstrated that altered target genes of tsncRNAs were most enriched in MAPK signaling pathway. CONCLUSION SalB can promote the expression of tRF-Glu-CTC-014 to treat atherosclerosis.
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Affiliation(s)
- Xindi Chang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Min Du
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Jing Wei
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Yifan Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Xiaoteng Feng
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Bing Deng
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Ping Liu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
| | - Yiru Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
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29
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Wang M, Guo J, Chen W, Wang H, Hou X. Emerging roles of tRNA-derived small RNAs in injuries. PeerJ 2024; 12:e18348. [PMID: 39465146 PMCID: PMC11512806 DOI: 10.7717/peerj.18348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/27/2024] [Indexed: 10/29/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are a novel class of small noncoding RNAs, precisely cleaved from tRNA, functioning as regulatory molecules. The topic of tsRNAs in injuries has not been extensively discussed, and studies on tsRNAs are entering a new era. Here, we provide a fresh perspective on this topic. We systematically reviewed the classification, generation, and biological functions of tsRNAs in response to stress, as well as their potential as biomarkers and therapeutic targets in various injuries, including lung injury, liver injury, renal injury, cardiac injury, neuronal injury, vascular injury, skeletal muscle injury, and skin injury. We also provided a fresh perspective on the association between stress-induced tsRNAs and organ injury from a clinical perspective.
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Affiliation(s)
- Mengjun Wang
- Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Junfeng Guo
- Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Wei Chen
- Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Hong Wang
- Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Xiaotong Hou
- Center for Cardiac Intensive Care, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
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30
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Zhang H, Sim G, Kehling AC, Adhav VA, Savidge A, Pastore B, Tang W, Nakanishi K. Target cleavage and gene silencing by Argonautes with cityRNAs. Cell Rep 2024; 43:114806. [PMID: 39368090 PMCID: PMC11533134 DOI: 10.1016/j.celrep.2024.114806] [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: 02/22/2024] [Revised: 07/02/2024] [Accepted: 09/12/2024] [Indexed: 10/07/2024] Open
Abstract
TinyRNAs (tyRNAs) are ≤17-nt guide RNAs associated with Argonaute proteins (AGOs), and certain 14-nt cleavage-inducing tyRNAs (cityRNAs) catalytically activate human Argonaute3 (AGO3). We present the crystal structure of AGO3 in complex with a cityRNA, 14-nt miR-20a, and its complementary target, revealing a different trajectory for the guide-target duplex from that of its ∼22-nt microRNA-associated AGO counterpart. cityRNA-loaded Argonaute2 (AGO2) and AGO3 enhance their endonuclease activity when the immediate 5' upstream region of the tyRNA target site (UTy) includes sequences with low affinity for AGO. We propose a model where cityRNA-loaded AGO2 and AGO3 efficiently cleave fully complementary tyRNA target sites unless they directly recognize the UTy. To investigate their gene silencing, we devised systems for loading endogenous AGOs with specific tyRNAs and demonstrated that, unlike microRNAs, cityRNA-mediated silencing heavily relies on target cleavage. Our study uncovered that AGO exploits cityRNAs for target recognition differently from microRNAs and alters gene silencing.
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Affiliation(s)
- Huaqun Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - GeunYoung Sim
- Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Audrey C Kehling
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vishal Annasaheb Adhav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew Savidge
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Pastore
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Wen Tang
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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31
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Peng J, Bu F, Duan L, Song A, Wang G, Zhang Z. Serum extracellular vesicles 3'tRF-ThrCGTand 3'tRF-mtlleGAT combined with tumor markers can serve as minimally invasive diagnostic predictors for colorectal cancer. Front Oncol 2024; 14:1474095. [PMID: 39497718 PMCID: PMC11532659 DOI: 10.3389/fonc.2024.1474095] [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: 08/01/2024] [Accepted: 09/30/2024] [Indexed: 11/07/2024] Open
Abstract
Background Colorectal cancer (CRC) is a leading cause of morbidity and mortality, and timely diagnosis and intervention are crucial for cancer patients. Transfer RNA-derived fragments (tRFs) play a noncoding regulatory role in organisms. Serum EV(extracellular vesicles), as an integral mediator of intercellular transmission of genetic information vesicles in Transfer RNA-derived fragment (tRF RNA), are expected to be minimally invasive diagnostic and predictive biologic factors of CRC. Methods Collect serum samples from 205 CRC patients, and then isolate extracellular vesicles from the serum. Captured the physical morphology of EV through transmission electron microscopy. The particle size was detected by particle size assay, and protein expression on the surface of EV was verified by Western blot. Gene microarrays were screened for differentially expressed tRF-RNA. TRF RNAs were verified by qPCR for differential expression in 205 CRC patients and 201 healthy donors, assessing the CRC diagnostic efficiency by area under the curve (AUC). Results Compared with 201 healthy donors, CRC patients experienced significantly down-regulated serum EV 3'tRF-ThrCGT while significantly up-regulated 3'tRF-mtlleGAT. Serum EV 3'tRF-ThrCGT and 3'tRF-mtlleGAT predictive diagnostic efficiency: 0.669 and 0.656, and the combination of CEA and CA724 predictive diagnostic efficiency was 0.938. Conclusion The study data showed that 3'tRF-ThrCGT and 3'tRF-mtlelGAT can be minimally invasive diagnostic CRC indicators. The combination of tumor markers CEA and CA724 has important diagnostic significance.
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Affiliation(s)
- Jiefei Peng
- Department of Clinical Laboratory, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-Drug Resistant Drug Research, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Fan Bu
- Department of Clinical Laboratory, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-Drug Resistant Drug Research, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Lei Duan
- Department of Clinical Laboratory, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-Drug Resistant Drug Research, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Anna Song
- Department of Reproduction and Genetics, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Guojun Wang
- Department of Neurosurgery, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Zhijun Zhang
- Department of Clinical Laboratory, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-Drug Resistant Drug Research, Affiliated Taian City Central Hospital of Qingdao University, Taian, China
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Lidonnici J, Oberkersch RE. Reciprocal Dynamics of Metabolism and mRNA Translation in Tumor Angiogenesis. Int J Mol Sci 2024; 25:11284. [PMID: 39457064 PMCID: PMC11508371 DOI: 10.3390/ijms252011284] [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: 09/26/2024] [Revised: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024] Open
Abstract
Angiogenesis, the process of formation of new blood vessels from pre-existing vasculature, is essential for tumor growth and metastasis. Anti-angiogenic treatment targeting vascular endothelial growth factor (VEGF) signaling is a powerful tool to combat tumor growth; however, anti-tumor angiogenesis therapy has shown limited efficacy, with survival benefits ranging from only a few weeks to months. Compensation by upregulation of complementary growth factors and switches to different modes of vascularization have made these types of therapies less effective. Recent evidence suggests that targeting specific players in endothelial metabolism is a valuable therapeutic strategy against tumor angiogenesis. Although it is clear that metabolism can modulate the translational machinery, the reciprocal relationship between metabolism and mRNA translational control during tumor angiogenesis is not fully understood. In this review, we explore emerging examples of how endothelial cell metabolism affects mRNA translation during the formation of blood vessels. A deeper comprehension of these mechanisms could lead to the development of innovative therapeutic strategies for both physiological and pathological angiogenesis.
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Affiliation(s)
- Jacopo Lidonnici
- Department of Surgery, Oncology and Gastroenterology, Section of Oncology and Immunology, University of Padova, 35128 Padova, Italy;
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33
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Do AN, Magesh S, Uzelac M, Chen T, Li WT, Bouvet M, Brumund KT, Wang-Rodriguez J, Ongkeko WM. Computational Analysis Suggests That AsnGTT 3'-tRNA-Derived Fragments Are Potential Biomarkers in Papillary Thyroid Carcinoma. Int J Mol Sci 2024; 25:10631. [PMID: 39408960 PMCID: PMC11476591 DOI: 10.3390/ijms251910631] [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: 09/09/2024] [Revised: 09/29/2024] [Accepted: 09/30/2024] [Indexed: 10/20/2024] Open
Abstract
Transfer-RNA-derived fragments (tRFs) are a novel class of small non-coding RNAs that have been implicated in oncogenesis. tRFs may act as post-transcriptional regulators by recruiting AGO proteins and binding to highly complementary regions of mRNA at seed regions, resulting in the knockdown of the transcript. Therefore, tRFs may be critical to tumorigenesis and warrant investigation as potential biomarkers. Meanwhile, the incidence of papillary thyroid carcinoma (PTC) has increased in recent decades and current diagnostic technology stands to benefit from new detection methods. Although small non-coding RNAs have been studied for their role in oncogenesis, there is currently no standard for their use as PTC biomarkers, and tRFs are especially underexplored. Accordingly, we aim to identify dysregulated tRFs in PTC that may serve as biomarker candidates. We identified dysregulated tRFs and driver genes between PTC primary tumor samples (n = 511) and adjacent normal tissue samples (n = 59). Expression data were obtained from MINTbase v2.0 and The Cancer Genome Atlas. Dysregulated tRFs and genes were analyzed in tandem to find pairs with anticorrelated expression. Significantly anticorrelated tRF-gene pairs were then tested for potential binding affinity using RNA22-if a heteroduplex can form via complementary binding, this would support the hypothesized RNA silencing mechanism. Four tRFs were significantly dysregulated in PTC tissue (p < 0.05), with only AsnGTT 3'-tRF being upregulated. Binding affinity analysis revealed that tRF-30-RY73W0K5KKOV (AsnGTT 3'-tRF) exhibits sufficient complementarity to potentially bind to and regulate transcripts of SLC26A4, SLC5A8, DIO2, and TPO, which were all found to be downregulated in PTC tissue. In the present study, we identified dysregulated tRFs in PTC and found that AsnGTT 3'-tRF is a potential post-transcriptional regulator and biomarker.
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Affiliation(s)
- Annie N. Do
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; (A.N.D.); (S.M.); (M.U.); (T.C.); (W.T.L.)
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
| | - Shruti Magesh
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; (A.N.D.); (S.M.); (M.U.); (T.C.); (W.T.L.)
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
| | - Matthew Uzelac
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; (A.N.D.); (S.M.); (M.U.); (T.C.); (W.T.L.)
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
- Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tianyi Chen
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; (A.N.D.); (S.M.); (M.U.); (T.C.); (W.T.L.)
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
| | - Wei Tse Li
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; (A.N.D.); (S.M.); (M.U.); (T.C.); (W.T.L.)
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
- UCSF School of Medicine, University of California, San Francisco, CA 94143, USA
| | - Michael Bouvet
- Department of Surgery, UC San Diego School of Medicine, University of Calfornia, La Jolla, CA 92093, USA;
- Department of Surgery, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Kevin T. Brumund
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
| | - Jessica Wang-Rodriguez
- Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA;
- Department of Pathology, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA
| | - Weg M. Ongkeko
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA; (A.N.D.); (S.M.); (M.U.); (T.C.); (W.T.L.)
- Department of Otolaryngology-Head and Neck Surgery, UC San Diego School of Medicine, University of California, La Jolla, CA 92093, USA;
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Fan Y, Pavani KC, Broeckx BJG, Smits K, Van Soom A, Peelman L. Circular RNAs from bovine blastocysts can interact with miRNAs/tsRNAs from embryonic extracellular vesicles and regulate hatching. Int J Biol Macromol 2024; 277:134018. [PMID: 39032885 DOI: 10.1016/j.ijbiomac.2024.134018] [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: 03/14/2024] [Revised: 07/05/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Circular RNAs (circRNAs) are endogenous biological macromolecules that regulate various biological processes including embryo development. However, little is known about which circRNAs are present in bovine preimplantation embryos and their respective roles. Here, we characterized the expression profile of circRNAs in bovine blastocysts for the first time. We detected 25,700 circRNAs in total, with 12,630 circRNAs uniquely expressed in blastocysts compared to degenerated embryos. CircRNA alternative splicing (AS) events were also found more frequently in blastocysts than in degenerated embryos (299 vs 258). Additionally, 410 circRNAs, among which 11 circRNAs with a high potential to encode polypeptides, were found differentially expressed between blastocysts and degenerated embryos. We further predicted and constructed a circRNA-miRNA-mRNA network, wherein differentially expressed circRNAs were shown to bind to bovine preimplantation embryo development-related miRNAs. Employing bioinformatic algorithms we found that differentially expressed circRNAs are associated with differentially expressed miRNAs and transfer RNA-derived small RNAs (tsRNAs) enclosed in embryonic extracellular vesicles (EVs). Furthermore, functional analysis revealed that knockdown of the evolutionarily conserved circAGO2 can inhibit blastocyst hatching. Overall, our study provides the first landscape of circRNAs in bovine preimplantation embryos and highlights the novel role of circRNAs as tsRNA binding partners influencing small RNA sorting and loading into EVs, with circAGO2 playing a regulatory role in bovine blastocyst hatching.
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Affiliation(s)
- Yuan Fan
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Krishna Chaitanya Pavani
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Bart J G Broeckx
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Luc Peelman
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium.
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Liang Y, Ji D, Ying X, Ma R, Ji W. tsRNA modifications: An emerging layer of biological regulation in disease. J Adv Res 2024:S2090-1232(24)00401-6. [PMID: 39260796 DOI: 10.1016/j.jare.2024.09.010] [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: 04/07/2024] [Revised: 08/02/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Transfer RNA (tRNA)-derived small RNA (tsRNA) represents an important and increasingly valued type of small non-coding RNA (sncRNA). The investigation of tRNA and tsRNA modification crosswalks has not only provided novel insights into the information and functions of tsRNA, but has also expanded the diversity and complexity of the tsRNA biological regulation network. AIM OF REVIEW Comparing with other sncRNAs, tsRNA biogenesis show obvious correlation with RNA modifications from mature tRNA and harbor various tRNA modifications. In this review, we aim to present the current aspect of tsRNA modifications and that modified tsRNA shape different regulatory mechanisms in physiological and pathological processes. KEY SCIENTIFIC CONCEPTS OF REVIEW Strategies for studying tsRNA mechanisms include its specific generation and functional effects induced by sequence/RNA modification/secondary structure. tsRNAs could harbor more than one tRNA modifications such as 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudouridine (Ψ) and N7-methylguanosine (m7G). This review consolidates the current knowledge of tRNA modification regulating tsRNA biogenesis, outlines the functional roles of various modified tsRNA and highlights their specific contributions in various disease pathogenesis. Therefore, the improvement of tsRNA modification detection technology and the introduction of experimental methods of tsRNA modification are conducive to further broadening the understanding of tsRNA function at the level of RNA modification.
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Affiliation(s)
- Yaomin Liang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Ding Ji
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510220, PR China
| | - Xiaoling Ying
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510220, PR China
| | - Renqiang Ma
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510220, PR China.
| | - Weidong Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China.
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Liu S, Holmes AD, Katzman S, Sharma U. A sperm-enriched 5'fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607197. [PMID: 39211093 PMCID: PMC11361008 DOI: 10.1101/2024.08.08.607197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sperm small RNAs have been implicated in intergenerational epigenetic inheritance of paternal environmental effects; however, their biogenesis and functions remain poorly understood. We previously identified a 5' fragment of tRNA-Valine-CAC-2 (tRFValCAC) as one of the most abundant small RNA in mature sperm. tRFValCAC is specifically enriched in sperm during post-testicular maturation in the epididymis, and we found that it is delivered to sperm from epididymis epithelial cells via extracellular vesicles. Here, we investigated the mechanistic basis of tRFValCAC delivery to sperm and its functions in the early embryo. We show that tRFValCAC interacts with an RNA binding protein, heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB), in the epididymis, and this interaction regulates the sorting and packing of tRFValCAC into extracellular vesicles. In the embryo, we found that tRFValCAC regulates early embryonic mRNA processing and splicing. Inhibition of tRFValCAC in preimplantation embryos altered the transcript abundance of genes involved in RNA splicing and mRNA processing. Importantly, tRFValCAC-inhibited embryos showed altered mRNA splicing, including alternative splicing of various splicing factors and genes important for proper preimplantation embryonic development. Finally, we find that inhibition of tRFValCAC in zygotes delayed preimplantation embryonic development. Together, our results reveal a novel function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.
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Affiliation(s)
- Simeiyun Liu
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Andrew D. Holmes
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Sol Katzman
- Genomics Institute, University of California, Santa Cruz, California, 95064
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
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37
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Li X, Mills WT, Jin DS, Meffert MK. Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. CELL REPORTS METHODS 2024; 4:100836. [PMID: 39127045 PMCID: PMC11384083 DOI: 10.1016/j.crmeth.2024.100836] [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: 04/15/2024] [Revised: 05/30/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024]
Abstract
Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types.
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Affiliation(s)
- Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William T Mills
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel S Jin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mollie K Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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38
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Hashimoto S, Hasan MDN, Arif M, Nozaki N, Husna AA, Furusawa Y, Sogawa T, Takahashi K, Kuramoto T, Noguchi A, Takahashi M, Yamato O, Rahman MM, Miura N. Aberrantly Expressed tRNA-Val Fragments Can Distinguish Canine Hepatocellular Carcinoma from Canine Hepatocellular Adenoma. Genes (Basel) 2024; 15:1024. [PMID: 39202384 PMCID: PMC11353709 DOI: 10.3390/genes15081024] [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: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
Hepatocellular adenoma (HCA) and hepatocellular carcinoma (HCC) can be difficult to differentiate but must be diagnosed correctly as treatment and prognosis for these tumors differ markedly. Relevant diagnostic biomarkers are thus needed, and those identified in dogs may have utility in human medicine because of the similarities between human and canine HCA and HCC. A tRNA-derived fragment (tRF), tRNA-Val, is a promising potential biomarker for canine mammary gland tumors but has not previously been investigated in hepatic tumors. Accordingly, we aimed to elucidate the potential utility of tRNA-Val as a biomarker for canine HCA and HCC using clinical samples (tumor tissue and plasma extracellular vesicles [EVs]) and tumor cell lines with qRT-PCR assays. We also investigated relevant functions and signaling pathways with bioinformatic analyses (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes). tRNA-Val was markedly downregulated in HCC tumor tissue versus HCA tumor tissue and normal liver tissue, and a similar trend was shown in plasma EVs and HCC cell lines versus healthy controls. Based on areas under the receiver operating characteristic curves (AUCs), tRNA-Val significantly distinguished HCC (AUC = 1.00, p = 0.001) from healthy controls in plasma EVs and HCC from HCA (AUC = 0.950, p = 0.01). Bioinformatics analysis revealed that tRNA-Val may be primarily involved in DNA repair, mRNA processing, and splicing and may be linked to the N-glycan and ubiquitin-mediated proteasome pathways. This is the first report on the expression of tRNA-Val in canine HCC and HCA and its possible functions and signaling pathways. We suggest that tRNA-Val could be a promising novel biomarker to distinguish canine HCC from HCA. This study provides evidence for a greater understanding of the role played by tRNA-Val in the development of canine HCC.
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MESH Headings
- Animals
- Dogs
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/veterinary
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Liver Neoplasms/genetics
- Liver Neoplasms/veterinary
- Liver Neoplasms/pathology
- Biomarkers, Tumor/genetics
- Dog Diseases/genetics
- Dog Diseases/diagnosis
- Adenoma, Liver Cell/genetics
- Adenoma, Liver Cell/veterinary
- Adenoma, Liver Cell/pathology
- Adenoma, Liver Cell/metabolism
- Adenoma, Liver Cell/diagnosis
- Gene Expression Regulation, Neoplastic
- Diagnosis, Differential
- Cell Line, Tumor
- Female
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Affiliation(s)
- Saki Hashimoto
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - MD Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Mohammad Arif
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Nobuhiro Nozaki
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Al Asmaul Husna
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yu Furusawa
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Takeshi Sogawa
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kaori Takahashi
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tomohide Kuramoto
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Aki Noguchi
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Masashi Takahashi
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Osamu Yamato
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Md Mahfuzur Rahman
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoki Miura
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Hao Y, Li B, Yin F, Liu W. tRNA-derived small RNA (tsr007330) regulates myocardial fibrosis after myocardial infarction through NAT10-mediated ac4C acetylation of EGR3 mRNA. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167267. [PMID: 38810917 DOI: 10.1016/j.bbadis.2024.167267] [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: 10/30/2023] [Revised: 04/27/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024]
Abstract
Small non-coding ribonucleic acids (sncRNAs) play an important role in cell regulation and are closely related to the pathogenesis of heart diseases. However, the role and molecular mechanism of transfer RNA-derived small RNAs (tsRNAs) in myocardial fibrosis after myocardial infarction (MI) remain unknown. In this study, we identified and validated sncRNAs (mainly miRNA and tsRNA) associated with myocardial fibrosis after MI through PANDORA sequencing of rat myocardial tissue. As a key enzyme of N4-acetylcytidine (ac4C) acetylation modification, N-acetyltransferase 10 (NAT10) plays an important role in regulating messenger RNA (mRNA) stability and translation efficiency. We found that NAT10 is highly expressed in infarcted myocardial tissue, and the results of acetylated RNA immunoprecipitation sequencing (acRIP-seq) analysis suggest that early growth response 3 (EGR3) may be an important molecule in the pathogenesis of NAT10-mediated myocardial fibrosis. Both in vivo and in vitro experiments have shown that inhibition of NAT10 can reduce the expression of EGR3 and alleviate myocardial fibrosis after MI. tsRNA can participate in gene regulation by inhibiting target genes. The expression of tsr007330 was decreased in myocardial infarction tissue. We found that overexpression of tsr007330 in rat myocardial tissue could antagonize NAT10, improve myocardial function in MI and alleviate myocardial fibrosis. In conclusion, tsRNAs (rno-tsr007330) may regulate the occurrence of myocardial fibrosis by regulating NAT10-mediated EGR3 mRNA acetylation. This study provides new insights into the improvement of myocardial fibrosis after MI by targeting tsRNA therapy.
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Affiliation(s)
- Yan Hao
- Harbin Medical University, Harbin, Heilongjiang 150001, China; Department of Cardiology, the fourth affiliated hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Bohan Li
- Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Feiya Yin
- University of Sydney, NSW 2006, Australia
| | - Wei Liu
- Harbin Medical University, Harbin, Heilongjiang 150001, China; Department of Geriatric Cardiovascular Division, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
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40
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Peng J, Zhang Y, Zhou G, Shao L, Li L, Zhang Z. Circulating serum exosomes i-tRF-AspGTC and tRF-1-SerCGA as diagnostic indicators for non-small cell lung cancer. Clin Transl Oncol 2024; 26:1988-1997. [PMID: 38502292 DOI: 10.1007/s12094-024-03423-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND tRF-RNA-a representative of non-coding RNA (ncRNA)-is a precursor or fragment of mature tRNA and plays a crucial regulatory role in the occurrence and development of cancer. There is currently little research on tRF-RNA as a diagnostic marker in cancer, especially for NSCLC from serum exosomes. METHOD Serum exosomes were successfully extracted from serum; their physical morphology was captured by transmission electron microscopy (TEM); appropriate particle size detection was performed using qNano; surface labeling was verified through western blotting. Serum exosomes i-tRF-AspGTC and tRF-1-SerCGA were selected through gene microarray, and qPCR was used to validate their significance in 242 patients and 201 healthy individuals. The area under the curve (AUC) was used to evaluate the diagnostic indicators of non-small cell lung cancer (NSCLC). RESULT Compared with 201 healthy individuals, i-tRF-AspGTC and tRF-1-SerCGA were significantly downregulated in 242 NSCLC patients and 95 early-stage patients. For tRF-AspGTC and tRF-1-SerCGA, the predictive diagnostic efficiency rates of AUC were 0.690 and 0.680, respectively, whereas the early diagnostic efficiency rates were 0.656 and 0.688, respectively. The result of combined diagnosis with CEA and CYFRA21-1 was 0.928, and the early diagnostic efficiency was 0.843, which is a very high biological predictive factor for NSCLC. CONCLUSION The expression of serum exosomes i-tRF-AspGTC and tRF-1-SerCGA was significantly downregulated in NSCLC patients. These exosomes could be used as predictive indicators for diagnosis or early diagnosis of NSCLC.
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Affiliation(s)
- Jiefei Peng
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-drug Resistant Drug Research, Taian City Central Hospital, Taian, 271000, China
| | - Yue Zhang
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Guangfei Zhou
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Luolin Shao
- Department of Dermatology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Lin Li
- Pharmacy Intravenous Admixture Services, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China.
| | - Zhijun Zhang
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China.
- Shandong Provincial Key Medical and Health Laboratory of Anti-drug Resistant Drug Research, Taian City Central Hospital, Taian, 271000, China.
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41
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Yuan W, Zhang R, Lyu H, Xiao S, Guo D, Zhang Q, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies. Cell Death Discov 2024; 10:327. [PMID: 39019857 PMCID: PMC11254935 DOI: 10.1038/s41420-024-02097-x] [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: 03/26/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.
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Affiliation(s)
- Wenbin Yuan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Qi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
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42
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Wang F, Zhou C, Zhu Y, Keshavarzi M. The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers. Cell Biol Toxicol 2024; 40:42. [PMID: 38836981 PMCID: PMC11153289 DOI: 10.1007/s10565-024-09884-3] [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: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
Many types of gynecological cancer (GC) are often silent until they reach an advanced stage, and are therefore often diagnosed too late for effective treatment. Hence, there is a real need for more efficient diagnosis and treatment for patients with GC. During recent years, researchers have increasingly studied the impact of microRNAs cancer development, leading to a number of applications in detection and treatment. MicroRNAs are a particular group of tiny RNA molecules that regulate regular gene expression by affecting the translation process. The downregulation of numerous miRNAs has been observed in human malignancies. Let-7 is an example of a miRNA that controls cellular processes as well as signaling cascades to affect post-transcriptional gene expression. Recent research supports the hypothesis that enhancing let-7 expression in those cancers where it is downregulated may be a potential treatment option. Exosomes are tiny vesicles that move through body fluids and can include components like miRNAs (including let-7) that are important for communication between cells. Studies proved that exosomes are able to enhance tumor growth, angiogenesis, chemoresistance, metastasis, and immune evasion, thus suggesting their importance in GC management.
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Affiliation(s)
- Fei Wang
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Chundi Zhou
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Yanping Zhu
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China.
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Tehran, Iran.
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43
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Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592122. [PMID: 38746336 PMCID: PMC11092647 DOI: 10.1101/2024.05.01.592122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.
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Affiliation(s)
- Aidan C. Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M. Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R. Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M. Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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44
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Li Z, Barnaby R, Nymon A, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in cystic fibrosis. Am J Physiol Lung Cell Mol Physiol 2024; 326:L574-L588. [PMID: 38440830 PMCID: PMC11380944 DOI: 10.1152/ajplung.00018.2024] [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: 01/17/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates of P. aeruginosa. The 5' tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lungs, increased expression of the 5' tRNA-fMet halves in OMVs attenuated KC (murine homolog of IL-8) secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice and in vitro studies on CF-HBEC that tobramycin reduces inflammation by increasing 5' tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin for P. aeruginosa infection.NEW & NOTEWORTHY The experiments in this report identify a novel mechanism, whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet halves in OMVs secreted by P. aeruginosa, which reduced the OMV-LPS-induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF.
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Affiliation(s)
- Zhongyou Li
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Roxanna Barnaby
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Amanda Nymon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Carolyn Roche
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
- Pulmonary and Critical Care Medicine, Dartmouth Health Medical Center, Lebanon, New Hampshire, United States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Scott A Gerber
- Dartmouth Health Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States
| | - Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Center for Biomedical Shared Resources, Larner College of Medicine, University of Vermont, Burlington, Vermont, United States
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
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45
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Muthukumar S, Li CT, Liu RJ, Bellodi C. Roles and regulation of tRNA-derived small RNAs in animals. Nat Rev Mol Cell Biol 2024; 25:359-378. [PMID: 38182846 DOI: 10.1038/s41580-023-00690-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.
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Affiliation(s)
- Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
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46
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Zhang Q, Zhao X, Sun M, Dong D. Novel insights into transfer RNA-derived small RNA (tsRNA) in cardio-metabolic diseases. Life Sci 2024; 341:122475. [PMID: 38309576 DOI: 10.1016/j.lfs.2024.122475] [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: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Cardio-metabolic diseases, including a cluster of metabolic disorders and their secondary affections on cardiovascular physiology, are gradually brought to the forefront by researchers due to their high prevalence and mortality, as well as an unidentified pathogenesis. tRNA-derived small RNAs (tsRNAs), cleaved by several specific enzymes and once considered as some "metabolic junks" in the past, have been proved to possess numerous functions in human bodies. More interestingly, such a potential also seems to influence the progression of cardio-metabolic diseases to some extent. In this review, the biogenesis, classification and mechanisms of tsRNAs will be discussed based on some latest studies, and their relations with several cardio-metabolic diseases will be highlighted in sequence. Lastly, some future prospects, such as their clinical applications as biomarkers and therapeutic targets will also be mentioned, in order to provide researchers with a comprehensive understanding of the research status of tsRNAs as well as its association with cardio-metabolic diseases, thus presenting as a beacon to indicate directions for the next stage of study.
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Affiliation(s)
- Qingya Zhang
- Innovation Institute, China Medical University, Shenyang 110122, Liaoning, China
| | - Xiaopeng Zhao
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Mingli Sun
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Dan Dong
- College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning, China.
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47
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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: 7] [Impact Index Per Article: 7.0] [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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48
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Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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49
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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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50
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Li Z, Barnaby R, Nymon A, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.03.578737. [PMID: 38352468 PMCID: PMC10862835 DOI: 10.1101/2024.02.03.578737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates of P. aeruginosa . The 5' tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lung, increased expression of the 5' tRNA-fMet halves in OMVs attenuated KC secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice and in vitro studies on CF-HBEC that tobramycin reduces inflammation by increasing 5' tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin for P. aeruginosa infection. New and noteworthy The experiments in this report identify a novel mechanim whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet haves in OMVs secreted by P. aeruginiosa , which reduced the OMV-LPS induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF. Graphical abstract The anti-inflammatory effect of tobramycin mediated by 5' tRNA-fMet halves secreted in P. aeruginosa OMVs. (A) P. aeruginosa colonizes the CF lungs and secrets OMVs. OMVs diffuse through the mucus layer overlying bronchial epithelial cells and induce IL-8 secretion, which recruits neutrophils that causes lung damage. ( B ) Tobramycin increases 5' tRNA-fMet halves in OMVs secreted by P. aeruginosa . 5' tRNA-fMet halves are delivered into host cells after OMVs fuse with lipid rafts in CF-HBEC and down-regulate protein expression of MAPK10, IKBKG, and EP300, which suppresses IL-8 secretion and neutrophils in the lungs. A reduction in neutrophils in CF BALF is predicted to improve lung function and decrease lung damage.
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