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Stillinovic M, Sarangdhar MA, Andina N, Tardivel A, Greub F, Bombaci G, Ansermet C, Zatti M, Saha D, Xiong J, Sagae T, Yokogawa M, Osawa M, Heller M, Keogh A, Keller I, Angelillo-Scherrer A, Allam R. Ribonuclease inhibitor and angiogenin system regulates cell type-specific global translation. SCIENCE ADVANCES 2024; 10:eadl0320. [PMID: 38820160 PMCID: PMC11141627 DOI: 10.1126/sciadv.adl0320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Translation of mRNAs is a fundamental process that occurs in all cell types of multicellular organisms. Conventionally, it has been considered a default step in gene expression, lacking specific regulation. However, recent studies have documented that certain mRNAs exhibit cell type-specific translation. Despite this, it remains unclear whether global translation is controlled in a cell type-specific manner. By using human cell lines and mouse models, we found that deletion of the ribosome-associated protein ribonuclease inhibitor 1 (RNH1) decreases global translation selectively in hematopoietic-origin cells but not in the non-hematopoietic-origin cells. RNH1-mediated cell type-specific translation is mechanistically linked to angiogenin-induced ribosomal biogenesis. Collectively, this study unravels the existence of cell type-specific global translation regulators and highlights the complex translation regulation in vertebrates.
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Affiliation(s)
- Martina Stillinovic
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Mayuresh Anant Sarangdhar
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Nicola Andina
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Aubry Tardivel
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Frédéric Greub
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Giuseppe Bombaci
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Camille Ansermet
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Marco Zatti
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Dipanjali Saha
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Jieyu Xiong
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Takeru Sagae
- Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Mariko Yokogawa
- Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, Keio University, Minato-ku, Tokyo, Japan
| | - Manfred Heller
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Adrian Keogh
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Anne Angelillo-Scherrer
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ramanjaneyulu Allam
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
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2
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Martinez-Feduchi P, Jin P, Yao B. Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci 2024; 17:1398026. [PMID: 38726308 PMCID: PMC11079283 DOI: 10.3389/fnmol.2024.1398026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder and the most common form of dementia. There are two main types of AD: familial and sporadic. Familial AD is linked to mutations in amyloid precursor protein (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2). On the other hand, sporadic AD is the more common form of the disease and has genetic, epigenetic, and environmental components that influence disease onset and progression. Investigating the epigenetic mechanisms associated with AD is essential for increasing understanding of pathology and identifying biomarkers for diagnosis and treatment. Chemical covalent modifications on DNA and RNA can epigenetically regulate gene expression at transcriptional and post-transcriptional levels and play protective or pathological roles in AD and other neurodegenerative diseases.
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Affiliation(s)
| | | | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
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3
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Hamidpour SK, Amiri M, Ketabforoush AHME, Saeedi S, Angaji A, Tavakol S. Unraveling Dysregulated Cell Signaling Pathways, Genetic and Epigenetic Mysteries of Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04128-1. [PMID: 38573414 DOI: 10.1007/s12035-024-04128-1] [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: 12/16/2023] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Parkinson's disease (PD) is a prevalent and burdensome neurodegenerative disorder that has been extensively researched to understand its complex etiology, diagnosis, and treatment. The interplay between genetic and environmental factors in PD makes its pathophysiology difficult to comprehend, emphasizing the need for further investigation into genetic and epigenetic markers involved in the disease. Early diagnosis is crucial for optimal management of the disease, and the development of novel diagnostic biomarkers is ongoing. Although many efforts have been made in the field of recognition and interpretation of the mechanisms involved in the pathophysiology of the disease, the current knowledge about PD is just the tip of the iceberg. By scrutinizing genetic and epigenetic patterns underlying PD, new avenues can be opened for dissecting the pathology of the disorder, leading to more precise and efficient diagnostic and therapeutic approaches. This review emphasizes the importance of studying dysregulated cell signaling pathways and molecular processes associated with genes and epigenetic alterations in understanding PD, paving the way for the development of novel therapeutic strategies to combat this devastating disease.
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Affiliation(s)
- Shayesteh Kokabi Hamidpour
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Mobina Amiri
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | | | - Saeedeh Saeedi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, 1449614535, Iran.
- Department of Research and Development, Tavakol BioMimetic Technologies Company, Tehran, Iran.
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4
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Ng N, Gibriel HAY, Halang L, Jirström E, Ioana JA, Burke M, Byrne MM, Prehn JHM. tRNA-derived fragments are altered in diabetes. Diabet Med 2024; 41:e15258. [PMID: 37935454 DOI: 10.1111/dme.15258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023]
Abstract
AIMS Maternally inherited diabetes and deafness (MIDD) is a rare form of adult-onset diabetes that can be difficult to diagnose due to its variable clinical phenotype. Transfer RNA-derived small fragments are a novel, emerging class of small non-coding RNAs (sncRNAs) that have significant potential as serum biomarkers due to their stress-induced generation, abundance, stability and ease of detection. METHODS We investigated the levels of tiRNA 5'ValCAC (alone and in combination with miR-23b-3p) identified from small RNA sequencing studies in serum samples from healthy controls, type 1 diabetes, type 2 diabetes and MIDD subjects. RESULTS Serum levels of 5'ValCAC were reduced in MIDD and type 2 diabetes subjects compared to controls. Type 2 diabetes subjects had higher serum levels of miR-23b-3p compared to all other subjects. Receiver Operating Characteristic analysis showed the potential of 5'ValCAC and miR-23b-3p as MIDD biomarkers, with the combination showing excellent separation from type 2 diabetes subjects. CONCLUSIONS This is the first report showing altered serum levels of tiRNAs in diabetes subjects. The combined use of 5'ValCAC and miR-23b-3p as serum biomarkers could potentially differentiate between MIDD subjects and type 2 diabetes subjects.
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Affiliation(s)
- N Ng
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - H A Y Gibriel
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - L Halang
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - E Jirström
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - J A Ioana
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - M Burke
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - M M Byrne
- Department of Diabetes and Endocrinology, Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - J H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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5
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Suleiman AA, Al-Chalabi R, Shaban SA. Integrative role of small non-coding RNAs in viral immune response: a systematic review. Mol Biol Rep 2024; 51:107. [PMID: 38227137 DOI: 10.1007/s11033-023-09141-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Various viruses cause viral infection, and these viruses have different microscopic sizes, genetic material, and morphological forms. Due to a viral infection, the host body induces defense mechanisms that activate the innate and adaptive immune system. sncRNAs are involved in various biological processes and play an essential role in antiviral response in viruses including ZIKV, HCV, DENV, SARS-CoV, and West Nile virus, and regulate the complex interactions between the viruses and host cells. This review discusses the role of miRNAs, siRNAs, piRNAs, and tiRNAs in antiviral response. Cellular miRNAs bind with virus mRNA and perform their antiviral response in multiple viruses. However, the chemical modifications of miRNA necessary to avoid nuclease attack, which is then involved with intracellular processing, have proven challenging for therapeutic replacement of miRNAs. siRNAs have significant antiviral responses by targeting any gene of interest along the correct nucleotide of targeting mRNA. Due to this ability, siRNAs have valuable characteristics in antiviral response for therapeutic purposes. Additionally, the researchers noted the involvement of piRNAs and tiRNAs in the antiviral response, yet their findings were deemed insignificant.
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Affiliation(s)
| | | | - Semaa A Shaban
- Biology Department, College of Sciences, Tikrit University, Tikrit, Iraq
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6
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Fatica T, Naas T, Liwak U, Slaa H, Souaid M, Frangione B, Kattini R, Gaudreau-Lapierre A, Trinkle-Mulcahy L, Chakraborty P, Holcik M. TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins. Genes (Basel) 2023; 14:genes14051043. [PMID: 37239403 DOI: 10.3390/genes14051043] [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: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondrial diseases are a group of heterogeneous disorders caused by dysfunctional mitochondria. Interestingly, a large proportion of mitochondrial diseases are caused by defects in genes associated with tRNA metabolism. We recently discovered that partial loss-of-function mutations in tRNA Nucleotidyl Transferase 1 (TRNT1), the nuclear gene encoding the CCA-adding enzyme essential for modifying both nuclear and mitochondrial tRNAs, causes a multisystemic and clinically heterogenous disease termed SIFD (sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay; SIFD). However, it is not clear how mutations in a general and essential protein like TRNT1 cause disease with such clinically broad but unique symptomatology and tissue involvement. Using biochemical, cell, and mass spectrometry approaches, we demonstrate that TRNT1 deficiency is associated with sensitivity to oxidative stress, which is due to exacerbated, angiogenin-dependent cleavage of tRNAs. Furthermore, reduced levels of TRNT1 lead to phosphorylation of Eukaryotic Translation Initiation Factor 2 Subunit Alpha (eIF2α), increased reactive oxygen species (ROS) production, and changes in the abundance of distinct proteins. Our data suggest that the observed variable SIFD phenotypes are likely due to dysregulation of tRNA maturation and abundance, which in turn negatively affects the translation of distinct proteins.
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Affiliation(s)
- Thet Fatica
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Turaya Naas
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Urszula Liwak
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Hannah Slaa
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Maryam Souaid
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Brianna Frangione
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Ribal Kattini
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | | | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
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Xu J, Cai M, Wang Z, Chen Q, Han X, Tian J, Jin S, Yan Z, Li Y, Lu B, Lu H. Phenylacetylglutamine as a novel biomarker of type 2 diabetes with distal symmetric polyneuropathy by metabolomics. J Endocrinol Invest 2023; 46:869-882. [PMID: 36282471 PMCID: PMC10105673 DOI: 10.1007/s40618-022-01929-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE Type 2 diabetes mellitus (T2DM) with distal symmetric polyneuropathy (DSPN) is a disease involving the nervous system caused by metabolic disorder, while the metabolic spectrum and key metabolites remain poorly defined. METHODS Plasma samples of 30 healthy controls, 30 T2DM patients, and 60 DSPN patients were subjected to nontargeted metabolomics. Potential biomarkers of DSPN were screened based on univariate and multivariate statistical analyses, ROC curve analysis, and logistic regression. Finally, another 22 patients with T2DM who developed DSPN after follow-up were selected for validation of the new biomarker based on target metabolomics. RESULTS Compared with the control group and the T2DM group, 6 metabolites showed differences in the DSPN group (P < 0.05; FDR < 0.1; VIP > 1) and a rising step trend was observed. Among them, phenylacetylglutamine (PAG) and sorbitol displayed an excellent discriminatory ability and associated with disease severity. The verification results demonstrated that when T2DM progressed to DSPN, the phenylacetylglutamine content increased significantly (P = 0.004). CONCLUSION The discovered and verified endogenous metabolite PAG may be a novel potential biomarker of DSPN and involved in the disease pathogenesis.
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Affiliation(s)
- J. Xu
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - M. Cai
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Z. Wang
- Department of Emergency, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Q. Chen
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - X. Han
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - J. Tian
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - S. Jin
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Z. Yan
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
| | - Y. Li
- Department of Endocrinology and Metabolism, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - B. Lu
- Department of Endocrinology and Metabolism, Huashan Hospital, Fudan University, Shanghai, 200040 China
| | - H. Lu
- Department of Endocrinology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China
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Chen X, Wolin SL. Transfer RNA halves are found as nicked tRNAs in cells: evidence that nicked tRNAs regulate expression of an RNA repair operon. RNA (NEW YORK, N.Y.) 2023; 29:620-629. [PMID: 36781286 PMCID: PMC10159003 DOI: 10.1261/rna.079575.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/01/2023] [Indexed: 05/06/2023]
Abstract
Transfer RNA fragments are proposed to regulate numerous processes in eukaryotes, including translation inhibition, epigenetic inheritance, and cancer. In the bacterium Salmonella enterica serovar Typhimurium, 5' tRNA halves ending in 2',3' cyclic phosphate are proposed to bind the RtcR transcriptional activator, resulting in transcription of an RNA repair operon. However, since 5' and 3' tRNA halves can remain base paired after cleavage, the 5' tRNA halves could potentially bind RtcR as nicked tRNAs. Here we report that nicked tRNAs are ligands for RtcR. By isolating RNA from bacteria under conditions that preserve base pairing, we show that many tRNA halves are in the form of nicked tRNAs. Using a circularly permuted tRNA that mimics a nicked tRNA, we show that nicked tRNA ending in 2',3' cyclic phosphate is a better ligand for RtcR than the corresponding 5' tRNA half. In human cells, we show that some tRNA halves similarly remain base paired as nicked tRNAs following cleavage by anticodon nucleases. Our work supports a role for the RNA repair operon in repairing nicked tRNAs and has implications for the functions proposed for tRNA fragments in eukaryotes.
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Affiliation(s)
- Xinguo Chen
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Sandra L Wolin
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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9
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Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [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: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
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Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
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10
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Fu M, Gu J, Wang M, Zhang J, Chen Y, Jiang P, Zhu T, Zhang X. Emerging roles of tRNA-derived fragments in cancer. Mol Cancer 2023; 22:30. [PMID: 36782290 PMCID: PMC9926655 DOI: 10.1186/s12943-023-01739-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.
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Affiliation(s)
- Min Fu
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China ,grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jianmei Gu
- grid.260483.b0000 0000 9530 8833Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226361 Jiangsu China
| | - Maoye Wang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jiahui Zhang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Yanke Chen
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Pengcheng Jiang
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China
| | - Taofeng Zhu
- Department of Pulmonary and Critical Care Medicine, Yixing Hospital Affiliated to Jiangsu University, Yixing, 214200, Jiangsu, China.
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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11
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Shen L, Liao T, Chen Q, Lei Y, Wang L, Gu H, Qiu Y, Zheng T, Yang Y, Wei C, Chen L, Zhao Y, Niu L, Zhang S, Zhu Y, Li M, Wang J, Li X, Gan M, Zhu L. tRNA-derived small RNA, 5'tiRNA-Gly-CCC, promotes skeletal muscle regeneration through the inflammatory response. J Cachexia Sarcopenia Muscle 2023; 14:1033-1045. [PMID: 36755335 PMCID: PMC10067481 DOI: 10.1002/jcsm.13187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/07/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Increasing evidence shows that tRNA-derived small RNAs (tsRNAs) are not only by-products of transfer RNAs, but they participate in numerous cellular metabolic processes. However, the role of tsRNAs in skeletal muscle regeneration remains unknown. METHODS Small RNA sequencing revealed the relationship between tsRNAs and skeletal muscle injury. The dynamic expression level of 5'tiRNA-Gly after muscle injury was confirmed by real-time quantitative PCR (q-PCR). In addition, q-PCR, flow cytometry, the 5-ethynyl-2'-deoxyuridine (Edu), cell counting kit-8, western blotting and immunofluorescence were used to explore the biological function of 5'tiRNA-Gly. Bioinformatics analysis and dual-luciferase reporter assay were used to further explore the mechanism of action under the biological function of 5'tiRNA-Gly. RESULTS Transcriptome analysis revealed that tsRNAs were significantly enriched during inflammatory response immediately after muscle injury. Interestingly, we found that 5'tiRNA-Gly was significantly up-regulated after muscle injury (P < 0.0001) and had a strong positive correlation with inflammation in vivo. In vitro experiments showed that 5'tiRNA-Gly promoted the mRNA expression of proinflammatory cytokines (IL-1β, P = 0.0468; IL-6, P = 0.0369) and the macrophages of M1 markers (TNF-α, P = 0.0102; CD80, P = 0.0056; MCP-1, P = 0.0002). On the contrary, 5'tiRNA-Gly inhibited the mRNA expression of anti-inflammatory cytokines (IL-4, P = 0.0009; IL-10, P = 0.0007; IL-13, P = 0.0008) and the mRNA expression of M2 markers (TGF-β1, P = 0.0016; ARG1, P = 0.0083). Flow cytometry showed that 5'tiRNA-Gly promoted the percentage of CD86+ macrophages (16%, P = 0.011) but inhibited that of CD206+ macrophages (10.5%, P = 0.012). Immunofluorescence showed that knockdown of 5'tiRNA-Gly increased the infiltration of M2 macrophages to the skeletal muscles (13.9%, P = 0.0023) and inhibited the expression of Pax7 (P = 0.0089) in vivo. 5'tiRNA-Gly promoted myoblast the expression of myogenic differentiation marker genes (MyoD, P = 0.0002; MyoG, P = 0.0037) and myotube formation (21.3%, P = 0.0016) but inhibited the positive rate of Edu (27.7%, P = 0.0001), cell viability (22.6%, P = 0.003) and the number of myoblasts in the G2 phase (26.3%, P = 0.0016) in vitro. Mechanistically, we found that the Tgfbr1 gene is a direct target of 5'tiRNA-Gly mediated by AGO1 and AGO3. 5'tiRNA-Gly dysregulated the expression of downstream genes related to inflammatory response, activation of satellite cells and differentiation of myoblasts through the TGF-β signalling pathway by targeting Tgfbr1. CONCLUSIONS These results reveal that 5'tiRNA-Gly potentially regulated skeletal muscle regeneration by inducing inflammation via the TGF-β signalling pathway. The findings of this study uncover a new potential target for skeletal muscle regeneration treatment.
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Affiliation(s)
- Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Tianci Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Qiuyang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yuhang Lei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Linghui Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Hao Gu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yanhao Qiu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Ting Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yiting Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Chenggang Wei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mailin Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
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12
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Akiyama Y, Takenaka Y, Kasahara T, Abe T, Tomioka Y, Ivanov P. RTCB Complex Regulates Stress-Induced tRNA Cleavage. Int J Mol Sci 2022; 23:ijms232113100. [PMID: 36361884 PMCID: PMC9655011 DOI: 10.3390/ijms232113100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
Abstract
Under stress conditions, transfer RNAs (tRNAs) are cleaved by stress-responsive RNases such as angiogenin, generating tRNA-derived RNAs called tiRNAs. As tiRNAs contribute to cytoprotection through inhibition of translation and prevention of apoptosis, the regulation of tiRNA production is critical for cellular stress response. Here, we show that RTCB ligase complex (RTCB-LC), an RNA ligase complex involved in endoplasmic reticulum (ER) stress response and precursor tRNA splicing, negatively regulates stress-induced tiRNA production. Knockdown of RTCB significantly increased stress-induced tiRNA production, suggesting that RTCB-LC negatively regulates tiRNA production. Gel-purified tiRNAs were repaired to full-length tRNAs by RtcB in vitro, suggesting that RTCB-LC can generate full length tRNAs from tiRNAs. As RTCB-LC is inhibited under oxidative stress, we further investigated whether tiRNA production is promoted through the inhibition of RTCB-LC under oxidative stress. Although hydrogen peroxide (H2O2) itself did not induce tiRNA production, it rapidly boosted tiRNA production under the condition where stress-responsive RNases are activated. We propose a model of stress-induced tiRNA production consisting of two factors, a trigger and booster. This RTCB-LC-mediated boosting mechanism may contribute to the effective stress response in the cell.
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Affiliation(s)
- Yasutoshi Akiyama
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
- Correspondence: (Y.A.); (P.I.)
| | - Yoshika Takenaka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
| | - Tomoko Kasahara
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Takaaki Abe
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai 980-8574, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: (Y.A.); (P.I.)
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13
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Chu X, He C, Sang B, Yang C, Yin C, Ji M, Qian A, Tian Y. Transfer RNAs-derived small RNAs and their application potential in multiple diseases. Front Cell Dev Biol 2022; 10:954431. [PMID: 36072340 PMCID: PMC9441921 DOI: 10.3389/fcell.2022.954431] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022] Open
Abstract
The role of tRNAs is best known as adapter components of translational machinery. According to the central dogma of molecular biology, DNA is transcribed to RNA and in turn is translated into proteins, in which tRNA outstands by its role of the cellular courier. Recent studies have led to the revision of the canonical function of transfer RNAs (tRNAs), which indicates that tRNAs also serve as a source for short non-coding RNAs called tRNA-derived small RNAs (tsRNAs). tsRNAs play key roles in cellular processes by modulating complicated regulatory networks beyond translation and are widely involved in multiple diseases. Herein, the biogenesis and classification of tsRNAs were firstly clarified. tsRNAs are generated from pre-tRNAs or mature tRNAs and are classified into tRNA-derived fragments (tRFs) and tRNA halves (tiRNA). The tRFs include five types according to the incision loci: tRF-1, tRF-2, tRF-3, tRF-5 and i-tRF which contain 3′ tiRNA and 5′ tiRNA. The functions of tsRNAs and their regulation mechanisms involved in disease processes are systematically summarized as well. The mechanisms can elaborate on the specific regulation of tsRNAs. In conclusion, the current research suggests that tsRNAs are promising targets for modulating pathological processes, such as breast cancer, ischemic stroke, respiratory syncytial virus, osteoporosis and so on, and maintain vital clinical implications in diagnosis and therapeutics of various diseases.
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Affiliation(s)
- Xiaohua Chu
- Lab for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an, SN, China
| | - Chenyang He
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Bo Sang
- Lab for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an, SN, China
| | - Chaofei Yang
- Lab for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an, SN, China
| | - Chong Yin
- Department of Clinical Laboratory, Academician (expert) Workstation, Lab of Epigenetics and RNA Therapy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Mili Ji
- Lab for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an, SN, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an, SN, China
- *Correspondence: Airong Qian, ; Ye Tian,
| | - Ye Tian
- Lab for Bone Metabolism, Xi’an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi’an, SN, China
- *Correspondence: Airong Qian, ; Ye Tian,
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14
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Wolzak K, Nölle A, Farina M, Abbink TE, van der Knaap MS, Verhage M, Scheper W. Neuron-specific translational control shift ensures proteostatic resilience during ER stress. EMBO J 2022; 41:e110501. [PMID: 35791631 PMCID: PMC9379547 DOI: 10.15252/embj.2021110501] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Proteostasis is essential for cellular survival and particularly important for highly specialised post‐mitotic cells such as neurons. Transient reduction in protein synthesis by protein kinase R‐like endoplasmic reticulum (ER) kinase (PERK)‐mediated phosphorylation of eukaryotic translation initiation factor 2α (p‐eIF2α) is a major proteostatic survival response during ER stress. Paradoxically, neurons are remarkably tolerant to PERK dysfunction, which suggests the existence of cell type‐specific mechanisms that secure proteostatic stress resilience. Here, we demonstrate that PERK‐deficient neurons, unlike other cell types, fully retain the capacity to control translation during ER stress. We observe rescaling of the ATF4 response, while the reduction in protein synthesis is fully retained. We identify two molecular pathways that jointly drive translational control in PERK‐deficient neurons. Haem‐regulated inhibitor (HRI) mediates p‐eIF2α and the ATF4 response and is complemented by the tRNA cleaving RNase angiogenin (ANG) to reduce protein synthesis. Overall, our study elucidates an intricate back‐up mechanism to ascertain translational control during ER stress in neurons that provides a mechanistic explanation for the thus far unresolved observation of neuronal resilience to proteostatic stress.
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Affiliation(s)
- Kimberly Wolzak
- Department of Functional Genomics, Faculty of Science, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands.,Functional Genomics Section, Department of Human Genetics, Amsterdam University Medical Centers (UMC) Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Anna Nölle
- Department of Pathology, Amsterdam University Medical Centers (UMC) Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Margherita Farina
- Department of Functional Genomics, Faculty of Science, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands
| | - Truus Em Abbink
- Department of Child Neurology, Amsterdam University Medical Centers (UMC) Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Marjo S van der Knaap
- Department of Functional Genomics, Faculty of Science, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands.,Department of Child Neurology, Amsterdam University Medical Centers (UMC) Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Matthijs Verhage
- Department of Functional Genomics, Faculty of Science, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands.,Functional Genomics Section, Department of Human Genetics, Amsterdam University Medical Centers (UMC) Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Wiep Scheper
- Department of Functional Genomics, Faculty of Science, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit (VU) Amsterdam, Amsterdam, The Netherlands.,Functional Genomics Section, Department of Human Genetics, Amsterdam University Medical Centers (UMC) Location Vrije Universiteit, Amsterdam, The Netherlands
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15
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A hypothesis: Retrotransposons as a relay of epigenetic marks in intergenerational epigenetic inheritance. Gene 2022; 817:146229. [PMID: 35063571 DOI: 10.1016/j.gene.2022.146229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022]
Abstract
Epigenetic marks in gametes, which both respond to the parental environmental factors and shape offspring phenotypes, are usually positioned to mediate intergenerational or transgenerational epigenetic inheritance. Nonetheless, the mechanisms through which gametic epigenetic signatures encode parental acquired phenotypes, and further initiate a cascade of molecular events to affect offspring phenotypes during early embryonic development, remain unclear. Retrotransposons are mobile DNA elements that could resist to genomic epigenetic reprogramming at specific loci and rewire the core regulatory networks of embryogenesis. Increasing evidences show that retrotransposons in the embryonic genome could interact with gametic epigenetic marks, which provides a tentative possibility that retrotransposons may serve as a relay of gametic epigenetic marks to transmit parental acquired traits. Here, we summarize the recent progress in exploring the crosstalk between gametic epigenetic marks and retrotransposons, and the regulation of gene expression and early embryonic development by retrotransposons. Accordingly, deciphering the mystery of interactions between gametic epigenetic marks and retrotransposons during early embryonic development will provide valuable insights into the intergenerational or transgenerational transmission of acquired traits.
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16
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Zeng L, Zhou J, Zhang Y, Wang X, Wang M, Su P. Differential Expression Profiles and Potential Intergenerational Functions of tRNA-Derived Small RNAs in Mice After Cadmium Exposure. Front Cell Dev Biol 2022; 9:791784. [PMID: 35047503 PMCID: PMC8762212 DOI: 10.3389/fcell.2021.791784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/07/2021] [Indexed: 12/18/2022] Open
Abstract
Cadmium (Cd) is a toxic heavy metal and ubiquitous environmental endocrine disruptor. Previous studies on Cd-induced damage to male fertility mainly focus on the structure and function of testis, including cytoskeleton, blood-testis barrier, and steroidogenesis. Nevertheless, to date, no studies have investigated the effects of Cd exposure on sperm epigenetic inheritance and intergenerational inheritance. In our study, we systematically revealed the changes in sperm tRNA-derived small RNAs (tsRNA) profiles and found that 14 tsRNAs (9 up-regulated and 5 down-regulated) were significantly altered after Cd exposure. Bioinformatics of tsRNA-mRNA-pathway interactions revealed that the altered biological functions mainly were related to ion transmembrane transport, lipid metabolism and cell membrane system. In addition, we focused on two stages of early embryo development and selected two organs to study the impact of these changes on cell membrane system, especially mitochondrion and lysosome, two typical membrane-enclosed organelles. Surprisingly, we found that the content of mitochondrion was significantly decreased in 2-cell stage, whereas remarkably increased in the morula stage. The contents of mitochondrion and lysosome were increased in the testes of 6-day-old offspring and livers of adult offspring, whereas remarkably decreased in the testes of adult offspring. This provides a possible basis to further explore the effects of paternal Cd exposure on offspring health.
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Affiliation(s)
- Ling Zeng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinzhao Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanwei Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaofei Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Wang
- Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ping Su
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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Xu XJ, Yang MS, Zhang B, Ge QQ, Niu F, Dong JQ, Zhuang Y, Liu BY. Genome-wide interrogation of transfer RNA-derived small RNAs in a mouse model of traumatic brain injury. Neural Regen Res 2022; 17:386-394. [PMID: 34269214 PMCID: PMC8463968 DOI: 10.4103/1673-5374.314315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that tsRNAs are involved in neurological disorders and play a role in the pathogenesis of neurodegenerative disease. However, whether tsRNAs are involved in traumatic brain injury-induced secondary injury remains poorly understood. In this study, a mouse controlled cortical impact model of traumatic brain injury was established, and integrated tsRNA and messenger RNA (mRNA) transcriptome sequencing were used. The results revealed that 103 tsRNAs were differentially expressed in the mouse model of traumatic brain injury at 72 hours, of which 56 tsRNAs were upregulated and 47 tsRNAs were downregulated. Based on microRNA-like seed matching and Pearson correlation analysis, 57 differentially expressed tsRNA-mRNA interaction pairs were identified, including 29 tsRNAs and 26 mRNAs. Moreover, Gene Ontology annotation of target genes revealed that the significantly enriched terms were primarily associated with inflammation and synaptic function. Collectively, our findings suggest that tsRNAs may be associated with traumatic brain injury-induced secondary brain injury, and are thus a potential therapeutic target for traumatic brain injury. The study was approved by the Beijing Neurosurgical Institute Animal Care and Use Committee (approval No. 20190411) on April 11, 2019.
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Affiliation(s)
- Xiao-Jian Xu
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Meng-Shi Yang
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bin Zhang
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qian-Qian Ge
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fei Niu
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jin-Qian Dong
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuan Zhuang
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bai-Yun Liu
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University; Nerve Injury and Repair Center of Beijing Institute for Brain Disorders; China National Clinical Research Center for Neurological Diseases, Beijing, China
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18
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Liu B, Cao J, Wang X, Guo C, Liu Y, Wang T. Deciphering the tRNA-derived small RNAs: origin, development, and future. Cell Death Dis 2021; 13:24. [PMID: 34934044 PMCID: PMC8692627 DOI: 10.1038/s41419-021-04472-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 01/04/2023]
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs), a novel category of small noncoding RNAs, are enzymatically cleaved from tRNAs. Previous reports have shed some light on the roles of tsRNAs in the development of human diseases. However, our knowledge about tsRNAs is still relatively lacking. In this paper, we review the biogenesis, classification, subcellular localization as well as action mechanism of tsRNAs, and discuss the association between chemical modifications of tRNAs and the production and functions of tsRNAs. Furthermore, using immunity, metabolism, and malignancy as examples, we summarize the molecular mechanisms of tsRNAs in diseases and evaluate the potential of tsRNAs as new biomarkers and therapeutic targets. At the same time, we compile and introduce several resource databases that are currently publicly available for analyzing tsRNAs. Finally, we discuss the challenges associated with research in this field and future directions.
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Affiliation(s)
- Bowen Liu
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China.
| | - Jinling Cao
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China
| | - Xiangyun Wang
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China
| | - Chunlei Guo
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China
| | - Yunxia Liu
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Tianjiao Wang
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, 300071, Tianjin, PR China
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19
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Angiogenin and Copper Crossing in Wound Healing. Int J Mol Sci 2021; 22:ijms221910704. [PMID: 34639045 PMCID: PMC8509573 DOI: 10.3390/ijms221910704] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 02/06/2023] Open
Abstract
Angiogenesis plays a key role in the wound healing process, involving the migration, growth, and differentiation of endothelial cells. Angiogenesis is controlled by a strict balance of different factors, and among these, the angiogenin protein plays a relevant role. Angiogenin is a secreted protein member of the ribonuclease superfamily that is taken up by cells and translocated to the nucleus when the process of blood vessel formation has to be promoted. However, the chemical signaling that activates the protein, normally present in the plasma, and the transport pathways through which the protein enters the cell are still largely unclear. Copper is also an angiogenic factor that regulates angiogenin expression and participates in the activation of common signaling pathways. The interaction between angiogenin and copper could be a relevant mechanism in regulating the formation of new blood vessel pathways and paving the way to the development of new drugs for chronic non-healing wounds.
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Wang J, Dong PK, Xu XF, Huang T, Mao S, Wang QG, Hao J, Liu XH, Sun XD, Kang K, Zhang Q, Li JT, Wang T. Identification of tRNA-derived Fragments and Their Potential Roles in Atherosclerosis. Curr Med Sci 2021; 41:712-721. [PMID: 34403096 DOI: 10.1007/s11596-021-2406-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Atherosclerosis (AS), a chronic inflammatory disease, is the basis of cardiovascular disease (CVD). Although the treatment has been greatly improved, AS still imposes a large burden on human health and the medical system, and we still need to further study its pathogenesis. As a novel biomolecule, transfer RNA-derived fragments (tRFs) play a key role in the progression of various disease. However, whether tRFs contribute to atherosclerosis pathogenesis remains unexplored. METHODS With deep sequencing technology, the change of tRFs expression profiles in patients with AS compared to healthy control group was identified. The accuracy of the sequencing data was validated using RT qPCR. Subsequently, we predicted the potential target genes of tRFs by online miRNA target prediction algorithms. The potential functions of tRFs were evaluated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. RESULTS There were 13 tRFs differentially expressed between patients with AS and healthy controls, of which 2 were up-regulated and 11 were down-regulated. Validation by RT-qPCR analysis confirmed the sequencing results, and tRF-Gly-GCC-009 was highly up-regulated in the AS group based on the results of sequencing which was confirmed by RT-qPCR analysis. Furthermore, GO enrichment and KEGG pathway analyses indicated that 10 signaling pathways were related to tRF-Gly-GCC-009. These pathways might be physiopathological fundamentals of AS, mainly involving in Apelin signaling, Notch signaling and calcium signaling. CONCLUSION The results of our study provide important novel insight into the underlying pathogenesis and demonstrate that tRFs might be potential biomarkers and therapeutic targets for AS in the future.
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Affiliation(s)
- Jian Wang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Pei-Kang Dong
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Xiu-Feng Xu
- Department of Neurology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Tao Huang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Shuai Mao
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Qing-Guo Wang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Jie Hao
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Xiao-Hong Liu
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Xiao-Dong Sun
- Department of Endocrinology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Kai Kang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Quan Zhang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China
| | - Jing-Tian Li
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China.
| | - Tao Wang
- Department of Cardiology, Affiliated Hospital of Weifang Medical University, Weifang, 261031, China.
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21
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Fagan SG, Helm M, Prehn JHM. tRNA-derived fragments: A new class of non-coding RNA with key roles in nervous system function and dysfunction. Prog Neurobiol 2021; 205:102118. [PMID: 34245849 DOI: 10.1016/j.pneurobio.2021.102118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
tRNA-derived small RNAs (tsRNA) are a recently identified family of non-coding RNA that have been associated with a variety of cellular functions including the regulation of protein translation and gene expression. Recent sequencing and bioinformatic studies have identified the broad spectrum of tsRNA in the nervous system and demonstrated that this new class of non-coding RNA is produced from tRNA by specific cleavage events catalysed by ribonucleases such as angiogenin and dicer. Evidence is also accumulating that production of tsRNA is increased during disease processes where they regulate stress responses, proteostasis, and neuronal survival. Mutations to tRNA cleaving and modifying enzymes have been implicated in several neurodegenerative disorders, and tsRNA levels in the blood are advancing as biomarkers for neurological disease. In this review we summarize the physiological importance of tsRNA in the central nervous system and their relevance to neurological disease.
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Affiliation(s)
- Steven G Fagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences - IPBS, Johannes Gutenberg-University, 55128, Mainz, Germany
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.
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22
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Abstract
tRNA-derived small RNA (tsRNA) is a novel class of non-coding RNA that is usually produced from tRNA following endonuclease cleavage which occurs under stress conditions. There are two types of tsRNAs: tRNA-derived fragments (tRFs) and stress-induced tRNA halves (tiRNAs), which differ in their cleavage position. Many studies have demonstrated that tsRNAs are involved in various physiological and pathological processes apart from cancer and gene expression. In this review, we briefly described the biogenesis, classification, and characteristics of tsRNAs and summarized the current research progress of tsRNAs in metabolic diseases, senescence, reproduction, stress, and organ injury, and finally put forward some problems to be solved.
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Affiliation(s)
- Qiyu Pan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
| | - Tingting Han
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
| | - Guoping Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
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23
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Rashad S, Tominaga T, Niizuma K. The cell and stress-specific canonical and noncanonical tRNA cleavage. J Cell Physiol 2021; 236:3710-3724. [PMID: 33043995 DOI: 10.1002/jcp.30107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 12/18/2022]
Abstract
Following stress, transfer RNA (tRNA) is cleaved to generate tRNA halves (tiRNAs). These tiRNAs have been shown to repress protein translation. Angiogenin was considered the main enzyme that cleaves tRNA at its anticodon to generate 35-45 nucleotide long tiRNA halves, however, the recent reports indicate the presence of angiogenin-independent cleavage. We previously observed tRNA cleavage pattern occurring away from the anticodon site. To explore this noncanonical cleavage, we analyze tRNA cleavage patterns in rat model of ischemia-reperfusion and in two rat cell lines. In vivo mitochondrial tRNAs were prone to this noncanonical cleavage pattern. In vitro, however, cytosolic and mitochondrial tRNAs could be cleaved noncanonically. Our results show an important regulatory role of mitochondrial stress in angiogenin-mediated tRNA cleavage. Neither angiogenin nor RNH1 appear to regulate the noncanonical tRNA cleavage. Finally, we verified our previous findings of the role of Alkbh1 in regulating tRNA cleavage and its impact on noncanonical tRNA cleavage.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
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24
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Mo D, He F, Zheng J, Chen H, Tang L, Yan F. tRNA-Derived Fragment tRF-17-79MP9PP Attenuates Cell Invasion and Migration via THBS1/TGF-β1/Smad3 Axis in Breast Cancer. Front Oncol 2021; 11:656078. [PMID: 33912465 PMCID: PMC8072113 DOI: 10.3389/fonc.2021.656078] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/18/2021] [Indexed: 12/19/2022] Open
Abstract
tRNA derivatives have been identified as a new kind of potential biomarker for cancer. Previous studies have identified that there were 30 differentially expressed tRNAs derivatives in breast cancer tissue with the high-throughput sequencing technique. This study aimed to investigate the possible biological function and mechanism of tRNA derivatives in breast cancer cells. One such tRF, a 5'-tRF fragment of tRF-17-79MP9PP (tRF-17) was screened in this study, which is processed from the mature tRNA-Val-AAC and tRNA-Val-CAC. tRF-17 with significantly low expression in breast cancer tissues and serum. The level of tRF-17 differentiated breast cancer from healthy controls with sensitivity of 70.4% and specificity of 68.4%. Overexpression of tRF-17 suppressed cells malignant activity. THBS1 (Thrombospondin-1) as a downstream target of tRF-17, and reduction of THBS1 expression also partially recovered the effects of tRF-17 inhibition on breast cancer cell viability, invasion and migration. Besides, THBS1, TGF-β1, Smad3, p-Smad3 and epithelial-to-mesenchymal transition related genes N-cadherin, MMP3, MMP9 were markedly down-regulated in tRF-17 overexpressing cells. Moreover, tRF-17 attenuated the THBS1-mediated TGF-β1/Smad3 signaling pathway in breast cancer cells. In general, the tRF-17/THBS1/TGF-β1/smad3 axis elucidates the molecular mechanism of breast cancer cells invasion and migration and could lead to a potential therapeutic target for breast cancer.
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Affiliation(s)
- Dongping Mo
- Department of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Fang He
- Department of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Junyu Zheng
- Department of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Huanhuan Chen
- Department of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Li Tang
- Department of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Feng Yan
- Department of Clinical Laboratory, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
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25
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Pereira M, Ribeiro DR, Pinheiro MM, Ferreira M, Kellner S, Soares AR. m 5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Int J Mol Sci 2021; 22:ijms22062941. [PMID: 33799331 PMCID: PMC8001983 DOI: 10.3390/ijms22062941] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023] Open
Abstract
Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification and tsRNA formation. More specifically, m5U54 hypomodification is followed by overexpression of the ribonuclease angiogenin (ANG) that cleaves tRNAs near the anticodon, resulting in accumulation of 5′tRNA-derived stress-induced RNAs (5′tiRNAs), namely 5′tiRNA-GlyGCC and 5′tiRNA-GluCTC, among others. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tiRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tiRNA formation in mammalian cells. These results establish a link between tRNA hypomethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
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Affiliation(s)
- Marisa Pereira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Diana R. Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Miguel M. Pinheiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Margarida Ferreira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, 81377 Munich, Germany;
- Institute of Pharmaceutical Chemistry, Goethe-University, 60438 Frankfurt, Germany
| | - Ana R. Soares
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810 Aveiro, Portugal; (M.P.); (D.R.R.); (M.M.P.); (M.F.)
- Correspondence:
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26
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Tao EW, Wang HL, Cheng WY, Liu QQ, Chen YX, Gao QY. A specific tRNA half, 5'tiRNA-His-GTG, responds to hypoxia via the HIF1α/ANG axis and promotes colorectal cancer progression by regulating LATS2. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:67. [PMID: 33588913 PMCID: PMC7885485 DOI: 10.1186/s13046-021-01836-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/10/2021] [Indexed: 02/06/2023]
Abstract
Background Currently, tRNA-derived small RNAs (tsRNAs) are recognized as a novel and potential type of non-coding RNAs (ncRNAs), which participate in various cellular processes and play an essential role in cancer progression. However, tsRNAs involvement in colorectal cancer (CRC) progression remains unclear. Methods Sequencing analyses were performed to explore the tsRNAs with differential expression in CRC. Gain- and loss-of functions of 5’tiRNA-His-GTG were performed in CRC cells and xenograft tumor to discover its role in the progression of CRC. Hypoxia culture and hypoxia inducible factor 1 subunit alpha (HIF1α) inhibitors were performed to uncover the biogenesis of 5’tiRNA-His-GTG. The regulation of 5’tiRNA-His-GTG for large tumor suppressor kinase 2 (LATS2) were identified by luciferase reporter assay, western blot, and rescue experiments. Results Here, our study uncovered the profile of tsRNAs in human CRC tissues and confirmed a specific tRNA half, 5’tiRNA-His-GTG, is upregulated in CRC tissues. Then, in vitro and in vivo experiments revealed the oncogenic role of 5’tiRNA-His-GTG in CRC and found that targeting 5’tiRNA-His-GTG can induce cell apoptosis. Mechanistically, the generation of 5’tiRNA-His-GTG seems to be a responsive process of tumor hypoxic microenvironment, and it is regulated via the HIF1α/angiogenin (ANG) axis. Remarkably, LATS2 was found to be an important and major target of 5’tiRNA-His-GTG, which renders 5’tiRNA-His-GTG to “turn off” hippo signaling pathway and finally promotes the expression of pro-proliferation and anti-apoptosis related genes. Conclusions In summary, the findings revealed a specific 5’tiRNA-His-GTG-engaged pathway in CRC progression and provided clues to design a novel therapeutic target in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01836-7.
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Affiliation(s)
- En-Wei Tao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Hao-Lian Wang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Wing Yin Cheng
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Qian-Qian Liu
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China.
| | - Qin-Yan Gao
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine, Renji Hospital, 145 Middle Shandong Road, 200001, Shanghai, China.
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Angiogenin (ANG)-Ribonuclease Inhibitor (RNH1) System in Protein Synthesis and Disease. Int J Mol Sci 2021; 22:ijms22031287. [PMID: 33525475 PMCID: PMC7866052 DOI: 10.3390/ijms22031287] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
Protein synthesis is a highly complex process executed by well-organized translation machinery. Ribosomes, tRNAs and mRNAs are the principal components of this machinery whereas RNA binding proteins and ribosome interacting partners act as accessory factors. Angiogenin (ANG)-Ribonuclease inhibitor (RNH1) system is one such accessory part of the translation machinery that came into focus afresh due to its unconventional role in the translation. ANG is conventionally known for its ability to induce blood vessel formation and RNH1 as a "sentry" to protect RNAs from extracellular RNases. However, recent studies suggest them to be important in translation regulation. During cell homeostasis, ANG in the nucleus promotes rRNA transcription. While under stress, ANG translocates to the cytosol and cleaves tRNA into fragments which inhibit ribosome biogenesis and protein synthesis. RNH1, which intimately interacts with ANG to inhibit its ribonucleolytic activity, can also bind to the 40S ribosomes and control translation by yet to be known mechanisms. Here, we review recent advancement in the knowledge of translation regulation by the ANG-RNH1 system. We also gather information about this system in cell homeostasis as well as in pathological conditions such as cancer and ribosomopathies. Additionally, we discuss the future research directions and therapeutic potential of this system.
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28
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Yu X, Xie Y, Zhang S, Song X, Xiao B, Yan Z. tRNA-derived fragments: Mechanisms underlying their regulation of gene expression and potential applications as therapeutic targets in cancers and virus infections. Am J Cancer Res 2021; 11:461-469. [PMID: 33391486 PMCID: PMC7681095 DOI: 10.7150/thno.51963] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/02/2020] [Indexed: 12/17/2022] Open
Abstract
tRNA-derived fragments (tRFs) are a new category of regulatory noncoding RNAs with distinct biological functions in cancers and stress-induced diseases. Herein, we first summarize the classification and biogenesis of tRFs. tRFs are produced from pre-tRNAs or mature tRNAs. Based on the incision loci, tRFs are classified into several types: tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. Some tRFs participate in posttranscriptional regulation through microRNA-like actions or by displacing RNA binding proteins and regulating protein translation by promoting ribosome biogenesis or interfering with translation initiation. Other tRFs prevent cell apoptosis by binding to cytochrome c or promoting virus replication. More importantly, the dysregulation of tRFs has important clinical implications. They are potential diagnostic and prognostic biomarkers of gastric cancer, liver cancer, breast cancer, prostate cancer, and chronic lymphocytic leukemia. tRFs may become new therapeutic targets for the treatment of diseases such as hepatocellular carcinoma and respiratory syncytial virus infection. Finally, we point out the existing problems and future research directions associated with tRFs. In conclusion, the current progress in the research of tRFs reveals that they have important clinical implications and may constitute novel molecular therapeutic targets for modulating pathological processes.
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29
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Avcilar-Kucukgoze I, Kashina A. Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology. Front Mol Biosci 2020; 7:610617. [PMID: 33392265 PMCID: PMC7773854 DOI: 10.3389/fmolb.2020.610617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Transfer tRNAs (tRNAs) are small non-coding RNAs that are highly conserved in all kingdoms of life. Originally discovered as the molecules that deliver amino acids to the growing polypeptide chain during protein synthesis, tRNAs have been believed for a long time to play exclusive role in translation. However, recent studies have identified key roles for tRNAs and tRNA-derived small RNAs in multiple other processes, including regulation of transcription and translation, posttranslational modifications, stress response, and disease. These emerging roles suggest that tRNAs may be central players in the complex machinery of biological regulatory pathways. Here we overview these non-canonical roles of tRNA in normal physiology and disease, focusing largely on eukaryotic and mammalian systems.
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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30
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Ishida T, Inoue T, Niizuma K, Konno N, Suzuki C, Inoue T, Ezura M, Uenohara H, Abe T, Tominaga T. Prediction of Functional Outcome in Patients with Acute Stroke by Measuring tRNA Derivatives. Cerebrovasc Dis 2020; 49:639-646. [PMID: 33207351 DOI: 10.1159/000511627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/15/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND PURPOSE Transfer RNA (tRNA) is a noncoding RNA that delivers amino acids to ribosomes for protein synthesis. tRNA is also involved in cell stress response programs. Oxidative stress induces direct conformational change in tRNA structure that promotes subsequent tRNA fragmentation. Using an antibody against tRNA-specific modified nucleoside 1-methyladenosine (m1A), we can detect tRNA derivatives such as conformationally changed tRNA, tRNA-derived fragments, and mononucleotide-free m1A. Based on these findings, tRNA derivatives may have potential as an early tissue damage marker. The purpose of this study was to investigate the plasma tRNA derivatives in stroke patients to clarify whether tRNA derivatives in the acute phase can detect early brain damage and then predict the functional outcome. METHODS Patients (75 patients with ischemic and 66 with hemorrhagic stroke) and 22 healthy volunteers were prospectively enrolled for this study between November 2016 and February 2019. Plasma samples were collected within 24 h and at 1 day, 7 days, and 30 days from the onset. Plasma tRNA derivative concentrations were measured by ELISA kit using the anti-m1A antibody. RESULTS The plasma tRNA derivative level on admission was significantly increased in both ischemic (mean ± standard error, 232.2 ± 33.1 ng/mL) and hemorrhagic stroke patients (212 ± 23.4 ng/mL) compared to the healthy volunteers (86.0 ± 7.9 ng/mL) (p = 0.00042 and p = 0.00018, respectively). The infarction size (r = 0.445, p = 0.00018) and hematoma volumes (r = 0.33, p = 0.0072) were also significantly correlated with tRNA derivatives. The concentrations of tRNA derivatives were associated with poor functional outcome (Modified Rankin Scale score 3-6 at 30 days from the onset) in patients with ischemic stroke at 7 days after onset (p = 0.020). CONCLUSIONS Stress-induced tRNA derivatives can detect brain tissue damage, predicting functional outcome in patients with ischemic stroke.
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Affiliation(s)
- Tomohisa Ishida
- Department of Neurosurgery, National Hospital Organization Sendai Medical Center, Sendai, Japan.,Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Inoue
- Department of Neurosurgery, National Hospital Organization Sendai Medical Center, Sendai, Japan,
| | - Kuniyasu Niizuma
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Natsumi Konno
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chitose Suzuki
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoo Inoue
- Department of Neurosurgery, National Hospital Organization Sendai Medical Center, Sendai, Japan
| | - Masayuki Ezura
- Department of Neurosurgery, National Hospital Organization Sendai Medical Center, Sendai, Japan
| | - Hiroshi Uenohara
- Department of Neurosurgery, National Hospital Organization Sendai Medical Center, Sendai, Japan
| | - Takaaki Abe
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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31
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Jia Y, Tan W, Zhou Y. Transfer RNA-derived small RNAs: potential applications as novel biomarkers for disease diagnosis and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1092. [PMID: 33145311 PMCID: PMC7575943 DOI: 10.21037/atm-20-2797] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s. tsRNAs have been reported to play essential roles and possess different biological functions in a variety of physiological activities. Recently, tsRNAs have been implicated in a large number of diseases, such as cancers (including breast cancer, ovarian cancer, lung cancer, prostate cancer, colorectal cancer, etc.), neurological disorders, viral infections, metabolic diseases and angiogenesis-related diseases. Although the biological functions of tsRNAs are still poorly understood, correlations between dysregulated tsRNA expression and disease development have been recently reported. Additionally, their capabilities as potential biomarkers for disease diagnosis and prognosis have been revealed in clinical studies. In this review, we summarize the current knowledge of tsRNAs, and discuss their potential clinical applications as biomarkers in different diseases. Although the regulation of tsRNAs is similar to miRNAs in regards to the related physiological and pathological processes, the higher stability and expression levels of tsRNAs place them as ideal biomarkers for the diagnosis and prognosis in cancer and other diseases. Therefore, it is worth to verify the possibility and reliability of these reported tsRNAs as potential biomarkers for clinical applications in disease diagnosis and prognosis.
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Affiliation(s)
- Yang Jia
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
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32
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Rashad S, Han X, Sato K, Mishima E, Abe T, Tominaga T, Niizuma K. The stress specific impact of ALKBH1 on tRNA cleavage and tiRNA generation. RNA Biol 2020; 17:1092-1103. [PMID: 32521209 PMCID: PMC7549645 DOI: 10.1080/15476286.2020.1779492] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 10/24/2022] Open
Abstract
tiRNAs are small non-coding RNAs produced when tRNA is cleaved under stress. tRNA methylation modifications has emerged in recent years as important regulators for tRNA structural stability and sensitivity to cleavage and tiRNA generation during stress, however, the specificity and higher regulation of such a process is not fully understood. Alkbh1 is a m1A demethylase that leads to destabilization of tRNA and enhanced tRNA cleavage. We examined the impact of Alkbh1 targeting via gene knockdown or overexpression on B35 rat neuroblastoma cell line fate following stresses and on tRNA cleavage. We show that Alkbh1 impact on cell fate and tRNA cleavage is a stress specific process that is impacted by the demethylating capacity of the cellular stress in question. We also show that not all tRNAs are cleaved equally following Alkbh1 manipulation and stress, and that Alkbh1 KD fails to rescue tRNAs from cleavage following demethylating stresses. These findings shed a light on the specificity and higher regulation of tRNA cleavage and should act as a guide for future work exploring the utility of Alkbh1 as a therapeutic target for cancers or ischaemic insult.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Xiaobo Han
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kanako Sato
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Eikan Mishima
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takaaki Abe
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
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33
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Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci 2020; 21:ijms21134684. [PMID: 32630140 PMCID: PMC7370119 DOI: 10.3390/ijms21134684] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed “epitranscriptomics”, in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome’s characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications (“stages”) until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.
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Affiliation(s)
- Julia Mathlin
- Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Loredana Le Pera
- CNR-Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Teresa Colombo
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
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34
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Sato K, Rashad S, Niizuma K, Tominaga T. Stress Induced tRNA Halves (tiRNAs) as Biomarkers for Stroke and Stroke Therapy; Pre-clinical Study. Neuroscience 2020; 434:44-54. [DOI: 10.1016/j.neuroscience.2020.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 01/10/2023]
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35
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Ghosh A, Shcherbik N. Effects of Oxidative Stress on Protein Translation: Implications for Cardiovascular Diseases. Int J Mol Sci 2020; 21:E2661. [PMID: 32290431 PMCID: PMC7215667 DOI: 10.3390/ijms21082661] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are a group of disorders that affect the heart and blood vessels. Due to their multifactorial nature and wide variation, CVDs are the leading cause of death worldwide. Understanding the molecular alterations leading to the development of heart and vessel pathologies is crucial for successfully treating and preventing CVDs. One of the causative factors of CVD etiology and progression is acute oxidative stress, a toxic condition characterized by elevated intracellular levels of reactive oxygen species (ROS). Left unabated, ROS can damage virtually any cellular component and affect essential biological processes, including protein synthesis. Defective or insufficient protein translation results in production of faulty protein products and disturbances of protein homeostasis, thus promoting pathologies. The relationships between translational dysregulation, ROS, and cardiovascular disorders will be examined in this review.
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Affiliation(s)
- Arnab Ghosh
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
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36
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Qin C, Feng H, Zhang C, Zhang X, Liu Y, Yang DG, Du LJ, Sun YC, Yang ML, Gao F, Li JJ. Differential Expression Profiles and Functional Prediction of tRNA-Derived Small RNAs in Rats After Traumatic Spinal Cord Injury. Front Mol Neurosci 2020; 12:326. [PMID: 31998075 PMCID: PMC6968126 DOI: 10.3389/fnmol.2019.00326] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Spinal cord injury (SCI) is mostly caused by trauma. As the primary mechanical injury is unavoidable, a focus on the underlying molecular mechanisms of the SCI-induced secondary injury is necessary to develop promising treatments for patients with SCI. Transfer RNA-derived small RNA (tsRNA) is a novel class of short, non-coding RNA, possessing potential regulatory functions in various diseases. However, the functional roles of tsRNAs in traumatic SCI have not been determined yet. We used a combination of sequencing, quantitative reverse transcription-polymerase chain reaction (qRT-PCR), bioinformatics, and luciferase reporter assay to screen the expression profiles and identify the functional roles of tsRNAs after SCI. As a result, 297 differentially expressed tsRNAs were identified in rats' spinal cord 1 day after contusion. Of those, 155 tsRNAs were significantly differentially expressed: 91 were significantly up-regulated, whereas 64 were significantly down-regulated after SCI (fold change > 1.5; P < 0.05). Bioinformatics analyses revealed candidate tsRNAs (tiRNA-Gly-GCC-001, tRF-Gly-GCC-012, tRF-Gly-GCC-013, and tRF-Gly-GCC-016) that might play regulatory roles through the mitogen-activated protein kinase (MAPK) and neurotrophin signaling pathways by targeting brain-derived neurotrophic factor (BDNF). We validated the candidate tsRNAs and found opposite trends in the expression levels of the tsRNAs and BDNF after SCI. Finally, tiRNA-Gly-GCC-001 was identified to target BDNF using the luciferase reporter assay. In summary, we found an altered tsRNA expression pattern and predicted tiRNA-Gly-GCC-001 might be involved in the MAPK and neurotrophin pathways by targeting the BDNF, thus regulating the post-SCI pathophysiologic processes. This study provides novel insights for future investigations to explore the mechanisms and therapeutic targets for SCI.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Hao Feng
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Yi Liu
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ying-Chun Sun
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,TCM Treatment Center, China Rehabilitation Research Center, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University, Beijing, China.,Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China.,Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,Chinese Institute of Rehabilitation Science, Beijing, China.,Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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37
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Abstract
Over the past decades, tRNA was found to be a rich hub of RNA modifications such as 1-methyladenosine and 5-methycytosine modifications and others, holding more than half of all modifications occurring in RNA molecules. Moreover, tRNA was discovered to be a source of various small noncoding RNA species, such as the stress induced angiogenin cleaved tRNA halves (tiRNA) or the miRNA like tRNA derived fragments. tRNA cleavage under stress was fist discovered in bacteria and later was found to be conserved across different species, including mammals. Under cellular stress conditions, tRNA undergoes conformational changes and angiogenin cleaves it into 3' and 5' halves. 5'tiRNA halves were shown to repress protein translations. tRNA cleavage is thought of to be a cytoprotective mechanism by which cells evade apoptosis, however some data hints to the opposite; that tiRNA are cytotoxic or at least related to apoptosis initiation. tRNA cleavage also was shown to be affected by tRNA modifications via different enzymes in the cytosol and mitochondria. In this review, we will highlight the biology of tRNA cleavage, show the evidence of it being cytoprotective or a marker of cell death and shed a light on its role in disease models and human diseases as well as possible future directions in this field of RNA research.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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38
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Qin C, Xu PP, Zhang X, Zhang C, Liu CB, Yang DG, Gao F, Yang ML, Du LJ, Li JJ. Pathological significance of tRNA-derived small RNAs in neurological disorders. Neural Regen Res 2020; 15:212-221. [PMID: 31552886 PMCID: PMC6905339 DOI: 10.4103/1673-5374.265560] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs (tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs (tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points: (1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes. (2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress. (3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma. (4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Pei-Pei Xu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chang-Bin Liu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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39
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Kim HK. Transfer RNA-Derived Small Non-Coding RNA: Dual Regulator of Protein Synthesis. Mol Cells 2019; 42:687-692. [PMID: 31656062 PMCID: PMC6821453 DOI: 10.14348/molcells.2019.0214] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/16/2023] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) play a role in various cellular processes. Accumulating evidence has revealed that tsRNAs are deeply implicated in human diseases, such as various cancers and neurological disorders, suggesting that tsRNAs should be investigated to develop novel therapeutic intervention. tsRNAs provide more complexity to the physiological role of transfer RNAs by repressing or activating protein synthesis with distinct mechanisms. Here, we highlight the detailed mechanism of tsRNA-mediated dual regulation in protein synthesis and discuss the necessity of novel sequencing technology to learn more about tsRNAs.
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Affiliation(s)
- Hak Kyun Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974,
Korea
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40
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Valdez F, Salvador J, Palermo PM, Mohl JE, Hanley KA, Watts D, Llano M. Schlafen 11 Restricts Flavivirus Replication. J Virol 2019; 93:e00104-19. [PMID: 31118262 PMCID: PMC6639263 DOI: 10.1128/jvi.00104-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/14/2019] [Indexed: 02/07/2023] Open
Abstract
Schlafen 11 (Slfn11) is an interferon-stimulated gene that controls the synthesis of proteins by regulating tRNA abundance. Likely through this mechanism, Slfn11 has previously been shown to impair human immunodeficiency virus type 1 (HIV-1) infection and the expression of codon-biased open reading frames. Because replication of positive-sense single-stranded RNA [(+)ssRNA] viruses requires the immediate translation of the incoming viral genome, whereas negative-sense single-stranded RNA [(-)ssRNA] viruses carry at infection an RNA replicase that makes multiple translation-competent copies of the incoming viral genome, we reasoned that (+)ssRNA viruses will be more sensitive to the effect of Slfn11 on protein synthesis than (-)ssRNA viruses. To evaluate this hypothesis, we tested the effects of Slfn11 on the replication of a panel of ssRNA viruses in the human glioblastoma cell line A172, which naturally expresses Slfn11. Depletion of Slfn11 significantly increased the replication of (+)ssRNA viruses from the Flavivirus genus, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV), but had no significant effect on the replication of the (-)ssRNA viruses vesicular stomatitis virus (VSV) (Rhabdoviridae family) and Rift Valley fever virus (RVFV) (Phenuiviridae family). Quantification of the ratio of genome-containing viral particles to PFU indicated that Slfn11 impairs WNV infectivity. Intriguingly, Slfn11 prevented WNV-induced downregulation of a subset of tRNAs implicated in the translation of 11.8% of the viral polyprotein. Low-abundance tRNAs might promote optimal protein folding and enhance viral infectivity, as previously reported. In summary, this study demonstrates that Slfn11 restricts flavivirus replication by impairing viral infectivity.IMPORTANCE We provide evidence that the cellular protein Schlafen 11 (Slfn11) impairs replication of flaviviruses, including West Nile virus (WNV), dengue virus (DENV), and Zika virus (ZIKV). However, replication of single-stranded negative RNA viruses was not affected. Specifically, Slfn11 decreases the infectivity of WNV potentially by preventing virus-induced modifications of the host tRNA repertoire that could lead to enhanced viral protein folding. Furthermore, we demonstrate that Slfn11 is not the limiting factor of this novel broad antiviral pathway.
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Affiliation(s)
- Federico Valdez
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Julienne Salvador
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Pedro M Palermo
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Jonathon E Mohl
- Department of Bioinformatics, The University of Texas at El Paso, El Paso, Texas, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Douglas Watts
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
| | - Manuel Llano
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, USA
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41
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A tRNA fragment, 5′-tiRNAVal, suppresses the Wnt/β-catenin signaling pathway by targeting FZD3 in breast cancer. Cancer Lett 2019; 457:60-73. [DOI: 10.1016/j.canlet.2019.05.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022]
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42
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Elkordy A, Rashad S, Shehabeldeen H, Mishima E, Niizuma K, Abe T, Tominaga T. tiRNAs as a novel biomarker for cell damage assessment in in vitro ischemia-reperfusion model in rat neuronal PC12 cells. Brain Res 2019; 1714:8-17. [DOI: 10.1016/j.brainres.2019.02.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/04/2019] [Accepted: 02/15/2019] [Indexed: 11/17/2022]
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43
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Toro-Urrego N, Vesga-Jiménez DJ, Herrera MI, Luaces JP, Capani F. Neuroprotective Role of Hypothermia in Hypoxic-ischemic Brain Injury: Combined Therapies using Estrogen. Curr Neuropharmacol 2019; 17:874-890. [PMID: 30520375 PMCID: PMC7052835 DOI: 10.2174/1570159x17666181206101314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/26/2018] [Accepted: 11/28/2018] [Indexed: 12/15/2022] Open
Abstract
Hypoxic-ischemic brain injury is a complex network of factors, which is mainly characterized by a decrease in levels of oxygen concentration and blood flow, which lead to an inefficient supply of nutrients to the brain. Hypoxic-ischemic brain injury can be found in perinatal asphyxia and ischemic-stroke, which represent one of the main causes of mortality and morbidity in children and adults worldwide. Therefore, knowledge of underlying mechanisms triggering these insults may help establish neuroprotective treatments. Selective Estrogen Receptor Modulators and Selective Tissue Estrogenic Activity Regulators exert several neuroprotective effects, including a decrease of reactive oxygen species, maintenance of cell viability, mitochondrial survival, among others. However, these strategies represent a traditional approach of targeting a single factor of pathology without satisfactory results. Hence, combined therapies, such as the administration of therapeutic hypothermia with a complementary neuroprotective agent, constitute a promising alternative. In this sense, the present review summarizes the underlying mechanisms of hypoxic-ischemic brain injury and compiles several neuroprotective strategies, including Selective Estrogen Receptor Modulators and Selective Tissue Estrogenic Activity Regulators, which represent putative agents for combined therapies with therapeutic hypothermia.
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Affiliation(s)
- Nicolás Toro-Urrego
- Address correspondence to this author at the Laboratorio de Citoarquitectura y Plasticidad Neuronal, Instituto de Investigaciones Cardiológicas, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina; E-mail:
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