151
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Fu BF, Xu CY. Transfer RNA-Derived Small RNAs: Novel Regulators and Biomarkers of Cancers. Front Oncol 2022; 12:843598. [PMID: 35574338 PMCID: PMC9096126 DOI: 10.3389/fonc.2022.843598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/06/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are conventional non-coding RNAs (ncRNAs) with a length between18 and 40 nucleotides (nt) playing a crucial role in treating various human diseases including tumours. Nowadays, with the use of high-throughput sequencing technologies, it has been proven that certain tsRNAs are dysregulated in multiple tumour tissues as well as in the blood serum of cancer patients. Meanwhile, data retrieved from the literature show that tsRNAs are correlated with the regulation of the hallmarks of cancer, modification of tumour microenvironment, and modulation of drug resistance. On the other side, the emerging role of tsRNAs as biomarkers for cancer diagnosis and prognosis is promising. In this review, we focus on the specific characteristics and biological functions of tsRNAs with a focus on their impact on various tumours and discuss the possibility of tsRNAs as novel potential biomarkers for cancer diagnosis and prognosis.
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Affiliation(s)
- Bi-Fei Fu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Chao-Yang Xu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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152
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Li J, Cao C, Fang L, Yu W. Serum transfer RNA-derived fragment tRF-31-79MP9P9NH57SD acts as a novel diagnostic biomarker for non-small cell lung cancer. J Clin Lab Anal 2022; 36. [PMID: 35576497 PMCID: PMC9279995 DOI: 10.1002/jcla.24492] [Citation(s) in RCA: 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: 04/14/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background tRNA‐derived fragments (tRFs) have been found to have a crucial function in the pathophysiology of cancers. However, the function of tRFs in non‐small cell lung cancer (NSCLC) is yet unknown. The goal of this study was to assess the tRF‐31‐79MP9P9NH57SD serum expression from NSCLC patients and to determine its diagnostic usefulness. Methods By using stem‐loop quantitative real‐time PCR, we were able to detect various tRF‐31‐79MP9P9NH57SD expressions in 96 NSCLC serum samples, 96 healthy controls, and 20 pairs of NSCLC serum samples pre‐ and post‐surgery (qRT‐PCR). After that, we analyzed its diagnostic effectiveness using the receiver operating characteristic (ROC) curve. Results Serum tRF‐31‐79MP9P9NH57SD expression was higher in NSCLC patients, and levels of tRF‐31‐79MP9P9NH57SD were linked to the clinical stage (p = 0.002) and the malignancy of lymph node (p = 0.012). In addition, after the procedure, the serum tRF‐31‐79MP9P9NH57SD expression in NSCLC patients dropped. With 48.96 percent sensitivity and 90.62 percent specificity, the area under ROC curve (AUC) was 0.733. Conclusion serum tRF‐31‐79MP9P9NH57SD possibly is a new and groundbreaking biomarker for the NSCLC.
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Affiliation(s)
- Jipeng Li
- Department of Central Laboratory, The Affiliated People's Hospital, Ningbo University, Ningbo, China
| | - Chao Cao
- Department of Respiratory and Critical Medicine, Ningbo First Hospital, Ningbo, China
| | - Laifu Fang
- Department of Pathology, The Affiliated People's Hospital, Ningbo University, Ningbo, China
| | - Wanjun Yu
- Department of Respiratory and Critical Medicine, The Affiliated People's Hospital, Ningbo University, Ningbo, China
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153
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Yang W, Gao K, Qian Y, Huang Y, Xiang Q, Chen C, Chen Q, Wang Y, Fang F, He Q, Chen S, Xiong J, Chen Y, Xie N, Zheng D, Zhai R. A novel tRNA-derived fragment AS-tDR-007333 promotes the malignancy of NSCLC via the HSPB1/MED29 and ELK4/MED29 axes. J Hematol Oncol 2022; 15:53. [PMID: 35526007 PMCID: PMC9077895 DOI: 10.1186/s13045-022-01270-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Background Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs. Recent studies suggest that tRFs participate in some pathological processes. However, the biological functions and mechanisms of tRFs in non-small cell lung cancer (NSCLC) are largely unknown.
Methods Differentially expressed tRFs were identified by tRF and tiRNA sequencing using 9 pairs of pre- and post-operation plasma from patients with NSCLC. Quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH) were used to determine the levels of tRF in tissues, plasma, and cells. Gain- and loss-of-function experiments were implemented to investigate the oncogenic effects of tRF on NSCLC cells in vitro and in vivo. Chromatin immunoprecipitation (ChIP), luciferase reporter, RNA pulldown, mass spectrum, RNA immunoprecipitation (RIP), Western blot, co-immunoprecipitation (Co-IP) assays, and rescue experiments were performed to explore the regulatory mechanisms of tRF in NSCLC. Results AS-tDR-007333 was an uncharacterized tRF and significantly up-regulated in NSCLC tissues, plasma, and cells. Clinically, AS-tDR-007333 overexpression could distinguish NSCLC patients from healthy controls and associated with poorer prognosis of NSCLC patients. Functionally, overexpression of AS-tDR-007333 enhanced proliferation and migration of NSCLC cells, whereas knockdown of AS-tDR-007333 resulted in opposite effects. Mechanistically, AS-tDR-007333 promoted the malignancy of NSCLC cells by activating MED29 through two distinct mechanisms. First, AS-tDR-007333 bound to and interacted with HSPB1, which activated MED29 expression by enhancing H3K4me1 and H3K27ac in MED29 promoter. Second, AS-tDR-007333 stimulated the expression of transcription factor ELK4, which bound to MED29 promoter and increased its transcription. Therapeutically, inhibition of AS-tDR-007333 suppressed NSCLC cell growth in vivo. Conclusions Our study identifies a new oncogenic tRF and uncovers a novel mechanism that AS-tDR-007333 promotes NSCLC malignancy through the HSPB1-MED29 and ELK4-MED29 axes. AS-tDR-007333 is a potential diagnostic or prognostic marker and therapeutic target for NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-022-01270-y.
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Affiliation(s)
- Wenhan Yang
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Kaiping Gao
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Youhui Qian
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, 3002 West Shungang Road, Shenzhen, 518035, China
| | - Yongyi Huang
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Qin Xiang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Cheng Chen
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Qianqian Chen
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yiling Wang
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Fuyuan Fang
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, 3002 West Shungang Road, Shenzhen, 518035, China
| | - Qihan He
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Siqi Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, 3002 West Shungang Road, Shenzhen, 518035, China
| | - Juan Xiong
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China.,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Yangchao Chen
- Faculty of Medicine, The Chinese University of Hong Kong, Rm508A, Lo Kwee-Seong Integrated Biomedical Sciences Bldg, Shatin, NT, Hong Kong, China
| | - Ni Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Shenzhen University, 3002 West Shungang Road, Shenzhen, 518035, China.
| | - Duo Zheng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China.
| | - Rihong Zhai
- School of Public Health, Shenzhen University Health Science Center, 1066 Xueyuan Ave., Shenzhen, 518055, China. .,Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China. .,Department of Thoracic Surgery, Shenzhen University General Hospital, 1098 Xueyuan Ave., Shenzhen, 518055, China.
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154
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A 5’-tiRNA fragment that inhibits proliferation and migration of laryngeal squamous cell carcinoma by targeting PIK3CD. Genomics 2022; 114:110392. [DOI: 10.1016/j.ygeno.2022.110392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/24/2022] [Accepted: 05/22/2022] [Indexed: 12/24/2022]
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155
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Su Z, Monshaugen I, Wilson B, Wang F, Klungland A, Ougland R, Dutta A. TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer. Nat Commun 2022; 13:2165. [PMID: 35444240 PMCID: PMC9021294 DOI: 10.1038/s41467-022-29790-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 03/16/2022] [Indexed: 01/11/2023] Open
Abstract
RNA modifications are important regulatory elements of RNA functions. However, most genome-wide mapping of RNA modifications has focused on messenger RNAs and transfer RNAs, but such datasets have been lacking for small RNAs. Here we mapped N1-methyladenosine (m1A) in the cellular small RNA space. Benchmarked with synthetic m1A RNAs, our workflow identified specific groups of m1A-containing small RNAs, which are otherwise disproportionally under-represented. In particular, 22-nucleotides long 3' tRNA-fragments are highly enriched for TRMT6/61A-dependent m1A located within the seed region. TRMT6/61A-dependent m1A negatively affects gene silencing by tRF-3s. In urothelial carcinoma of the bladder, where TRMT6/61A is over-expressed, higher m1A modification on tRFs is detected, correlated with a dysregulation of tRF targetome. Lastly, TRMT6/61A regulates tRF-3 targets involved in unfolded protein response. Together, our results reveal a mechanism of regulating gene expression via base modification of small RNA.
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Affiliation(s)
- Zhangli Su
- Department of Genetics, University of Alabama, Birmingham, AL, 35233, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA
| | - Ida Monshaugen
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
- Department of Surgery, Baerum Hospital Vestre Viken Hospital Trust, 1346, Gjettum, Norway
| | - Briana Wilson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. 10 Box 1066 Blindern, 0316, Oslo, Norway
| | - Rune Ougland
- Department of Microbiology, Oslo University Hospital Rikshospitalet, 0372, Oslo, Norway.
- Department of Surgery, Baerum Hospital Vestre Viken Hospital Trust, 1346, Gjettum, Norway.
| | - Anindya Dutta
- Department of Genetics, University of Alabama, Birmingham, AL, 35233, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, 22901, USA.
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156
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Wilson B, Dutta A. Function and Therapeutic Implications of tRNA Derived Small RNAs. Front Mol Biosci 2022; 9:888424. [PMID: 35495621 PMCID: PMC9043108 DOI: 10.3389/fmolb.2022.888424] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022] Open
Abstract
tRNA derived small RNAs are mainly composed of tRNA fragments (tRFs) and tRNA halves (tiRs). Several functions have been attributed to tRFs and tiRs since their initial characterizations, spanning all aspects of regulation of the Central Dogma: from nascent RNA silencing, to post-transcriptional gene silencing, and finally, to translational regulation. The length distribution, sequence diversity, and multifaceted functions of tRFs and tiRs positions them as attractive new models for small RNA therapeutics. In this review, we will discuss the principles of tRF biogenesis and function in order to highlight their therapeutic potential.
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Affiliation(s)
- Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Anindya Dutta
- Department of Genetics, University of Alabama, Birmingham, AL, United States
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157
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Liu Y, Cheng L, Zhan H, Li H, Li X, Huang Y, Li Y. The Roles of Noncoding RNAs in Systemic Sclerosis. Front Immunol 2022; 13:856036. [PMID: 35464474 PMCID: PMC9024074 DOI: 10.3389/fimmu.2022.856036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Noncoding RNAs (ncRNAs) constitute more than 90% of the RNAs in the human genome. In the past decades, studies have changed our perception of ncRNAs from “junk” transcriptional products to functional regulatory molecules that mediate critical processes, including chromosomal modifications, mRNA splicing and stability, and translation, as well as key signaling pathways. Emerging evidence suggests that ncRNAs are abnormally expressed in not only cancer but also autoimmune diseases, such as systemic sclerosis (SSc), and may serve as novel biomarkers and therapeutic targets for the diagnosis and treatment of SSc. However, the functions and underlying mechanisms of ncRNAs in SSc remain incompletely understood. In this review, we discuss the current findings on the biogenetic processes and functions of ncRNAs, including microRNAs and long noncoding RNAs, as well as explore emerging ncRNA-based diagnostics and therapies for SSc.
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Affiliation(s)
- Yongmei Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linlin Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haoting Zhan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaomeng Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuan Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Yongzhe Li,
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158
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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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159
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Watson OT, Buchmann G, Young P, Lo K, Remnant EJ, Yagound B, Shambrook M, Hill AF, Oldroyd BP, Ashe A. Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera. BMC Genomics 2022; 23:257. [PMID: 35379185 PMCID: PMC8978429 DOI: 10.1186/s12864-022-08478-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Results Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in the semen of other animals. Intriguingly we also find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. Conclusions We conclude that small RNAs may play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of-origin effects on gene expression and reproductive physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08478-9.
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Affiliation(s)
- Owen T Watson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gabriele Buchmann
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Paul Young
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute NSW 2010, Darlinghurst, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Emily J Remnant
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mitch Shambrook
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Andrew F Hill
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia.,Institute for Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Benjamin P Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia. .,Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany.
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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160
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Shi J, Zhou T, Chen Q. Exploring the expanding universe of small RNAs. Nat Cell Biol 2022; 24:415-423. [PMID: 35414016 PMCID: PMC9035129 DOI: 10.1038/s41556-022-00880-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
The world of small noncoding RNAs (sncRNAs) is ever-expanding, from small interfering RNA, microRNA and Piwi-interacting RNA to the recently emerging non-canonical sncRNAs derived from longer structured RNAs (for example, transfer, ribosomal, Y, small nucleolar, small nuclear and vault RNAs), showing distinct biogenesis and functional principles. Here we discuss recent tools for sncRNA identification, caveats in sncRNA expression analysis and emerging methods for direct sequencing of sncRNAs and systematic mapping of RNA modifications that are integral to their function.
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Affiliation(s)
- Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
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161
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Tian H, Hu Z, Wang C. The Therapeutic Potential of tRNA-derived Small RNAs in Neurodegenerative Disorders. Aging Dis 2022; 13:389-401. [PMID: 35371602 PMCID: PMC8947841 DOI: 10.14336/ad.2021.0903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 11/01/2022] Open
Abstract
Gene expressions and functions at various levels, namely post-transcriptional, transcriptional, and epigenetic, can be regulated by transfer RNA (tRNA)-derived small RNAs (tsRNAs), which are as well-established as tRNA fragments or tRFs. This regulation occurs when tsRNAs are created through the special endonuclease-mediated cleavage of mature or precursor tRNAs. However, tsRNAs are newly discovered entities, and molecular functions associated with tsRNAs are still not clearly understood. There is increasingly robust evidence suggesting that specific tsRNAs perform fundamental tasks in the pathogenesis of neurodevelopmental, neurodegenerative, and neurobehavioral disorders. Indeed, the patterns of tsRNA expression are uncertain and could be altered in patients suffering from Parkinson's disease, pontocerebellar hypoplasia, amyotrophic lateral sclerosis, Alzheimer's disease, and other neurodegenerative disorders. In the present article, a review is conducted of recent domestic and international progress in research on the potential cellular and molecular mechanisms of tsRNA biogenesis. We also describe endogenous tsRNAs during neuronal development and neurodegenerative disorders, thereby providing theoretical support and guidance for further revealing the therapeutic potential of tsRNAs in neurodegenerative disorders.
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Affiliation(s)
- Haihua Tian
- 1Ningbo Key Laboratory of Behavioral Neuroscience, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,2Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,3Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,4Department of Laboratory Medicine, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Zhenyu Hu
- 5Department of Child Psychiatry, Ningbo Kanning Hospital, Ningbo, Zhejiang, China
| | - Chuang Wang
- 1Ningbo Key Laboratory of Behavioral Neuroscience, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,2Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,3Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
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162
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Luo K, Li S, Zheng Z, Lai X, Ju M, Li C, Wan X. tsRNAs及其对植物响应非生物胁迫时基因表达的调控. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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163
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Qin C, Chen ZH, Cao R, Shi MJ, Tian Y. Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population. Genes (Basel) 2022; 13:genes13040601. [PMID: 35456407 PMCID: PMC9030102 DOI: 10.3390/genes13040601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have not yet been identified. Here, RNA sequencing, bioinformatics, and quantitative reverse transcription- polymerase chain reaction (qRT-PCR) were used to screen the expression profiles and predict the potential roles of tsRNAs in MIBC. Of 406 tsRNAs differentially expressed in MIBC tissues, 91 tsRNAs were significantly differentially expressed. Then, four candidate tsRNAs, tiRNA-1:34-Val-CAC-2, tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1, were selected. Next, a bioinformatics analysis showed the potential target genes and tsRNA–mRNA network. The most significant and meaningful terms of gene ontology were the positive regulation of the phosphate metabolic process, lamellipodium, and protein-cysteine S-acyltransferase activity in the biological process, cellular component, and molecular function, respectively. In addition, the top four pathways were predicted by the Kyoto Encyclopedia of Genes and Genomes database (KEGG). Finally, qRT-PCR demonstrated a similar expression pattern compared to sequencing data for the candidate tsRNAs. In short, we find differential expression profiles and predict that tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1 are very likely to engage in the pathophysiological process of MIBC via regulating the target genes in the key pathways.
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Affiliation(s)
| | | | | | | | - Ye Tian
- Correspondence: ; Tel.: +86-010-63138377
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164
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Xu Y, Zou H, Ding Q, Zou Y, Tang C, Lu Y, Xu X. tiRNA-Val promotes angiogenesis via Sirt1–Hif-1α axis in mice with diabetic retinopathy. Biol Res 2022; 55:14. [PMID: 35346383 PMCID: PMC8962541 DOI: 10.1186/s40659-022-00381-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/22/2022] [Indexed: 11/27/2022] Open
Abstract
Background Diabetic retinopathy (DR) is a specific microvascular complication arising from diabetes, and its pathogenesis is not completely understood. tRNA-derived stress-induced RNAs (tiRNAs), a new type of small noncoding RNA generated by specific cleavage of tRNAs, has become a promising target for several diseases. However, the regulatory function of tiRNAs in DR and its detailed mechanism remain unknown. Results Here, we analyzed the tiRNA profiles of normal and DR retinal tissues. The expression level of tiRNA-Val was significantly upregulated in DR retinal tissues. Consistently, tiRNA-Val was upregulated in human retinal microvascular endothelial cells (HRMECs) under high glucose conditions. The overexpression of tiRNA-Val enhanced cell proliferation and inhibited cell apoptosis in HRMECs, but the knockdown of tiRNA-Val decreased cell proliferation and promoted cell apoptosis. Mechanistically, tiRNA-Val, derived from mature tRNA-Val with Ang cleavage, decreased Sirt1 expression level by interacting with sirt1 3'UTR, leading to the accumulation of Hif-1α, a key target for DR. In addition, subretinal injection of adeno-associated virus to knock down tiRNA-Val in DR mice ameliorated the symptoms of DR. Conclusion tiRNA-Val enhance cell proliferation and inhibited cell apoptosis via Sirt1/Hif-1α pathway in HRMECs of DR retinal tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s40659-022-00381-7.
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165
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Di Fazio A, Schlackow M, Pong SK, Alagia A, Gullerova M. Dicer dependent tRNA derived small RNAs promote nascent RNA silencing. Nucleic Acids Res 2022; 50:1734-1752. [PMID: 35048990 PMCID: PMC8860591 DOI: 10.1093/nar/gkac022] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 12/09/2021] [Accepted: 01/10/2022] [Indexed: 12/14/2022] Open
Abstract
In mammalian cells, small non-coding RNAs (sncRNAs) negatively regulate gene expression in a pathway known as RNA interference (RNAi). RNAi can be categorized into post-transcriptional gene silencing (PTGS), which involves the cleavage of target messenger RNA (mRNA) or inhibition of translation in the cytoplasm, and transcriptional gene silencing (TGS), which is mediated by the establishment of repressive epigenetic marks at target loci. Transfer RNAs (tRNAs), which are essential for translation, can be processed into small ncRNAs, termed tRNA-derived small RNAs (tsRNAs). The biogenesis of tsRNAs and their role in gene expression regulation has not yet been fully understood. Here, we show that Dicer dependent tsRNAs promote gene silencing through a mechanism distinct from PTGS and TGS. tsRNAs can lead to downregulation of target genes by targeting introns via nascent RNA silencing (NRS) in nuclei. Furthermore, we show that Ago2 slicer activity is required for this mechanism. Synthetic tsRNAs can significantly reduce expression of a target gene at both RNA and protein levels. Target genes regulated by NRS are associated with various diseases, which further underpins its biological significance. Finally, we show that NRS is evolutionarily conserved and has the potential to be explored as a novel synthetic sRNA based therapeutic.
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Affiliation(s)
- Arianna Di Fazio
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Margarita Schlackow
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sheng Kai Pong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Adele Alagia
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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166
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Xiao L, Wang J, Ju S, Cui M, Jing R. Disorders and roles of tsRNA, snoRNA, snRNA and piRNA in cancer. J Med Genet 2022; 59:623-631. [PMID: 35145038 DOI: 10.1136/jmedgenet-2021-108327] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/24/2022] [Indexed: 11/04/2022]
Abstract
Most small non-coding RNAs (sncRNAs) with regulatory functions are encoded by majority sequences in the human genome, and the emergence of high-throughput sequencing technology has greatly expanded our understanding of sncRNAs. sncRNAs are composed of a variety of RNAs, including tRNA-derived small RNA (tsRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), PIWI-interacting RNA (piRNA), etc. While for some, sncRNAs' implication in several pathologies is now well established, the potential involvement of tsRNA, snoRNA, snRNA and piRNA in human diseases is only beginning to emerge. Recently, accumulating pieces of evidence demonstrate that tsRNA, snoRNA, snRNA and piRNA play an important role in many biological processes, and their dysregulation is closely related to the progression of cancer. Abnormal expression of tsRNA, snoRNA, snRNA and piRNA participates in the occurrence and development of tumours through different mechanisms, such as transcriptional inhibition and post-transcriptional regulation. In this review, we describe the research progress in the classification, biogenesis and biological function of tsRNA, snoRNA, snRNA and piRNA. Moreover, we emphasised their dysregulation and mechanism of action in cancer and discussed their potential as diagnostic and prognostic biomarkers or therapeutic targets.
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Affiliation(s)
- Lin Xiao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Department of Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Jie Wang
- Department of Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Department of Medical School of Nantong University, Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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167
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Han Y, Peng Y, Liu S, Wang X, Cai C, Guo C, Chen Y, Gao L, Huang Q, He M, Shen E, Long J, Yu J, Shen H, Zeng S. tRF3008A suppresses the progression and metastasis of colorectal cancer by destabilizing FOXK1 in an AGO-dependent manner. J Exp Clin Cancer Res 2022; 41:32. [PMID: 35065674 PMCID: PMC8783529 DOI: 10.1186/s13046-021-02190-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/20/2021] [Indexed: 01/05/2023] Open
Abstract
Abstract
Background
tRNA-derived fragments (tRFs) have been shown to have critical regulatory roles in cancer biology. However, the contributions of tRFs to colorectal cancer (CRC) remain largely unknown.
Methods
tRF3008A (a tRFRNA derived from tRNAVal) was identified by RNA sequencing and validated by quantitative reverse transcription PCR. The role of tRF3008A in CRC progression was assessed both in vitro and in vivo, and its downstream target genes were identified and validated in CRC cells. RNA pull-down with mass spectrometry and AGO-RIP were used to confirm the interaction of tRF3008A and AGO proteins. The clinical implications of tRF3008A were assessed in CRC tissues and blood samples.
Results
The expression of tRF3008A was reduced in colorectal cancer, and its reduction was significantly correlated with advanced and metastatic disease in CRC. Patients with low tRF3008A expression showed significantly shorter DFS, and multivariate analysis identified tRF3008A as an independent prognostic biomarker in CRC. Functionally, tRF3008A inhibits the proliferation and migration of CRC in vivo and in vitro by repressing endogenous FOXK1, a positive regulator of the Wnt/β-catenin pathway. Mechanistically, tRF3008A binds to AGO proteins as a guide to destabilize oncogenic FOXK1 transcript.
Conclusions
tRF3008A suppresses the metastasis and progression of colorectal cancer by destabilizing FOXK1 in an AGO-dependent manner.
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168
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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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169
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Zhou Y, Cui Q, Zhou Y. Screening and Comprehensive Analysis of Cancer-Associated tRNA-Derived Fragments. Front Genet 2022; 12:747931. [PMID: 35095997 PMCID: PMC8795687 DOI: 10.3389/fgene.2021.747931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
tRNA-derived fragments (tRFs) constitute a novel class of small non-coding RNA cleaved from tRNAs. In recent years, researches have shown the regulatory roles of a few tRFs in cancers, illuminating a new direction for tRF-centric cancer researches. Nonetheless, more specific screening of tRFs related to oncogenesis pathways, cancer progression stages and cancer prognosis is continuously demanded to reveal the landscape of the cancer-associated tRFs. In this work, by combining the clinical information recorded in The Cancer Genome Atlas (TCGA) and the tRF expression profiles curated by MINTbase v2.0, we systematically screened 1,516 cancer-associated tRFs (ca-tRFs) across seven cancer types. The ca-tRF set collectively combined the differentially expressed tRFs between cancer samples and control samples, the tRFs significantly correlated with tumor stage and the tRFs significantly correlated with patient survival. By incorporating our previous tRF-target dataset, we found the ca-tRFs tend to target cancer-associated genes and onco-pathways like ATF6-mediated unfolded protein response, angiogenesis, cell cycle process regulation, focal adhesion, PI3K-Akt signaling pathway, cellular senescence and FoxO signaling pathway across multiple cancer types. And cell composition analysis implies that the expressions of ca-tRFs are more likely to be correlated with T-cell infiltration. We also found the ca-tRF expression pattern is informative to prognosis, suggesting plausible tRF-based cancer subtypes. Together, our systematic analysis demonstrates the potentially extensive involvements of tRFs in cancers, and provides a reasonable list of cancer-associated tRFs for further investigations.
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Affiliation(s)
- Yiran Zhou
- MOE Key Lab of Cardiovascular Sciences, Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Lab of Cardiovascular Sciences, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qinghua Cui
- MOE Key Lab of Cardiovascular Sciences, Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Lab of Cardiovascular Sciences, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan Zhou
- MOE Key Lab of Cardiovascular Sciences, Department of Biomedical Informatics, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- MOE Key Lab of Cardiovascular Sciences, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, School of Basic Medical Sciences, Peking University, Beijing, China
- *Correspondence: Yuan Zhou,
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170
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Long D, Xu Y, Mao G, Xin R, Deng Z, Liao H, Li Z, Yang Z, Yu B, Yang Z, He A, Zhang Z, Kang Y. tRNA-derived fragment TRF365 regulates the metabolism of anterior cruciate ligament cells by targeting IKBKB. Cell Death Dis 2022; 8:19. [PMID: 35013149 PMCID: PMC8748987 DOI: 10.1038/s41420-021-00806-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
Abstract
tRNA-derived fragments (tRFs) are new noncoding RNAs, and recent studies have shown that tRNAs and tRFs have important functions in cell metabolism via posttranscriptional regulation of gene expression. However, whether tRFs regulate cellular metabolism of the anterior cruciate ligament (ACL) remains elusive. The aim of this study was to investigate the role and action mechanism of tRFs in ACL cell metabolism. A tRF array was used to determine tRF expression profiles in different human ACL cells, and quantitative real-time polymerase chain reaction and fluorescence in situ hybridisation were used to determine TRF365 expression. ACL cells were transfected with a TRF365 mimic or a TRF365 inhibitor to determine whether TRF365 regulates IKBKB expression. A rescue experiment and dual-luciferase reporter assay were conducted to determine whether the 3′-untranslated region (UTR) of IKBKB has a TRF365-binding site. TRF365 was weakly expressed in osteoarthritis (OA) ACL and interleukin-1β-treated ACL cells. IKBKB was highly expressed in OA ACL and interleukin-1β-treated ACL cells; transfection with the TRF365 mimic suppressed IKBKB expression, whereas transfection with the TRF365 inhibitor had the opposite effect. A dual-luciferase reporter assay showed that TRF365 silenced the expression of IKBKB by binding to its 3′-UTR. Thus, TRF365 regulates the metabolism of ACL cells by targeting IKBKB. In summary, TRF365 may provide a new direction for the study of ACL degeneration and on the pathophysiological process of OA.
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Affiliation(s)
- Dianbo Long
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Yiyang Xu
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Department of Orthopedics, Shengli Clinical Medical College, Fujian Provincial Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China
| | - Guping Mao
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Ruobing Xin
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zengfa Deng
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Hongyi Liao
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhiwen Li
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhi Yang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Baoxi Yu
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhijian Yang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Aishan He
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Ziji Zhang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Yan Kang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
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171
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Lu Z, Su K, Wang X, Zhang M, Ma S, Li H, Qiu Y. Expression Profiles of tRNA-Derived Small RNAs and Their Potential Roles in Primary Nasopharyngeal Carcinoma. Front Mol Biosci 2022; 8:780621. [PMID: 34988117 PMCID: PMC8722782 DOI: 10.3389/fmolb.2021.780621] [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] [Received: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs, are divided into two categories: tRNA-related fragments (tRFs) and tRNA halves (tiRNAs). Abnormal expression of tsRNAs has been found in diverse cancers, which indicates that further understanding of the function of tsRNAs will help identify new biomarkers and potential therapeutic targets. Until now, the underlying roles of tsRNAs in primary nasopharyngeal carcinoma (NPC) are still unknown. Methods: tRF and tiRNA sequencing was performed on four pairs of NPC tissues and healthy controls. Thirty pairs of NPC samples were used for quantitative real-time polymerase chain reaction (qRT-PCR) verification, and the ROC analysis was used to evaluate the diagnostic efficiency initially. Target prediction and bioinformatics analysis of validated tRFs and tiRNAs were conducted to explore the mechanisms of tsRNAs in NPC’s pathogenesis. Results: A total of 158 differentially expressed tRFs and tiRNAs were identified, of which 88 are upregulated and 70 are downregulated in NPC. Three validated tRFs in the results of qRT-PCR were consistent with the sequencing data: two upregulations (tRF-1:28-Val-CAC-2 and tRF-1:24-Ser-CGA-1-M3) and one downregulation (tRF-55:76-Arg-ACG-1-M2). The GO and KEGG pathway enrichment analysis showed that the potential target genes of validated tRFs are widely enriched in cancer pathways. The related modules may play an essential role in the pathogenesis of NPC. Conclusions: The tsRNAs may become a novel class of biological diagnostic indicators and possible targets for NPC.
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Affiliation(s)
- Zhaoyi Lu
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China.,Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Kai Su
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Xiaomin Wang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Mingjie Zhang
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Shiyin Ma
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Hui Li
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Yuanzheng Qiu
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
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172
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Identifying Differentially Expressed tRNA-Derived Small Fragments as a Biomarker for the Progression and Metastasis of Colorectal Cancer. DISEASE MARKERS 2022; 2022:2646173. [PMID: 35035608 PMCID: PMC8758288 DOI: 10.1155/2022/2646173] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/17/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022]
Abstract
Objectives. The epithelial-to-mesenchymal transition (EMT) is one key step for the invasion and metastasis of colorectal cancer (CRC). Up until now, the underlying mechanism of EMT in CRC is still unpromising. Thus, it is essential to have a better understanding of its carcinogenesis. The transfer RNA-derived small fragments (tsRNAs) are a new group of small noncoding RNAs (sncRNAs), including tRNA-derived stress-induced RNAs (tiRNAs) and tRNA-derived fragments (tRFs), which have been observed to play an important role in many cancers. However, the relationship between tRFs and EMT in CRC is still unknown. Herein, we aimed to investigate the involvement of tRFs in EMT and its contribution to CRC development. Methods. We identified the differentially expressed tsRNAs in colorectal cancer cell line HT29 treated with TGF-β compared with control cells by using high-throughput sequencing and quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). QRT-PCR was conducted to validate the differentially expressed fragments in 68 CRC tumor samples (22 women and 46 men) and adjacent nontumor samples. The association of the expression of tRFs with CRC metastasis and clinical stage was analyzed. Meanwhile, the correlation between tRF expression and overall survival (OS) was also analyzed. TargetScan and miRanda and multiple bioinformatic approaches were used to predict the possible target genes of tsRNAs and analyze possible functions of the tRFs. Results. A series of differentially expressed tsRNAs were identified in TGF-β-treated HT29 cells compared with control cells. tRF-phe-GAA-031 and tRF-VAL-TCA-002 were found to be significantly upregulated in CRC tissues compared to adjacent nontumor tissues. They were significantly correlated with distant metastasis and clinical stage. We compared the differences between tumor samples and nontumor tissues from the ROC curves. The area under the ROC curve (AUC) was up to 0.7554 (95% confidence interval: 0.6739 to 0.8369,
) for tRF-Phe-GAA-031 and up to 0.7313 (95% confidence interval: 0.6474 to 0.8151,
) for tRF-VAL-TCA-002. For OS analysis, higher tRF-phe-GAA-031 and tRF-VAL-TCA-002 expressions were associated with shorter survival for CRC patients. Conclusion. A series of differentially expressed tsRNAs are identified in the EMT process of CRC. And tRF-phe-GAA-031 and tRF-VAL-TCA-002 are higher expressed in CRC tissues, and they might play an important role in the metastasis of CRC. Meanwhile, they may be potential biomarkers and intervention targets in the clinical treatment of CRC.
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173
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Wang Y, Weng Q, Ge J, Zhang X, Guo J, Ye G. tRNA-derived small RNAs: mechanisms and potential roles in cancers. Genes Dis 2022; 9:1431-1442. [PMID: 36157501 PMCID: PMC9485285 DOI: 10.1016/j.gendis.2021.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/08/2021] [Accepted: 12/18/2021] [Indexed: 11/02/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential for protein synthesis. Mature or pre-tRNAs may be cleaved to produce tRNA-derived small RNAs (tsRNAs). tsRNAs, divided into tRNA-derived stress-induced RNA (tiRNAs) and tRNA-derived fragments (tRFs), play versatile roles in a number of fundamental biological processes. tsRNAs not only play regulatory roles in gene silencing, RNA stability, reverse transcription, and translation, but are also closely related to cell proliferation, migration, cell cycle, and apoptosis. Their abnormal expression is associated with the occurrence and development of various human diseases, especially cancer. This paper reviews the classification, biogenesis, and mechanism of action of tsRNAs, and the research progress to date on tsRNAs in cancers. These findings provide new opportunities for diagnostic biomarkers and treatment targets of several types of cancers including gastric cancer, colorectal cancer, hepatocellular carcinomas, pancreatic cancer, breast cancer, prostate cancer, renal cell carcinoma, ovarian cancer, lung cancer, bladder cancer, thyroid cancer, oral cancer, and leukemia.
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174
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Bolatkan A, Asada K, Kaneko S, Suvarna K, Ikawa N, Machino H, Komatsu M, Shiina S, Hamamoto R. Downregulation of METTL6 mitigates cell progression, migration, invasion and adhesion in hepatocellular carcinoma by inhibiting cell adhesion molecules. Int J Oncol 2022; 60:4. [PMID: 34913069 PMCID: PMC8698744 DOI: 10.3892/ijo.2021.5294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
RNA modifications have attracted increasing interest in recent years because they have been frequently implicated in various human diseases, including cancer, highlighting the importance of dynamic post‑transcriptional modifications. Methyltransferase‑like 6 (METTL6) is a member of the RNA methyltransferase family that has been identified in many cancers; however, little is known about its specific role or mechanism of action. In the present study, we aimed to study the expression levels and functional role of METTL6 in hepatocellular carcinoma (HCC), and further investigate the relevant pathways. To this end, we systematically conducted bioinformatics analysis of METTL6 in HCC using gene expression data and clinical information from a publicly available dataset. The mRNA expression levels of METTL6 were significantly upregulated in HCC tumor tissues compared to that in adjacent non‑tumor tissues and strongly associated with poorer survival outcomes in patients with HCC. CRISPR/Cas9‑mediated knockout of METTL6 in HCC cell lines remarkably inhibited colony formation, cell proliferation, cell migration, cell invasion and cell attachment ability. RNA sequencing analysis demonstrated that knockout of METTL6 significantly suppressed the expression of cell adhesion‑related genes. However, chromatin immunoprecipitation sequencing results revealed no significant differences in enhancer activities between cells, which suggests that METTL6 may regulate genes of interest post‑transcriptionally. In addition, it was demonstrated for the first time that METTL6 was localized in the cytosol as detected by immunofluorescence analysis, which indicates the plausible location of RNA modification mediated by METTL6. Our findings provide further insight into the function of RNA modifications in cancer and suggest a possible role of METTL6 as a therapeutic target in HCC.
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Affiliation(s)
- Amina Bolatkan
- Department of Diagnostic Imaging and Interventional Oncology, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Ken Asada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Kruthi Suvarna
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Noriko Ikawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hidenori Machino
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Masaaki Komatsu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Shuichiro Shiina
- Department of Diagnostic Imaging and Interventional Oncology, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
- Department of National Cancer Center Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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175
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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: 9] [Impact Index Per Article: 4.5] [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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176
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Cui X, Huang X, Huang M, Zhou S, Guo L, Yu W, Duan M, Jiang B, Zeng J, Zhou J, Huang X, Liang P, Zhang P. miR-24-3p obstructs the proliferation and migration of HSFs after thermal injury by targeting PPAR-β and positively regulated by NF-κB. Exp Dermatol 2021; 31:841-853. [PMID: 34932851 DOI: 10.1111/exd.14517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 12/03/2021] [Accepted: 12/19/2021] [Indexed: 11/30/2022]
Abstract
Thermal injury repair is a complex process during which the maintenance of the proliferation and migration of human skin fibroblasts (HSFs) exert a crucial role. MicroRNAs have been proven to exert an essential function in repairing skin burns. This study delves into the regulatory effects of miR-24-3p on the migration and proliferation of HSFs that have sustained a thermal injury; thereby, providing deeper insight into thermal injury repair pathogenesis. The PPAR-β protein expression level progressively increased in a time-dependent manner on the 12th , 24th , and 48th hour following the thermal injury of the HSFs. The knockdown of PPAR-β markedly suppressed the proliferation of and migration of HSF. Following thermal injury, the knockdown also promoted the inflammatory cytokine IL-6, TNF-, PTGS-2, and P65 expression. PPAR-β contrastingly exhibited an opposite trend. A targeted relationship between PPAR-β and miR-24-3p was predicted and verified. miR-24-3p inhibited thermal injured-HSFs proliferation and migration and facilitated inflammatory cytokine expression through the regulation of PPAR-β. p65 directly targeted the transcriptional precursor of miR-24 and promoted miR-24 expression. A negative correlation between miR-24-3p expression level and PPAR-β expression level in rats burnt dermal tissues was observed. Our findings reveal that miR-24-3p is conducive to rehabilitating the denatured dermis, which may be beneficial in providing effective therapy of skin burns.
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Affiliation(s)
- Xu Cui
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Xu Huang
- Department of Hyperbaric Oxygen, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Mitao Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Situo Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Le Guo
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Wenchang Yu
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Mengting Duan
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Bimei Jiang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Jizhang Zeng
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Jie Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Xiaoyuan Huang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Pihong Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
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177
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Yang ZY, Li PF, Li ZQ, Tang T, Liu W, Wang Y. Altered Expression of Transfer-RNA-Derived Small RNAs in Human With Rheumatic Heart Disease. Front Cardiovasc Med 2021; 8:716716. [PMID: 34926598 PMCID: PMC8671610 DOI: 10.3389/fcvm.2021.716716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
Rheumatic heart disease (RHD) remains a severe public health problem in developing countries. Atrial fibrillation (AF) is a medical complication of RHD. Although the understanding of disease pathogenesis has advanced in recent years, the key questions need to be addressed. Transfer RNA–derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs with potential regulatory functions in various physiological and pathological processes. The present study used tsRNAs sequencing to investigate the relationship between RHD and atrial fibrillation (AF). Three paired cardiac papillary muscles were taken from six rheumatic RHD patients with AF (3 cases) or without AF (3 cases) from January 2016 to January 2017 in Xiangya Hospital, Central South University. A total of 219 precisely matched tsRNAs were identified, and 77 tsRNAs (fold change > 2.0 and P < 0.05) were differently changed. Three tsRNAs (AS-tDR-001269, AS-tDR-001363, AS-tDR-006049) were randomly selected and confirmed by qRT-PCR. The results of qRT-PCR were consistent with tsRNAs sequencing, suggesting the tsRNAs sequencing was reliable. Subsequently, we predicted the target mRNAs of the three tsRNAs. Moreover, we verified the functions of tsRNAs targeting mRNAs in vitro. Finally, bioinformatics analysis indicated that the target genes were abundant in regulation of transcription, DNA binding, intracellular. Most of the genes were predicted to interplay with cytokine-cytokine receptor by KEGG analysis. Our findings uncover the pathological process of AF in RHD through tsRNAs sequencing. This research provides a new perspective for future research on elucidating the mechanism of AF in RHD and offers potential new candidates for the treatment and diagnosis.
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Affiliation(s)
- Zhao-Yu Yang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Peng-Fei Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhi-Qing Li
- Hunan University of Chinese Medicine, Changsha, China
| | - Tao Tang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Liu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yang Wang
- Department of Integrated Traditional Chinese and Western Medicine, Institute of Integrative Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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178
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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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179
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tRNA modifications and their potential roles in pancreatic cancer. Arch Biochem Biophys 2021; 714:109083. [PMID: 34785212 DOI: 10.1016/j.abb.2021.109083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022]
Abstract
Since the breakthrough discovery of N6-methyladenosine (m6A), the field of RNA epitranscriptomics has attracted increasing interest in the biological sciences. Transfer RNAs (tRNAs) are extensively modified, and various modifications play a crucial role in the formation and stability of tRNA, which is universally required for accurate and efficient functioning of tRNA. Abnormal tRNA modification can lead to tRNA degradation or specific cleavage of tRNA into fragmented derivatives, thus affecting the translation process and frequently accompanying a variety of human diseases. Increasing evidence suggests that tRNA modification pathways are also misregulated in human cancers. In this review, we summarize tRNA modifications and their biological functions, describe the type and frequency of tRNA modification alterations in cancer, and highlight variations in tRNA-modifying enzymes and the multiple functions that they regulate in different types of cancers. Furthermore, the current implications and the potential role of tRNA modifications in the progression of pancreatic cancer are discussed. Collectively, this review describes recent advances in tRNA modification in cancers and its potential significance in pancreatic cancer. Further study of the mechanism of tRNA modifications in pancreatic cancer may provide possibilities for therapies targeting enzymes responsible for regulating tRNA modifications in pancreatic cancer.
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180
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Qiu Z, Wang Q, Liu L, Li G, Hao Y, Ning S, Zhang L, Zhang X, Chen Y, Wu J, Wang X, Yang S, Lin Y, Xu S. Riddle of the Sphinx: Emerging Role of Transfer RNAs in Human Cancer. Front Pharmacol 2021; 12:794986. [PMID: 34975491 PMCID: PMC8714751 DOI: 10.3389/fphar.2021.794986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 01/16/2023] Open
Abstract
The dysregulation of transfer RNA (tRNA) expression contributes to the diversity of proteomics, heterogeneity of cell populations, and instability of the genome, which may be related to human cancer susceptibility. However, the relationship between tRNA dysregulation and cancer susceptibility remains elusive because the landscape of cancer-associated tRNAs has not been portrayed yet. Furthermore, the molecular mechanisms of tRNAs involved in tumorigenesis and cancer progression have not been systematically understood. In this review, we detail current knowledge of cancer-related tRNAs and comprehensively summarize the basic characteristics and functions of these tRNAs, with a special focus on their role and involvement in human cancer. This review bridges the gap between tRNAs and cancer and broadens our understanding of their relationship, thus providing new insights and strategies to improve the potential clinical applications of tRNAs for cancer diagnosis and therapy.
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Affiliation(s)
- Zhilin Qiu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qin Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guozheng Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yi Hao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shipeng Ning
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lei Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yihai Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiale Wu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinheng Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shuai Yang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yaoxin Lin
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Yaoxin Lin, ; Shouping Xu,
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181
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Wen JT, Huang ZH, Li QH, Chen X, Qin HL, Zhao Y. Research progress on the tsRNA classification, function, and application in gynecological malignant tumors. Cell Death Discov 2021; 7:388. [PMID: 34907180 PMCID: PMC8671397 DOI: 10.1038/s41420-021-00789-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
A large number of small non-coding RNAs derived from tRNAs, called tRNA-derived small RNA (tsRNAs), have been identified by high-throughput RNA sequencing of cell lines. Further research has revealed that they are not produced via random tRNA degradation, but through degradation by specific nuclease cleavages, such as Elac Ribonuclease Z 2 (ELAC2)/RNase Z, RNase L, Dicer, and angiogenin (ANG), the tsRNAs can be classified into the following types based on the location from which they have been derived from the parental tRNA: tRF-1s, tRF-3s, tRF-5s, tiRNA, and tRF-2s/i-tRFs. Moreover, tsRNAs are a type of small RNAs with diverse functions, including gene expression regulation, anti-apoptosis, translation inhibition, participation in epigenetic regulation, initial virus reverse transcription, promote virus replication and cell-to-cell communication. Certain types of tsRNAs are overexpressed in cancer tissues, but are underexpressed in normal tissues. Therefore, the relationship between tsRNAs and the occurrence and development of cancer has attracted significant research attention. Research advancements have contributed to further discoveries of the biological activities of tsRNAs, but the mechanisms of their biogenesis and functions have not been fully elucidated. This article reviews the classification and biological functions of tsRNAs, and introduces the research progress in gynecological malignancies.
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Affiliation(s)
- Jing-Tao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Zheng-Hao Huang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Hong-Lei Qin
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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182
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Hu F, Niu Y, Mao X, Cui J, Wu X, Simone CB, Kang HS, Qin W, Jiang L. tsRNA-5001a promotes proliferation of lung adenocarcinoma cells and is associated with postoperative recurrence in lung adenocarcinoma patients. Transl Lung Cancer Res 2021; 10:3957-3972. [PMID: 34858784 PMCID: PMC8577981 DOI: 10.21037/tlcr-21-829] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022]
Abstract
Background The biological role and clinical significance of transfer RNA-derived small RNAs (tsRNAs) remain largely unclear. The purpose of this study was to investigate the biological function, molecular mechanism, and clinical significance of tsRNA-5001a in lung adenocarcinoma. Methods The function of tsRNA-5001a on the growth of tumor cells was accessed by cell function experiments. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression of tsRNA-5001a in paired samples of lung adenocarcinoma. Cell localization of tsRNA-5001a was performed by nuclear-cytoplasmic separation assay. Transcriptome sequencing was used to screen the molecules involved in the regulatory network of tsRNA-5001a. Independent samples t-test was used to compare the two groups. Prism software (Prism 7.0) was used to analyze the statistical results. P<0.05 was considered statistically significant. Results tsRNA-5001a was significantly upregulated in lung adenocarcinoma tissues. Upregulation of tsRNA-5001a was found to increase the risk of postoperative recurrences in patients with lung adenocarcinoma and was associated with poor prognosis. Function assay showed that overexpression tsRNA-5001a could significantly promote cell proliferation. In contrast, knockdown of tsRNA-5001a significantly inhibited the proliferation of lung adenocarcinoma cells. In addition, nucleoplasmic isolation assay indicated that tsRNA-5001a was located mainly in the cytoplasm. According to the results of RNA sequencing and The Cancer Genome Atlas database (TCGA database) analysis, growth arrest and DNA damage 45G (GADD45G) was screened and may be the target gene of tsRNA-5001a. Conclusions tsRNA-5001a promotes the proliferation of lung adenocarcinoma cells and increases the risk of postoperative recurrences in lung adenocarcinoma patients.
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Affiliation(s)
- Fang Hu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Niu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Mao
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Cui
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoting Wu
- Department of Integrated Traditional Chinese and Western Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Charles B Simone
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center and New York Proton Center, New York, NY, USA
| | - Hye Seon Kang
- Division of Pulmonary, Critical Care and Allergy, Department of Internal Medicine, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, China
| | - Liyan Jiang
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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183
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Pandey KK, Madhry D, Ravi Kumar YS, Malvankar S, Sapra L, Srivastava RK, Bhattacharyya S, Verma B. Regulatory roles of tRNA-derived RNA fragments in human pathophysiology. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:161-173. [PMID: 34513302 PMCID: PMC8413677 DOI: 10.1016/j.omtn.2021.06.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hundreds of tRNA genes and pseudogenes are encoded by the human genome. tRNAs are the second most abundant type of RNA in the cell. Advancement in deep-sequencing technologies have revealed the presence of abundant expression of functional tRNA-derived RNA fragments (tRFs). They are either generated from precursor (pre-)tRNA or mature tRNA. They have been found to play crucial regulatory roles during different pathological conditions. Herein, we briefly summarize the discovery and recent advances in deciphering the regulatory role played by tRFs in the pathophysiology of different human diseases.
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Affiliation(s)
- Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Deeksha Madhry
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M.S. Ramaiah, Institute of Technology, MSR Nagar, Bengaluru, India
| | - Shivani Malvankar
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Leena Sapra
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rupesh K Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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184
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Kfoury YS, Ji F, Mazzola M, Sykes DB, Scherer AK, Anselmo A, Akiyama Y, Mercier F, Severe N, Kokkaliaris KD, Zhao T, Brouse T, Saez B, Seidl J, Papazian A, Ivanov P, Mansour MK, Sadreyev RI, Scadden DT. tiRNA signaling via stress-regulated vesicle transfer in the hematopoietic niche. Cell Stem Cell 2021; 28:2090-2103.e9. [PMID: 34551362 PMCID: PMC8642285 DOI: 10.1016/j.stem.2021.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/23/2021] [Accepted: 08/17/2021] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) transfer complex biologic material between cells. However, the role of this process in vivo is poorly defined. Here, we demonstrate that osteoblastic cells in the bone marrow (BM) niche elaborate extracellular vesicles that are taken up by hematopoietic progenitor cells in vivo. Genotoxic or infectious stress rapidly increased stromal-derived extracellular vesicle transfer to granulocyte-monocyte progenitors. The extracellular vesicles contained processed tRNAs (tiRNAs) known to modulate protein translation. 5'-ti-Pro-CGG-1 was preferentially abundant in osteoblast-derived extracellular vesicles and, when transferred to granulocyte-monocyte progenitors, increased protein translation, cell proliferation, and myeloid differentiation. Upregulating EV transfer improved hematopoietic recovery from genotoxic injury and survival from fungal sepsis. Therefore, EV-mediated tiRNA transfer provides a stress-modulated signaling axis in the BM niche distinct from conventional cytokine-driven stress responses.
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Affiliation(s)
- Youmna S Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Mazzola
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Allison K Scherer
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yasutoshi Akiyama
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Francois Mercier
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nicolas Severe
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Konstantinos D Kokkaliaris
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ting Zhao
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Brouse
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Borja Saez
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jefferson Seidl
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ani Papazian
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Michael K Mansour
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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185
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Mao Y, Huo Y, Li J, Zhao Y, Wang Y, Sun L, Kang Z. circRPS28 (hsa_circ_0049055) is a novel contributor for papillary thyroid carcinoma by regulating cell growth and motility via functioning as ceRNA for miR-345-5p to regulate frizzled family receptor 8 (FZD8). Endocr J 2021; 68:1267-1281. [PMID: 34108309 DOI: 10.1507/endocrj.ej21-0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Circular RNA 40S ribosomal protein S28 (circRPS28; hsa_circ_0049055) is upregulated in papillary thyroid carcinoma (PTC) patients. However, its role remained uncovered in the progression of PTC. Above all, expression of circRPS28 was determined in PTC samples by real-time quantitative PCR and circRPS28 was highly expressed in tumor tissues and cells. Besides, circRPS28 was predominantly distributed in the cytoplasm. Functional experiments were launched using colony formation assay, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, 5-ethynyl-2-deoxyuridine (EdU) assay, transwell assays, scratch wound assay, and flow cytometry. As a result, blocking circRPS28 restrained PTC cell viability, EdU positive cell rate, colony formation number, wounding healing rate, and numbers of migration and invasion cells, accompanied with apoptosis rate promotion. These effects paralleled with low B-cell lymphoma (Bcl)-2 level and high Bcl-2-associated X protein (Bax), matrix metalloproteinase-2 (MMP2), and MMP9 levels, as analyzed by western blotting. Overexpressing microRNA (miR)-345-5p exerted similar roles to circRPS28 silencing. Notably, dual-luciferase reporter assay and RNA immunoprecipitation confirmed the target relationship between circRPS28 and miR-345-5p, miR-345-5p and frizzled family receptor 8 (FZD8). Downregulating miR-345-5p abrogated effects of circRPS28 blockage in PTC cells, and restoring FZD8 counteracted miR-345-5p roles, either. Furthermore, xenograft tumor model was established in mice, and exhausting circRPS28 delayed the growth of PTC cells in vivo by regulating miR-345-5p and FZD8. In conclusion, we demonstrated that blocking circRPS28 and/or promoting miR-345-5p suppressed PTC cell growth and motility via regulating FZD8. This study might suggest a novel circRPS28/miR-345-5p/FZD8 competing endogenous RNA pathway in PTC.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Movement/physiology
- Cell Proliferation/physiology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mice
- Mice, Nude
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Thyroid Cancer, Papillary/genetics
- Thyroid Cancer, Papillary/metabolism
- Thyroid Cancer, Papillary/pathology
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
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Affiliation(s)
- Yu Mao
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
| | - Yajie Huo
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
| | - Jing Li
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
| | - Yanli Zhao
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
| | - Yuan Wang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
| | - Ling Sun
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
| | - Zhiqiang Kang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450007, China
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186
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Lin Y, Cai J, Huang D, Zhou B, Luo Z, Yu S, Lu J. Effects of dexmedetomidine on the expression profile of tsRNAs in LPS-induced acute lung injury. J Clin Lab Anal 2021; 36:e24115. [PMID: 34811808 PMCID: PMC8761442 DOI: 10.1002/jcla.24115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Acute lung injury (ALI) is characterized by impaired alveolar function and excessive inflammation, which is commonly seen in clinical anesthesia and intensive care units. tRNA-derived small RNA (tsRNA) is a non-coding RNA that can be used as a potential disease diagnostic biomarker. The connection between ALI and tsRNA remains unknown. We aimed to explore the possible regulatory functions and mechanisms of tsRNAs in ALI treated with DEX. METHODS Firstly, we established the ALI model by LPS injection and explored the effect of dexmedetomidine (DEX) treatment on lung damage. Then, the lung tissues were obtained from the LPS and LPS + DEX group for small RNA sequencing. RESULTS We proved that DEX could ameliorate pulmonary injury, and decreased inflammation, pulmonary edema, and ferroptosis (MDA down-regulation and GPX4 up-regulation) in ALI. Furthermore, in the tsRNA expression profile, the top 10 down-regulated tsRNAs were tsRNA-1018, tsRNA-3045b, tsRNA-5021a, tsRNA-1020, tsRNA-5002b, tsRNA-3045b, tsRNA-1026, tsRNA-5004a, tsRNA-5005b and tsRNA-1009, and the top 10 up-regulated tsRNAs were tsRNA-3025b, tsRNA-3025a, tsRNA-5016b, tsRNA-3042b, tsRNA-3029b, tsRNA-3028b, tsRNA-5006a, tsRNA-3027b, tsRNA-3027a, and tsRNA-5009b. The enrichment analysis of GO terms and KEGG pathways pointed that target genes of DE-tsRNAs were mainly enriched in regulation of transcription-associated GO terms, NF-kappa B signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway. The RT-qPCR results of tsRNA-1020 and tsRNA-1018 were in accordance with small RNA sequencing data. CONCLUSION DEX affected the abnormal expression of tsRNAs in ALI. These aberrantly expressed tsRNAs and enriched physiological processes provide a scientific basis for the diagnosis and treatment of ALI.
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Affiliation(s)
- Yue Lin
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Junying Cai
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Dan Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Bin Zhou
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Zhenzhong Luo
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Shuchun Yu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
| | - Jun Lu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang City, China
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187
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Chen L, Xu W, Liu K, Jiang Z, Han Y, Jin H, Zhang L, Shen W, Jia S, Sun Q, Meng A. 5' Half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos. SCIENCE ADVANCES 2021; 7:eabh0494. [PMID: 34797706 PMCID: PMC8604414 DOI: 10.1126/sciadv.abh0494] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
5′tRFls are small transfer RNA (tRNA) fragments derived from 5′ half of mature tRNAs. However, it is unknown whether 5′tRFls could feed back to regulate tRNA biogenesis. Here, we show that 5′tRFlGly/GCC and 5′tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5′tRFlGly/GCC and 5′tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino-mediated knockdown of 5′tRFlGly/GCC or 5′tRFlGlu/CTC down-regulates tRNAGly/GCC or tRNAGlu/CTC levels, respectively, and causes embryonic lethality that is efficiently rescued by coinjection of properly refolded corresponding tRNA. In zebrafish embryos, tRNA:DNA and 5′tRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically, unstable 5′tRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA gene transcription. The uncovered mechanism may be implicated in other physiological and pathological processes.
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Affiliation(s)
- Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kunpeng Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Jiang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Han
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongbin Jin
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- The Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Guangzhou Laboratory, Guangzhou 510320, Guangdong Province, China
- Corresponding author.
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188
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Pan L, Huang X, Liu ZX, Ye Y, Li R, Zhang J, Wu G, Bai R, Zhuang L, Wei L, Li M, Zheng Y, Su J, Deng J, Deng S, Zeng L, Zhang S, Wu C, Che X, Wang C, Chen R, Lin D, Zheng J. Inflammatory cytokine-regulated tRNA-derived fragment tRF-21 suppresses pancreatic ductal adenocarcinoma progression. J Clin Invest 2021; 131:148130. [PMID: 34779408 DOI: 10.1172/jci148130] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/28/2021] [Indexed: 01/11/2023] Open
Abstract
The tumorigenic mechanism for pancreatic ductal adenocarcinoma (PDAC) is not clear, although chronic inflammation is implicated. Here, we identified an inflammatory cytokine-regulated transfer RNA-derived (tRNA-derived) fragment, tRF-21-VBY9PYKHD (tRF-21), as a tumor suppressor in PDAC progression. We found that the biogenesis of tRF-21 could be inhibited by leukemia inhibitory factor and IL-6 via the splicing factor SRSF5. Reduced tRF-21 promoted AKT2/1-mediated heterogeneous nuclear ribonucleoprotein L (hnRNP L) phosphorylation, enhancing hnRNP L to interact with dead-box helicase 17 (DDX17) to form an alternative splicing complex. The provoked hnRNP L-DDX17 activity preferentially spliced Caspase 9 and mH2A1 pre-mRNAs to form Caspase 9b and mH2A1.2, promoting PDAC cell malignant phenotypes. The tRF-21 levels were significantly lower in PDACs than in normal tissues, and patients with low tRF-21 levels had a poor prognosis. Treatment of mouse PDAC xenografts or patient-derived xenografts (PDXs) with tRF-21 mimics repressed tumor growth and metastasis. These results demonstrate that tRF-21 has a tumor-suppressive effect and is a potential therapeutic agent for PDAC.
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Affiliation(s)
- Ling Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xudong Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ze-Xian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ying Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Rui Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jialiang Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Guandi Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ruihong Bai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lisha Zhuang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lusheng Wei
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanfen Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jiachun Su
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Junge Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shuang Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lingxing Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shaoping Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xu Che
- Department of Abdominal Surgery, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengfeng Wang
- Department of Abdominal Surgery, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rufu Chen
- Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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189
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Wang JH, Chen WX, Mei SQ, Yang YD, Yang JH, Qu LH, Zheng LL. tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data. Nucleic Acids Res 2021; 50:D421-D431. [PMID: 34755848 PMCID: PMC8728237 DOI: 10.1093/nar/gkab1023] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/21/2022] Open
Abstract
tRNA-derived small RNA (tsRNA), a novel type of regulatory small noncoding RNA, plays an important role in physiological and pathological processes. However, the understanding of the functional mechanism of tsRNAs in cells and their role in the occurrence and development of diseases is limited. Here, we integrated multiomics data such as transcriptome, epitranscriptome, and targetome data, and developed novel computer tools to establish tsRFun, a comprehensive platform to facilitate tsRNA research (http://rna.sysu.edu.cn/tsRFun/ or http://biomed.nscc-gz.cn/DB/tsRFun/). tsRFun evaluated tsRNA expression profiles and the prognostic value of tsRNAs across 32 types of cancers, identified tsRNA target molecules utilizing high-throughput CLASH/CLEAR or CLIP sequencing data, and constructed the interaction networks among tsRNAs, microRNAs, and mRNAs. In addition to its data presentation capabilities, tsRFun offers multiple real-time online tools for tsRNA identification, target prediction, and functional enrichment analysis. In summary, tsRFun provides a valuable data resource and multiple analysis tools for tsRNA investigation.
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Affiliation(s)
- Jun-Hao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China.,School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, P.R. China
| | - Wen-Xin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Shi-Qiang Mei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yue-Dong Yang
- National Supercomputer Center in Guangzhou, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jian-Hua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Liang-Hu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Ling-Ling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, P.R. China
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190
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Lu H, Liu L, Han S, Wang B, Qin J, Bu K, Zhang Y, Li Z, Ma L, Tian J, Zhang K, Li T, Cui H, Liu X. Expression of tiRNA and tRF in APP/PS1 transgenic mice and the change of related proteins expression. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1457. [PMID: 34734009 PMCID: PMC8506760 DOI: 10.21037/atm-21-4318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022]
Abstract
Background Transcriptomics, such as that of non-coding RNA (ncRNA), which include microRNA (miRNA), circular RNA, and the transfer RNA (tRNA)-derived fragments (tiRNA and tRF) in Alzheimer's disease (AD) have attracted much attention recently. The tiRNA and tRFs are produced when the tRNA splits at specific sites. The expression change and related function of tiRNA and tRFs in AD has not been fully investigated. Methods In our study, APP/PS1 transgenic mice (AD mice model) and healthy control mice were used to discover the differentially expressed tiRNA and tRFs with high-throughput sequencing. Among the differentially expressed tiRNA and tRFs, we chose two tRFs (tRF-Thr-CGT-003 and tRF-Leu-CAA-004) and predicted the target messenger RNAs (mRNAs) with miRanda and Target Scan. The target mRNAs of tRF-related function and pathways were analyzed, then we performed quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blot to validate the related target mRNAs and pathways. Results A total of 27 significantly different tiRNA and tRFs were detected between wild type (WT) and APP/PS1 groups, including 14 up-regulated and 13 down-regulated. Through analyzing the target mRNAs of all differentially expressed tiRNA and tRFs with GO enrichment, we found the target mRNAs could take part in the learning and memory biological process, synapse organization, cognition biological process, synaptic transmission, amyloid-β (Aβ) metabolic process, and so on. We then chose three differentially expressed tRFs for further qPCR validation and passed two tRFs: tRF-Thr-CGT-003 and tRF-Leu-CAA-004, that were found to regulate the calcium regulation-related proteins (the voltage-gated calcium channel γ2 subunit and the RYR1 endoplasmic reticulum calcium released protein) and the retinol metabolism-related proteins (retinoic acid metabolic enzymes CYP2S1, CYP2C68, CYP2S1). Conclusions The APP expression and presenilin mutation in APP/PS1 mice could cause tiRNA and tRFs expression change. Among the differentially expressed tiRNA and tRFs, we found some tRFs took part in the voltage-gated calcium channel γ2 subunit expression and regulation, influencing the neuron calcium homeostasis. Moreover, we also found the tRFs may participate in the regulation of retinol metabolism. Our findings suggest that the dysregulated tiRNA and tRFs may be beneficially exploited as potential diagnostic biomarkers and/or therapeutic targets of AD.
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Affiliation(s)
- Honglin Lu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lin Liu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shu Han
- Department of Electrocardiogram, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Binbin Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jin Qin
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Kailin Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yingzhen Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhongzhong Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lina Ma
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jing Tian
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Kun Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Tong Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huixian Cui
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
| | - Xiaoyun Liu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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191
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The neurobiology of non-coding RNAs and Alzheimer's disease pathogenesis: Pathways, mechanisms and translational opportunities. Ageing Res Rev 2021; 71:101425. [PMID: 34384901 DOI: 10.1016/j.arr.2021.101425] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
In the past two decades, advances in sequencing technology and analysis of the human and mouse genome have led to the discovery of many non-protein-coding RNAs (ncRNAs) including: microRNA, small-interfering RNAs, piwi-associated small RNAs, transfer RNA-derived small RNAs, long-non-coding RNAs and circular RNAs. Compared with healthy controls, levels of some ncRNAs are significantly altered in the central nervous system and blood of patients affected by neurodegenerative disorders like Alzheimer's disease (AD). Although the mechanisms are still not fully elucidated, studies have revealed that these highly conserved ncRNAs are important modulators of gene expression, amyloid-β production, tau phosphorylation, inflammation, synaptic plasticity and neuronal survival, all features considered central to AD pathogenesis. Despite considerable difficulties due to their large heterogeneity, and the complexity of their regulatory pathways, research in this rapidly growing field suggests that ncRNAs hold great potential as biomarkers and therapeutic targets against AD. Herein, we summarize the current knowledge regarding the neurobiology of ncRNA in the context of AD pathophysiology.
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192
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Gu H, Lian B, Yuan Y, Kong C, Li Y, Liu C, Qi Y. A 5' tRNA-Ala-derived small RNA regulates anti-fungal defense in plants. SCIENCE CHINA-LIFE SCIENCES 2021; 65:1-15. [PMID: 34705222 DOI: 10.1007/s11427-021-2017-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022]
Abstract
Apart from their primordial role in protein synthesis, tRNAs can be cleaved to produce tRNA-derived small RNAs (tsRNAs). The biological functions of tsRNAs in plants remain largely unknown. In this study, we developed RtcB ligation-based small RNA (sRNA) sequencing, a method that captures and distinguishes between 3'-2',3'-cyclic-phosphate (cP)/phosphate (P)-terminated sRNAs and 3'-OH-terminated sRNAs, and profiled 5' tsRNAs and 5' tRNA halves in Arabidopsis thaliana. We found that Arabidopsis 5' tsRNAs and 5' tRNA halves predominantly contain a cP at the 3' end and require S-like RNase 1 (RNS1) and RNS3 for their production. One of the most abundant 5' tsRNAs, 5' tsR-Ala, by associating with AGO1, negatively regulates Cytochrome P450 71A13 (CYP71A13) expression and camalexin biosynthesis to repress anti-fungal defense. Interestingly, 5' tsR-Ala is downregulated upon fungal infection. Our study provides a global view of 5' tsRNAs and 5' tRNA halves in Arabidopsis and unravels an important role of a 5' tsRNA in regulating anti-fungal defense.
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Affiliation(s)
- Hanqing Gu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bi Lian
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuxiang Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ci Kong
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chang Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
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193
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Chen Q, Zhang X, Shi J, Yan M, Zhou T. Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem Sci 2021; 46:790-804. [PMID: 34053843 PMCID: PMC8448906 DOI: 10.1016/j.tibs.2021.05.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation, RNA modifications, and protein-binding abilities. We summarize the mechanisms of tsRNA biogenesis and the impact of RNA modifications, and propose how thinking of tsRNA functionality from an evolutionary perspective urges the expansion of tsRNA research into a wider spectrum, including cross-tissue/cross-species regulation and harnessing of the 'tsRNA code' for precision medicine.
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Affiliation(s)
- Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA.
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, USA
| | - Menghong Yan
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China; Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
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194
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Zeng L, Peng H, Yu H, Wang W, Duan C, Fang C, Wu Y. Expression profiles of tRNA-derived small RNA and their potential roles in oral submucous fibrosis. J Oral Pathol Med 2021; 50:1057-1066. [PMID: 34558114 DOI: 10.1111/jop.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Although transfer RNA (tRNA) has been found to be the main source of a rich class of noncoding RNA, the tRNA-derived small RNA (tsRNA) has been proved to play an irreplaceable role in the human body, and its dynamic imbalance could affect the progress of the disease. However, the research on tsRNA in oral submucous fibrosis (OSF) is still scarce. METHODS We sequenced the OSF and validated it by PCR. We found that there were significant differences in their expression levels in OSF. Furthermore, bioinformatic analysis was performed to explore the roles of these fragments in oral submucous fibrosis. RESULTS Of 126 tsRNAs in OSF were dysregulated, including 73 upregulated tsRNAs and 53 downregulated tsRNAs. The downregulated tiRNA-Val-CAC-002, tRF-Asn-GTT-005, tRF-Trp-CCA-007 and upregulated tRF-Gly-TCC-016, tRF-Pro-TGG-009 showed significant differences by qRT-PCR validation, which were consistent with the results of RNA sequencing. Gene ontology and pathway analysis revealed that tRF-Gly-TCC-016 would possibly promote the formation and progress of OSF through cytokine-cytokine receptor interaction and cAMP signal pathway, while tiRNA-Val-CAC-002 could be primarily concerned with the transition from OSF to oral squamous cell carcinoma (OSCC). CONCLUSION tRNA-derived fragments are dysregulated and could be involved in the pathogenesis of oral submucous fibrosis. tRF-Gly-TCC-016 and tiRNA-Val-CAC-002 may be new regulatory molecules that could affect the process of OSF by regulating signal pathways through interacting with multiple genes.
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Affiliation(s)
- Liujun Zeng
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Hui Peng
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Huiqiao Yu
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Weiming Wang
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University.,Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Changyun Fang
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Yingfang Wu
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
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195
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Bakre AA, Duffy C, Abdullah H, Cosby SL, Tripp RA. Small Non-coding RNA Expression Following Respiratory Syncytial Virus or Measles Virus Infection of Neuronal Cells. Front Microbiol 2021; 12:671852. [PMID: 34539595 PMCID: PMC8446675 DOI: 10.3389/fmicb.2021.671852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022] Open
Abstract
Respiratory syncytial virus (RSV) or measles virus (MeV) infection modifies host responses through small non-coding RNA (sncRNA) expression. We show that RSV or MeV infection of neuronal cells induces sncRNAs including various microRNAs and transfer RNA fragments (tRFs). We show that these tRFs originate from select tRNAs (GCC and CAC for glycine, CTT and AAC for Valine, and CCC and TTT for Lysine). Some of the tRNAs are rarely used by RSV or MeV as indicated by relative synonymous codon usage indices suggesting selective cleavage of the tRNAs occurs in infected neuronal cells. The data implies that differentially expressed sncRNAs may regulate host gene expression via multiple mechanisms in neuronal cells.
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Affiliation(s)
- Abhijeet A Bakre
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Catherine Duffy
- Virology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Hani'ah Abdullah
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - S Louise Cosby
- Virology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Ralph A Tripp
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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196
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Li X, Liu X, Zhao D, Cui W, Wu Y, Zhang C, Duan C. tRNA-derived small RNAs: novel regulators of cancer hallmarks and targets of clinical application. Cell Death Discov 2021; 7:249. [PMID: 34537813 PMCID: PMC8449783 DOI: 10.1038/s41420-021-00647-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/19/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
tRNAs are a group of conventional noncoding RNAs (ncRNAs) with critical roles in the biological synthesis of proteins. Recently, tRNA-derived small RNAs (tsRNAs) were found to have important biological functions in the development of human diseases including carcinomas, rather than just being considered pure degradation material. tsRNAs not only are abnormally expressed in the cancer tissues and serum of cancer patients, but also have been suggested to regulate various vital cancer hallmarks. On the other hand, the application of tsRNAs as biomarkers and therapeutic targets is promising. In this review, we focused on the basic characteristics of tsRNAs, and their biological functions known thus far, and explored the regulatory roles of tsRNAs in cancer hallmarks including proliferation, apoptosis, metastasis, tumor microenvironment, drug resistance, cancer stem cell phenotype, and cancer cell metabolism. In addition, we also discussed the research progress on the application of tsRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Xizhe Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Xianyu Liu
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Weifang Cui
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China
| | - Yingfang Wu
- Centre of Stomatology, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China. .,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China. .,National Clinical Research Center for Geriatric Disorders, Changsha, 410008, Hunan, P. R. China.
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, P. R. China. .,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, P. R. China. .,Institute of Medical Sciences, Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, P. R. China.
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197
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Wang Y, Zhang Y, Kong L, Song C, Chen X, Fang X, Zhang C. tRNA-derived RNA fragments in the exosomes of bovine milk and colostrum. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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198
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Winek K, Soreq H, Meisel A. Regulators of cholinergic signaling in disorders of the central nervous system. J Neurochem 2021; 158:1425-1438. [PMID: 33638173 PMCID: PMC8518971 DOI: 10.1111/jnc.15332] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/23/2021] [Accepted: 02/21/2021] [Indexed: 12/14/2022]
Abstract
Cholinergic signaling is crucial in cognitive processes, and degenerating cholinergic projections are a pathological hallmark in dementia. Use of cholinesterase inhibitors is currently the main treatment option to alleviate symptoms of Alzheimer's disease and has been postulated as a therapeutic strategy in acute brain damage (stroke and traumatic brain injury). However, the benefits of this treatment are still not clear. Importantly, cholinergic receptors are expressed both by neurons and by astrocytes and microglia, and binding of acetylcholine to the α7 nicotinic receptor in glial cells results in anti-inflammatory response. Similarly, the brain fine-tunes the peripheral immune response over the cholinergic anti-inflammatory axis. All of these processes are of importance for the outcome of acute and chronic neurological disease. Here, we summarize the main findings about the role of cholinergic signaling in brain disorders and provide insights into the complexity of molecular regulators of cholinergic responses, such as microRNAs and transfer RNA fragments, both of which may fine-tune the orchestra of cholinergic mRNAs. The available data suggest that these small noncoding RNA regulators may include promising biomarkers for predicting disease course and assessing treatment responses and might also serve as drug targets to attenuate signaling cascades during overwhelming inflammation and to ameliorate regenerative capacities of neuroinflammation.
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Affiliation(s)
- Katarzyna Winek
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain SciencesThe Hebrew University of JerusalemJerusalemIsrael
- The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Andreas Meisel
- Department of Neurology with Experimental NeurologyCenter for Stroke Research BerlinNeuroCure Clinical Research CenterCharité‐Universitätsmedizin BerlinBerlinGermany
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199
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Fang Y, Liu Y, Yan Y, Shen Y, Li Z, Li X, Zhang Y, Xue Z, Peng C, Chen X, Cao K, Zhou J. Differential Expression Profiles and Function Predictions for tRFs & tiRNAs in Skin Injury Induced by Ultraviolet Irradiation. Front Cell Dev Biol 2021; 9:707572. [PMID: 34447751 PMCID: PMC8383935 DOI: 10.3389/fcell.2021.707572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
Ultraviolet (UV) radiation is a major environmental factor contributing skin damage. As UV exposure is inevitable, it is necessary to pay attention to the underlying molecular mechanisms of UV-induced skin damage to develop effective therapies. tRNA-derived stress-induced RNAs (tiRNAs) and tRNA-derived fragments (tRFs) are tRNA-derived small RNAs (tsRNAs) that are a novel class of short, non-coding RNAs. However, the functions behind tRFs & tiRNAs in UV-induced skin injury are not yet clear. Firstly, the animal model of ultraviolet irradiation induced skin damage was established. Then the skin samples were preserved for the follow-up experiment. Sequencing was used to screen expression profiles and predict target genes. Compared with normal skin, a total of 31 differentially expressed tRFs & tiRNAs were screened. Among these, 10 tRFs & tiRNAs were shown to be significantly different in expression levels, where there were 4 up-regulated and 6 down-regulated target genes. Bioinformatics analyses revealed potential up-regulated tsRNAs (tRF-Val-AAC-012, tRF-Pro-AGG-012, tRF-Val-CAC-018, tRF-Val-AAC-031) and down-regulated tsRNAs (tRF-Arg-CCT-002, tRF-Trp-TCA-001, tiRNA-Ser-GCT-001, tRF-Gly-CCC-019, tRF-Ala-TGC-001, tRF-Ala-TGC-002). In summary, it was speculated that tRF-Gly-CCC-019 plays an important role in acute skin injury induced by UVB radiation by regulating the ras-related C3 botulinum toxin substrate 1 (Rac1) gene in the WNT signaling pathway. This study provides new insights into the mechanisms and therapeutic targets of UV-induced skin injury.
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Affiliation(s)
- Yuan Fang
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yang Liu
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yu Yan
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yiyu Shen
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zenan Li
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xu Li
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yufang Zhang
- Anyang Tumor Hospital, The Fourth Affiliated Hospital of Henan University of Science and Technology, Anyang, China
| | - Zhigang Xue
- Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Cong Peng
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, China
| | - Xiang Chen
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, China
| | - Ke Cao
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianda Zhou
- Department of Plastic Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
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200
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Global view of dynamic expression and precise mapping of mitochondrial tRNAs-derived fragments during stressed conditions in S. pombe. Mitochondrion 2021; 60:219-227. [PMID: 34428580 DOI: 10.1016/j.mito.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/14/2021] [Accepted: 08/19/2021] [Indexed: 01/30/2023]
Abstract
In this study, we provide a global view of population and processing of mitochondrial tRNAs-derived fragments (mt-tRFs) in fission yeast Schizosaccharomyces pombe. Here, mt-tRFs of 15-30 nucleotides were retrieved from S. pombe small RNA libraries obtained from unstressed, stress, and during stationary phase conditions. We demonstrate that production of these fragments increase during heat stress and stationary phase conditions in S. pombe, especially (most notably) in stationary phase. Analysis of data also reveals depending on the tRNA, either 5'-mt-tRF or 3'-mt-tRF was found and major mt-tRNA processing sites have been precisely identified. Furthermore, RNA-seq reveals that inactivation of trz2 encoding S. pombe mitochondrial tRNase ZL globally impairs mt-tRF processing. Finally, our result showed mt-tRFs were predicted to target mitochondrial genome mapping mtDNA-encoded protein gene. These observations suggest that mitochondrial tRFs may play an important regulatory role in response to stress and development.
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