1
|
Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024; 67:292-306. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
Collapse
Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| |
Collapse
|
2
|
Wang K, Liu CY, Fang B, Li B, Li YH, Xia QQ, Zhao Y, Cheng XL, Yang SM, Zhang MH, Wang K. The function and therapeutic potential of transfer RNA-derived small RNAs in cardiovascular diseases: A review. Pharmacol Res 2024; 206:107279. [PMID: 38942340 DOI: 10.1016/j.phrs.2024.107279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are a class of small non-coding RNA (sncRNA) molecules derived from tRNA, including tRNA derived fragments (tRFs) and tRNA halfs (tiRNAs). tsRNAs can affect cell functions by participating in gene expression regulation, translation regulation, intercellular signal transduction, and immune response. They have been shown to play an important role in various human diseases, including cardiovascular diseases (CVDs). Targeted regulation of tsRNAs expression can affect the progression of CVDs. The tsRNAs induced by pathological conditions can be detected when released into the extracellular, giving them enormous potential as disease biomarkers. Here, we review the biogenesis, degradation process and related functional mechanisms of tsRNAs, and discuss the research progress and application prospects of tsRNAs in different CVDs, to provide a new perspective on the treatment of CVDs.
Collapse
Affiliation(s)
- Kai Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Ying-Hui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Qian-Qian Xia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xue-Li Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Su-Min Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| | - Mei-Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China.
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
| |
Collapse
|
3
|
Syu YC, Hatterschide J, Budding CR, Tang Y, Musier-Forsyth K. Human T-cell leukemia virus type 1 uses a specific tRNA Pro isodecoder to prime reverse transcription. RNA (NEW YORK, N.Y.) 2024; 30:967-976. [PMID: 38684316 PMCID: PMC11251516 DOI: 10.1261/rna.080006.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is the only oncogenic human retrovirus discovered to date. All retroviruses are believed to use a host cell tRNA to prime reverse transcription (RT). In HTLV-1, the primer-binding site (PBS) in the genomic RNA is complementary to the 3' 18 nucleotides (nt) of human tRNAPro The human genome encodes 20 cytoplasmic tRNAPro genes representing seven isodecoders, all of which share the same 3' 18 nt sequence but vary elsewhere. Whether all tRNAPro isodecoders are used to prime RT in cells is unknown. A previous study showed that a 3' 18 nt tRNAPro-derived fragment (tRFPro) is packaged into HTLV-1 particles and can serve as an RT primer in vitro. The role of this tRNA fragment in the viral life cycle is unclear. In retroviruses, N1-methylation of the tRNA primer at position A58 (m1A) is essential for successful plus-strand transfer. Using primer-extension assays performed in chronically HTLV-1-infected cells, we found that A58 of tRNAPro is m1A-modified, implying that full-length tRNAPro is capable of facilitating successful plus-strand transfer. Analysis of HTLV-1 RT primer extension products indicated that full-length tRNAPro is likely to be the primer. To determine which tRNAPro isodecoder is used as the RT primer, we sequenced the minus-strand strong-stop RT product containing the intact tRNA primer and established that HTLV-1 primes RT using a specific tRNAPro UGG isodecoder. Further studies are required to understand how this primer is annealed to the highly structured HTLV-1 PBS and to investigate the role of tRFPro in the viral life cycle.
Collapse
Affiliation(s)
- Yu-Ci Syu
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio 43210, USA
| | - Joshua Hatterschide
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio 43210, USA
| | - Christina R Budding
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yingke Tang
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
4
|
Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592122. [PMID: 38746336 PMCID: PMC11092647 DOI: 10.1101/2024.05.01.592122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.
Collapse
Affiliation(s)
- Aidan C. Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M. Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R. Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M. Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| |
Collapse
|
5
|
Muthukumar S, Li CT, Liu RJ, Bellodi C. Roles and regulation of tRNA-derived small RNAs in animals. Nat Rev Mol Cell Biol 2024; 25:359-378. [PMID: 38182846 DOI: 10.1038/s41580-023-00690-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.
Collapse
Affiliation(s)
- Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
| |
Collapse
|
6
|
Zhou M, He X, Zhang J, Mei C, Zhong B, Ou C. tRNA-derived small RNAs in human cancers: roles, mechanisms, and clinical application. Mol Cancer 2024; 23:76. [PMID: 38622694 PMCID: PMC11020452 DOI: 10.1186/s12943-024-01992-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are a new type of non-coding RNAs (ncRNAs) produced by the specific cleavage of precursor or mature tRNAs. tsRNAs are involved in various basic biological processes such as epigenetic, transcriptional, post-transcriptional, and translation regulation, thereby affecting the occurrence and development of various human diseases, including cancers. Recent studies have shown that tsRNAs play an important role in tumorigenesis by regulating biological behaviors such as malignant proliferation, invasion and metastasis, angiogenesis, immune response, tumor resistance, and tumor metabolism reprogramming. These may be new potential targets for tumor treatment. Furthermore, tsRNAs can exist abundantly and stably in various bodily fluids (e.g., blood, serum, and urine) in the form of free or encapsulated extracellular vesicles, thereby affecting intercellular communication in the tumor microenvironment (TME). Meanwhile, their abnormal expression is closely related to the clinicopathological features of tumor patients, such as tumor staging, lymph node metastasis, and poor prognosis of tumor patients; thus, tsRNAs can be served as a novel type of liquid biopsy biomarker. This review summarizes the discovery, production, and expression of tsRNAs and analyzes their molecular mechanisms in tumor development and potential applications in tumor therapy, which may provide new strategies for early diagnosis and targeted therapy of tumors.
Collapse
Affiliation(s)
- Manli Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jing Zhang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Cheng Mei
- Department of Blood Transfusion, Xiangya Hospital, Clinical Transfusion Research Center, Central South University, Changsha, Hunan, 410008, China.
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| |
Collapse
|
7
|
Zhang Q, Zhao X, Sun M, Dong D. Novel insights into transfer RNA-derived small RNA (tsRNA) in cardio-metabolic diseases. Life Sci 2024; 341:122475. [PMID: 38309576 DOI: 10.1016/j.lfs.2024.122475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Cardio-metabolic diseases, including a cluster of metabolic disorders and their secondary affections on cardiovascular physiology, are gradually brought to the forefront by researchers due to their high prevalence and mortality, as well as an unidentified pathogenesis. tRNA-derived small RNAs (tsRNAs), cleaved by several specific enzymes and once considered as some "metabolic junks" in the past, have been proved to possess numerous functions in human bodies. More interestingly, such a potential also seems to influence the progression of cardio-metabolic diseases to some extent. In this review, the biogenesis, classification and mechanisms of tsRNAs will be discussed based on some latest studies, and their relations with several cardio-metabolic diseases will be highlighted in sequence. Lastly, some future prospects, such as their clinical applications as biomarkers and therapeutic targets will also be mentioned, in order to provide researchers with a comprehensive understanding of the research status of tsRNAs as well as its association with cardio-metabolic diseases, thus presenting as a beacon to indicate directions for the next stage of study.
Collapse
Affiliation(s)
- Qingya Zhang
- Innovation Institute, China Medical University, Shenyang 110122, Liaoning, China
| | - Xiaopeng Zhao
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Mingli Sun
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Dan Dong
- College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning, China.
| |
Collapse
|
8
|
Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| |
Collapse
|
9
|
Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
Collapse
Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
| |
Collapse
|
10
|
Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580780. [PMID: 38405876 PMCID: PMC10888928 DOI: 10.1101/2024.02.16.580780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. Moreover, mounting evidence supports a noncanonical role for tRNA cleavage products in the control of gene expression during diverse conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to altered tRNA transcription, suggesting that tRNA regulation may play an important role in mediating viral replication or the host response. To better understand how viral infection alters tRNA expression, we combined Ordered Two Template Relay (OTTR) with tRNA-specific bioinformatic software called tRAX to profile full-length tRNAs and fragmented tRNA-derived RNAs (tDRs) during infection with MHV68. We find that OTTR-tRAX is a powerful sequencing strategy for combined tRNA/tDR profiling and reveals that MHV68 infection triggers pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tDRs. Fragments of virally-encoded tRNAs (virtRNAs), as well as virtRNA base modification signatures are also detectable during infection. We present evidence that tRNA splicing factors are involved in the biogenesis of MHV68-induced cleavage products from pre-tRNAs and, in the case of CLP1 kinase, impact infectious virus production. Our data offers new insights into the importance of tRNA processing during gammaherpesvirus infection.
Collapse
Affiliation(s)
- Aidan C Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| |
Collapse
|
11
|
Yang N, Li R, Liu R, Yang S, Zhao Y, Xiong W, Qiu L. The Emerging Function and Promise of tRNA-Derived Small RNAs in Cancer. J Cancer 2024; 15:1642-1656. [PMID: 38370372 PMCID: PMC10869971 DOI: 10.7150/jca.89219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/20/2024] Open
Abstract
Fragments derived from tRNA, called tRNA-derived small RNAs (tsRNAs), have attracted widespread attention in the past decade. tsRNAs are widespread in prokaryotic and eukaryotic transcriptome, which contains two main types, tRNA-derived fragments (tRFs) and tRNA-derived stress-inducing RNA (tiRNAs), derived from the precursor tRNAs or mature tRNAs. According to differences in the cleavage position, tRFs can be divided into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, whereas tiRNAs can be divided into 5'-tiRNA and 3'-tiRNA. Studies have found that tRFs and tiRNAs are abnormally expressed in a variety of human malignant tumors, promote or inhibit the proliferation and apoptosis of cancer cells by regulating the expression of oncogene, and play an important role in the aggressive metastasis and progression of tumors. This article reviews the biological origins of various tsRNAs, introduces their functions and new concepts of related mechanisms, and focuses on the molecular mechanisms of tsRNAs in cancer, including breast cancer, prostate cancer, colorectal cancer, lung cancer, b-cell lymphoma, and chronic lymphoma cell leukemia. Lastly, this article puts forward some unresolved problems and future research prospects.
Collapse
Affiliation(s)
- Na Yang
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Ruijun Li
- College of Foreign Languages, Chuxiong Normal University, Chuxiong 675000, China
| | - Ruai Liu
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Shengjie Yang
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Yi Zhao
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Wei Xiong
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Lu Qiu
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
| |
Collapse
|
12
|
Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
Collapse
Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
13
|
Aquino-Jarquin G. tRNA Thr-miR-720 mimicry in glioma cells. Hum Cell 2023; 36:2276-2277. [PMID: 37578573 DOI: 10.1007/s13577-023-00968-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Affiliation(s)
- Guillermo Aquino-Jarquin
- RNA Biology and Genome Editing Section, Genomics, Genetics, and Bioinformatics Research Laboratory, 'Federico Gómez' Children's Hospital of Mexico, Dr. Márquez 162, Doctores, Cuauhtémoc, C.P. 06720, Ciudad de México, Mexico.
| |
Collapse
|
14
|
Shi H, Xie J, Pei S, He D, Hou H, Xu S, Fu Z, Shi X. Digging out the biology properties of tRNA-derived small RNA from black hole. Front Genet 2023; 14:1232325. [PMID: 37953919 PMCID: PMC10637384 DOI: 10.3389/fgene.2023.1232325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
An unique subclass of functional non-coding RNAs generated by transfer RNA (tRNA) under stress circumstances is known as tRNA-derived small RNA (tsRNA). tsRNAs can be divided into tRNA halves and tRNA-derived fragments (tRFs) based on the different cleavage sites. Like microRNAs, tsRNAs can attach to Argonaute (AGO) proteins to target downstream mRNA in a base pairing manner, which plays a role in rRNA processing, gene silencing, protein expression and viral infection. Notably, tsRNAs can also directly bind to protein and exhibit functions in transcription, protein modification, gene expression, protein stabilization, and signaling pathways. tsRNAs can control the expression of tumor suppressor genes and participate in the initiation of cancer. It can also mediate the progression of diseases by regulating cell viability, migration ability, inflammatory factor content and autophagy ability. Precision medicine targeting tsRNAs and drug therapy of plant-derived tsRNAs are expected to be used in clinical practice. In addition, liquid biopsy technology based on tsRNAs indicates a new direction for the non-invasive diagnosis of diseases.
Collapse
Affiliation(s)
- Hengmei Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengbin Pei
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Danni He
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Huyang Hou
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Shipeng Xu
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoyan Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| |
Collapse
|
15
|
Cao W, Zeng Z, Lei S. 5'-tRF-19-Q1Q89PJZ Suppresses the Proliferation and Metastasis of Pancreatic Cancer Cells via Regulating Hexokinase 1-Mediated Glycolysis. Biomolecules 2023; 13:1513. [PMID: 37892195 PMCID: PMC10605356 DOI: 10.3390/biom13101513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/20/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
tRNA-derived small RNAs (tDRs) are dysregulated in several diseases, including pancreatic cancer (PC). However, only a limited number of tDRs involved in PC progression are known. Herein, a novel tDR, 5'-tRF-19-Q1Q89PJZ (tRF-19-Q1Q89PJZ), was verified in PC plasma using RNA and Sanger sequencing. tRF-19-Q1Q89PJZ was downregulated in PC tissues and plasma, which was related to advanced clinical characteristics and poor prognosis. tRF-19-Q1Q89PJZ overexpression inhibited the malignant activity of PC cells in vitro, while tRF-19-Q1Q89PJZ inhibition produced an opposite effect. The differentially expressed genes induced by tRF-19-Q1Q89PJZ overexpression were enriched in "pathways in cancer" and "glycolysis". Mechanistically, tRF-19-Q1Q89PJZ directly sponged hexokinase 1 (HK1) mRNA and inhibited its expression, thereby suppressing glycolysis in PC cells. HK1 restoration relieved the inhibitory effect of tRF-19-Q1Q89PJZ on glycolysis in PC cells and on their proliferation and mobility in vitro. tRF-19-Q1Q89PJZ upregulation inhibited PC cell proliferation and metastasis in vivo and suppressed HK1 expression in tumor tissues. Furthermore, tRF-19-Q1Q89PJZ expression was attenuated under hypoxia. Collectively, these findings indicate that tRF-19-Q1Q89PJZ suppresses the malignant activity of PC cells by regulating HK1-mediated glycolysis. Thus, tRF-19-Q1Q89PJZ may serve as a key target for PC therapy.
Collapse
Affiliation(s)
- Wenpeng Cao
- Department of Anatomy, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China
| | - Zhirui Zeng
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China;
| | - Shan Lei
- Department of Physiology, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China;
| |
Collapse
|
16
|
Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
Collapse
Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
| |
Collapse
|
17
|
Lee S, Kim J, Valdmanis PN, Kim HK. Emerging roles of tRNA-derived small RNAs in cancer biology. Exp Mol Med 2023:10.1038/s12276-023-01038-5. [PMID: 37430089 PMCID: PMC10393972 DOI: 10.1038/s12276-023-01038-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023] Open
Abstract
Transfer RNAs (tRNAs) play an essential role in mRNA translation by delivering amino acids to growing polypeptide chains. Recent data demonstrate that tRNAs can be cleaved by ribonucleases, and the resultant cleavage products, tRNA-derived small RNAs (tsRNAs), have crucial roles in physiological and pathological conditions. They are classified into more than six types according to their size and cleavage positions. Since the initial discovery of the physiological functions of tsRNAs more than a decade ago, accumulating data have demonstrated that tsRNAs play critical roles in gene regulation and tumorigenesis. These tRNA-derived molecules have various regulatory functions at the transcriptional, post-transcriptional, and translational levels. More than a hundred types of modifications are found on tRNAs, affecting the biogenesis, stability, function, and biochemical properties of tsRNA. Both oncogenic and tumor suppressor functions have been reported for tsRNAs, which play important roles in the development and progression of various cancers. Abnormal expression patterns and modification of tsRNAs are associated with various diseases, including cancer and neurological disorders. In this review, we will describe the biogenesis, versatile gene regulation mechanisms, and modification-mediated regulation mechanisms of tsRNA as well as the expression patterns and potential therapeutic roles of tsRNAs in various cancers.
Collapse
Affiliation(s)
- Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jungeun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98115, USA
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| |
Collapse
|
18
|
Wilson B, Su Z, Kumar P, Dutta A. XRN2 suppresses aberrant entry of tRNA trailers into argonaute in humans and Arabidopsis. PLoS Genet 2023; 19:e1010755. [PMID: 37146074 PMCID: PMC10191329 DOI: 10.1371/journal.pgen.1010755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/17/2023] [Accepted: 04/21/2023] [Indexed: 05/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a well-characterized class of small RNAs (sRNAs) that regulate gene expression post-transcriptionally. miRNAs function within a complex milieu of other sRNAs of similar size and abundance, with the best characterized being tRNA fragments or tRFs. The mechanism by which the RNA-induced silencing complex (RISC) selects for specific sRNAs over others is not entirely understood in human cells. Several highly expressed tRNA trailers (tRF-1s) are strikingly similar to microRNAs in length but are generally excluded from the microRNA effector pathway. This exclusion provides a paradigm for identifying mechanisms of RISC selectivity. Here, we show that 5' to 3' exoribonuclease XRN2 contributes to human RISC selectivity. Although highly abundant, tRF-1s are highly unstable and degraded by XRN2 which blocks tRF-1 accumulation in RISC. We also find that XRN mediated degradation of tRF-1s and subsequent exclusion from RISC is conserved in plants. Our findings reveal a conserved mechanism that prevents aberrant entry of a class of highly produced sRNAs into Ago2.
Collapse
Affiliation(s)
- Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Zhangli Su
- Department of Genetics, University of Alabama, Birmingham, Alabama, United States of America
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- Department of Genetics, University of Alabama, Birmingham, Alabama, United States of America
| |
Collapse
|
19
|
Fu M, Gu J, Wang M, Zhang J, Chen Y, Jiang P, Zhu T, Zhang X. Emerging roles of tRNA-derived fragments in cancer. Mol Cancer 2023; 22:30. [PMID: 36782290 PMCID: PMC9926655 DOI: 10.1186/s12943-023-01739-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.
Collapse
Affiliation(s)
- Min Fu
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China ,grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jianmei Gu
- grid.260483.b0000 0000 9530 8833Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226361 Jiangsu China
| | - Maoye Wang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jiahui Zhang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Yanke Chen
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Pengcheng Jiang
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China
| | - Taofeng Zhu
- Department of Pulmonary and Critical Care Medicine, Yixing Hospital Affiliated to Jiangsu University, Yixing, 214200, Jiangsu, China.
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| |
Collapse
|
20
|
Lu E, Wu L, Chen B, Xu S, Fu Z, Wu Y, Wu Y, Gu H. Maternal Serum tRNA-Derived Fragments (tRFs) as Potential Candidates for Diagnosis of Fetal Congenital Heart Disease. J Cardiovasc Dev Dis 2023; 10:jcdd10020078. [PMID: 36826574 PMCID: PMC9968204 DOI: 10.3390/jcdd10020078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/26/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is one of the most predominant birth defects that causes infant death worldwide. The timely and successful surgical treatment of CHD on newborns after delivery requires accurate detection and reliable diagnosis during pregnancy. However, there are no biomarkers that can serve as an early diagnostic factor for CHD patients. tRNA-derived fragments (tRFs) have been reported to play an important role in the occurrence and progression of numerous diseases, but their roles in CHD remains unknown. METHODS High-throughput sequencing was performed on the peripheral blood of pregnant women with an abnormal fetal heart and a normal fetal heart, and 728 differentially expressed tRFs/tiRNAs were identified, among which the top 18 tRFs/tiRNAs were selected as predictive biomarkers of CHD. Then, a quantitative reverse transcriptase polymerase chain reaction verified the expression of tRFs/tiRNAs in more clinical samples, and the correlation between tRFs/tiRNAs abnormalities and CHD was analyzed. RESULTS tRF-58:74-Gly-GCC-1 and tiRNA-1:35-Leu-CAG-1-M2 may be promising biomarkers. Through further bioinformatics analysis, we predicted that TRF-58:744-GLy-GCC-1 could induce CHD by influencing biological metabolic processes. CONCLUSIONS Our results provide a theoretical basis for the abnormally expressed tRF-58:74-Gly-GCC-1 in maternal peripheral blood as a new potential biomarker for the accurate diagnosis of CHD during pregnancy.
Collapse
Affiliation(s)
- Enkang Lu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Central Laboratory of Jiangsu Provincial Maternal and Child Health Care Hospital, Maternal and Child Branch of the First Affiliated Hospital of Nanjing Medical University, Nanjing 210036, China
| | - Lijun Wu
- Department of Ultrasound, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing 210004, China
| | - Bin Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shipeng Xu
- Department of Biomedical Engineering, University of California Davis, Davis, CA 95616, USA
| | - Ziyi Fu
- Central Laboratory of Jiangsu Provincial Maternal and Child Health Care Hospital, Maternal and Child Branch of the First Affiliated Hospital of Nanjing Medical University, Nanjing 210036, China
| | - Yun Wu
- Department of Ultrasound, Nanjing Maternity and Child Health Care Hospital, Women’s Hospital of Nanjing Medical University, Nanjing 210004, China
- Correspondence: (Y.W.); (Y.W.); (H.G.); Tel.: +86-189-0518-0170 (Y.W.); +86-139-5194-5999 (Y.W.); +86-139-0159-2427 (H.G.)
| | - Yanhu Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Correspondence: (Y.W.); (Y.W.); (H.G.); Tel.: +86-189-0518-0170 (Y.W.); +86-139-5194-5999 (Y.W.); +86-139-0159-2427 (H.G.)
| | - Haitao Gu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
- Correspondence: (Y.W.); (Y.W.); (H.G.); Tel.: +86-189-0518-0170 (Y.W.); +86-139-5194-5999 (Y.W.); +86-139-0159-2427 (H.G.)
| |
Collapse
|
21
|
Dremel SE, Jimenez AR, Tucker JM. "Transfer" of power: The intersection of DNA virus infection and tRNA biology. Semin Cell Dev Biol 2023; 146:31-39. [PMID: 36682929 PMCID: PMC10101907 DOI: 10.1016/j.semcdb.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Transfer RNAs (tRNAs) are at the heart of the molecular biology central dogma, functioning to decode messenger RNAs into proteins. As obligate intracellular parasites, viruses depend on the host translation machinery, including host tRNAs. Thus, the ability of a virus to fine-tune tRNA expression elicits the power to impact the outcome of infection. DNA viruses commonly upregulate the output of RNA polymerase III (Pol III)-dependent transcripts, including tRNAs. Decades after these initial discoveries we know very little about how mature tRNA pools change during viral infection, as tRNA sequencing methodology has only recently reached proficiency. Here, we review perturbation of tRNA biogenesis by DNA virus infection, including an emerging player called tRNA-derived fragments (tRFs). We discuss how tRNA dysregulation shifts the power landscape between the host and virus, highlighting the potential for tRNA-based antivirals as a future therapeutic.
Collapse
Affiliation(s)
- Sarah E Dremel
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ariana R Jimenez
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA
| | - Jessica M Tucker
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
22
|
Hou J, Li Q, Wang J, Lu W. tRFs and tRNA Halves: Novel Cellular Defenders in Multiple Biological Processes. Curr Issues Mol Biol 2022; 44:5949-5962. [PMID: 36547066 PMCID: PMC9777342 DOI: 10.3390/cimb44120405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA transcripts rather than via random degradation. tRFs and tRNA halves are highly involved in regulating transcription and translation in a canonical or non-canonical manner in response to cellular stress. In this review, we summarize the biogenesis and types of tRFs and tRNA halves, clarify the biological functions and molecular mechanisms of tRNA fragments in both physiological and pathological processes with a particular focus on their cytoprotective roles in defending against oxidation and apoptosis, and highlight their potential application as biomarkers in determining cell fate.
Collapse
Affiliation(s)
- Jiani Hou
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qianqing Li
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jun Wang
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
| | - Wenfa Lu
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
| |
Collapse
|
23
|
Wang S, Luo Z, Yuan L, Lin X, Tang Y, Yin L, Liang P, Jiang B. tRNA-Derived Small RNAs: Novel Insights into the Pathogenesis and Treatment of Cardiovascular Diseases. J Cardiovasc Transl Res 2022; 16:300-309. [PMID: 36190649 DOI: 10.1007/s12265-022-10322-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/12/2022] [Indexed: 12/05/2022]
Abstract
tRNA-derived small RNAs (tsRNAs) are non-coding RNAs with diverse functions in various diseases. Although research on tsRNAs has focused on their roles in cancer, such as gene expression regulation to influence cancer progression and realize clinical effects, a growing number of studies are investigating the association of tsRNAs with cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction, and pulmonary hypertension. tsRNA expression varies across these diseases and could be regulated by epigenetics, tsRNA structure, and tRNA-binding proteins. tsRNAs play key roles in CVD progression, including the regulation of protein synthesis, and the different mechanisms underlying these functional roles of tsRNAs have been elucidated. Furthermore, tsRNAs are potential diagnostic biomarkers and therapeutic targets in CVDs. In this review, we summarize the biogenesis, classification, and regulation of tsRNAs and their potential application for CVD diagnosis and therapy. We also highlight the current challenges and provide perspectives for further investigation.
Collapse
Affiliation(s)
- Shuxin Wang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Zhengyang Luo
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Ludong Yuan
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Xiaofang Lin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Yuting Tang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Leijing Yin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Bimei Jiang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China.
| |
Collapse
|
24
|
Ma X, Niu X, Huang S, Li S, Ran X, Wang J, Dai X. The piRNAs present in the developing testes of Chinese indigenous Xiang pigs. Theriogenology 2022; 189:92-106. [PMID: 35738035 DOI: 10.1016/j.theriogenology.2022.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/21/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
The piRNA pathway plays an essential role in defense against transposable elements in the germline tissues of animals and contributes to post-transcriptional regulation of genes. Xiang pigs present an earlier sexual maturation compared with most European pig breeds, but the role that the piRNA pathway plays in the development of Xiang pigs is currently not understood. In this study, we sequenced and analyzed piRNAs expressed in the testes of Xiang pigs at four different ages, and identified endogenous piRNAs which were highly abundant at each time point. The lengths of the identified piRNAs ranged from 24 to 34 nucleotides (nt), with the most abundant length being 29 nt. Additionally, there was a strong bias for uracil at the first position, a slight bias for adenine at position 10 and frequent 5'-10 nt complementary sequences, suggesting that ping-pong-mediated silencing is present in the Xiang pig germline. We observed that the piRNA composition changed from TE-associated piRNAs in two- and three-month-old testes to predominantly gene-derived and intergenic piRNAs in six- and twelve-month-old testes, with a gradual increase in the expression level of piRNAs over the course of testis development. And more than half of piRNA reads mapped to just a few of 473 predicted piRNA clusters. Additionally, we found that several genes were highly enriched by piRNA reads, including CYP19A1, PRMT8, SUZ12, WWOX, SGSM1 and MIF. The functions of these genes are primarily associated with steroidogenesis and histone modification. Changes in piRNA composition and widespread expression patterns during spermatid development indicate that these small ncRNAs may be responsible not only for transposon suppression but also for post-transcriptional regulation of several protein-coding genes essential for normal spermatogenesis.
Collapse
Affiliation(s)
- Xinrui Ma
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Shihui Huang
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Sheng Li
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xueqin Ran
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Jiafu Wang
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xinlan Dai
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| |
Collapse
|
25
|
Gu X, Zhang Y, Qin X, Ma S, Huang Y, Ju S. Transfer RNA-derived small RNA: an emerging small non-coding RNA with key roles in cancer. Exp Hematol Oncol 2022; 11:35. [PMID: 35658952 PMCID: PMC9164556 DOI: 10.1186/s40164-022-00290-1] [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] [Received: 05/01/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
Transfer RNAs (tRNAs) promote protein translation by binding to the corresponding amino acids and transporting them to the ribosome, which is essential in protein translation. tRNA-derived small RNAs (tsRNAs) are derived fragments of tRNAs that are cleaved explicitly under certain conditions. An increasing amount of research has demonstrated that tsRNAs have biological functions rather than just being degradation products. tsRNAs can exert functions such as regulating gene expression to influence cancer progression. Their dysregulation is closely associated with various cancers and can serve as diagnostic and prognostic biomarkers for cancer. This review summarizes the generation, classification, and biological functions of tsRNAs, and highlights the roles of tsRNAs in different cancers and their applications as tumor markers.
Collapse
Affiliation(s)
- Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xinyue Qin
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shuo Ma
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, China. .,Department of Medical Oncology, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.
| |
Collapse
|
26
|
Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs. Noncoding RNA 2022; 8:ncrna8030029. [PMID: 35645336 PMCID: PMC9149963 DOI: 10.3390/ncrna8030029] [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: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Sex-Specific Expression of Non-Coding RNA Fragments in Frontal Cortex, Hippocampus and Cerebellum of Rats. EPIGENOMES 2022; 6:epigenomes6020011. [PMID: 35466186 PMCID: PMC9036230 DOI: 10.3390/epigenomes6020011] [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: 02/02/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Non-coding RNA fragments (ncRFs) are processed from various non-coding RNAs (ncRNAs), with the most abundant being those produced from tRNAs. ncRFs were reported in many animal and plant species. Many ncRFs exhibit tissue specificity or/and are affected by stress. There is, however, only a handful of reports that describe differential expression of ncRFs in the brain regions. In this work, we analyzed the abundance of ncRFs processed from four major ncRNAs, including tRNA (tRFs), snoRNA (snoRFs), snRNA (snRFs), and rRNA (rRFs) in the frontal cortex (FC), hippocampus (HIP), and cerebellum (CER) of male and female rats. We found brain-specific and sex-specific differences. Reads mapping to lincRNAs were significantly larger in CER as compared to HIP and CER, while those mapping to snRNAs and tRNA were smaller in HIP than in FC and CER. tRF reads were the most abundant among all ncRF reads, and FC had more reads than HIP and CER. Reads mapping to antisense ncRNAs were significantly larger in females than in males in FC. Additionally, males consistently had more tRF, snRF, and snoRF reads in all brain regions. rRFs were more abundant in males in FC and females in HIP. Several tRFs were significantly underrepresented, including tRF-ValCAC, tRF-ValACC, and tRF-LysCTT in all brain regions. We also found brain- and sex-specific differences in the number of brain function-related mRNA targets. To summarize, we found sex-specific differences in the expression of several ncRNA fragments in various brain regions of healthy rats.
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Emerging function and clinical significance of extracellular vesicle noncoding RNAs in lung cancer. Mol Ther Oncolytics 2022; 24:814-833. [PMID: 35317517 PMCID: PMC8908047 DOI: 10.1016/j.omto.2022.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lung cancer (LC) is a commonly diagnosed cancer with an unsatisfactory prognosis. Extracellular vesicles (EVs) are lipid bilayer-delimited particles that mediate cell-cell communication by transporting various biomacromolecules, such as nucleic acids, proteins, and lipids. Noncoding RNAs (ncRNAs), including microRNAs, circular RNAs, and long noncoding RNAs, are important noncoding transcripts that play critical roles in a variety of physiological and pathological processes, especially in cancer. ncRNAs have been verified to be packaged into EVs and transported between LC cells and stromal cells, regulating multiple LC malignant phenotypes, such as proliferation, migration, invasion, epithelial-mesenchymal transition, metastasis, and treatment resistance. Additionally, EVs can be detected in various body fluids and are associated with the stage, grade, and metastasis of LC. Herein, we summarize the biological characteristics and functions of EV ncRNAs in the biological processes of LC, focusing on their potential to serve as diagnostic and prognostic biomarkers of LC as well as their probable role in the clinical treatment of LC. EV ncRNAs provide a new perspective for understanding the mechanism underlying LC pathogenesis and development, which might benefit numerous LC patients in the future.
Collapse
|
31
|
Meseguer S, Rubio MP. mt tRFs, New Players in MELAS Disease. Front Physiol 2022; 13:800171. [PMID: 35273517 PMCID: PMC8902416 DOI: 10.3389/fphys.2022.800171] [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: 10/22/2021] [Accepted: 01/20/2022] [Indexed: 12/22/2022] Open
Abstract
MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) is an OXPHOS disease mostly caused by the m.3243A>G mutation in the mitochondrial tRNALeu(UUR) gene. Recently, we have shown that the mutation significantly changes the expression pattern of several mitochondrial tRNA-derived small RNAs (mt tsRNAs or mt tRFs) in a cybrid model of MELAS and in fibroblasts from MELAS patients versus control cells. Among them are those derived from mt tRNA LeuUUR containing or not the m.3243A>G mutation (mt 5′-tRF LeuUUR-m.3243A>G and mt 5′-tRF LeuUUR), whose expression levels are, respectively, increased and decreased in both MELAS cybrids and fibroblasts. Here, we asked whether mt 5′-tRF LeuUUR and mt 5′-tRF LeuUUR-m.3243A>G are biologically relevant and whether these mt tRFs are detected in diverse patient samples. Treatment with a mimic oligonucleotide of mt tRNA LeuUUR fragment (mt 5′-tRF LeuUUR) showed a therapeutic potential since it partially restored mitochondrial respiration in MELAS cybrids. Moreover, these mt tRFs could be detected in biofluids like urine and blood. We also investigated the participation of miRNA pathway components Dicer and Ago2 in the mt tRFs biogenesis process. We found that Dicer and Ago2 localize in the mitochondria of MELAS cybrids and that immunoprecipitation of these proteins in cytoplasm and mitochondria fractions revealed an increased mt tRF/mt tRNA ratio in MELAS condition compared to WT. These preliminary results suggest an involvement of Dicer and Ago2 in the mechanism of mt tRF biogenesis and action.
Collapse
Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Mari-Paz Rubio
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| |
Collapse
|
32
|
Cao KY, Yan TM, Zhang JZ, Chan TF, Li J, Li C, Lai-Han Leung E, Gao J, Zhang BX, Jiang ZH. A tRNA-derived fragment from Chinese yew suppresses ovarian cancer growth via targeting TRPA1. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:718-732. [PMID: 35317282 PMCID: PMC8905250 DOI: 10.1016/j.omtn.2021.12.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022]
Abstract
Drug discovery from plants usually focuses on small molecules rather than such biological macromolecules as RNAs. Although plant transfer RNA (tRNA)-derived fragment (tRF) has been associated with the developmental and defense mechanisms in plants, its regulatory role in mammals remains unclear. By employing a novel reverse small interfering RNA (siRNA) screening strategy, we show that a tRF mimic (antisense derived from the 5' end of tRNAHis(GUG) of Chinese yew) exhibits comparable anti-cancer activity with that of taxol on ovarian cancer A2780 cells, with a 16-fold lower dosage than that of taxol. A dual-luciferase reporter assay revealed that tRF-T11 directly targets the 3' UTR of oncogene TRPA1 mRNA. Furthermore, an Argonaute-RNA immunoprecipitation (AGO-RIP) assay demonstrated that tRF-T11 can interact with AGO2 to suppress TRPA1 via an RNAi pathway. This study uncovers a new role of plant-derived tRFs in regulating endogenous genes. This holds great promise for exploiting novel RNA drugs derived from nature and sheds light on the discovery of unknown molecular targets of therapeutics.
Collapse
Affiliation(s)
- Kai-Yue Cao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| | - Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| | - Ji-Zhou Zhang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ting-Fung Chan
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jie Li
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chong Li
- Medical Research Institute, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| | - Jin Gao
- Increasepharm (Hengqin) Institute Co., Ltd, Zhuhai 519031, China
| | | | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, China
| |
Collapse
|
33
|
Yang H, Zhang H, Chen Z, Wang Y, Gao B. Effects of tRNA-derived fragments and microRNAs regulatory network on pancreatic acinar intracellular trypsinogen activation. Bioengineered 2022; 13:3207-3220. [PMID: 35045793 PMCID: PMC8973995 DOI: 10.1080/21655979.2021.2018880] [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] [Indexed: 12/29/2022] Open
Abstract
Acute pancreatitis (AP) is a common gastrointestinal disease with substantial morbidity and mortality. Pancreatic acinar intracellular trypsinogen activation (PAITA) is an important event in the early stage of AP. The present study aimed to investigate the effects of tRNA-derived fragments (tRFs) and the microRNA regulatory network on pancreatic acinar intracellular trypsinogen activation (PAITA) and identify novel key targets in AP. Taurolithocholic acid 3-sulfate (TLC-S)-treated AR42J cells were used to establish a PAITA model. Twenty differentially expressed tRFs and 35 DE microRNAs were identified in PAITA through gene sequencing. Based on these genes, we established the tRF-mRNA and microRNA-mRNA regulatory networks by using bioinformatics methods. The networks revealed 29 hub microRNAs (e.g., Let-7 family, miR-21-3p.) and 19 hub tRFs (e.g., tRF3-Thr-AGT, i-tRF-Met-CAT) in PAITA. GO analysis showed that the functions of the two networks were similar and mainly enriched in RNA splicing, mRNA processing, and so on. tRF3-Thr-AGT, targeting Btg2, Cd44, Zbp1, etc., was significantly decreased in PAITA. Moreover, the trypsinogen activation level was increased significantly in the tRF3-Thr-AGT deficiency groups, but rescued by tRF3-Thr-AGT mimics. The results revealed that downregulated tRF3-Thr-AGT was involved in PAITA. This study provides potential novel targets for researching the underlying mechanisms of AP.
Collapse
Affiliation(s)
- Hao Yang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Huairong Zhang
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhuomiaoyu Chen
- Department of General Surgery, Peking University People's Hospital, Beijing, China
| | - Yuan Wang
- Department of General Surgery, Peking University People's Hospital, Beijing, China
| | - Bo Gao
- Department of General Surgery, Peking University People's Hospital, Beijing, China
| |
Collapse
|
34
|
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.
Collapse
|
35
|
Abstract
There are strong incentives for human populations to develop antiviral systems. Similarly, genomes that encode antiviral systems have had strong selective advantages. Protein-guided immune systems, which have been well studied in mammals, are necessary for survival in our virus-laden environments. Small RNA–directed antiviral immune systems suppress invasion of cells by non-self genetic material via complementary base pairing with target sequences. These RNA silencing-dependent systems operate in diverse organisms. In mammals, there is strong evidence that microRNAs (miRNAs) regulate endogenous genes important for antiviral immunity, and emerging evidence that virus-derived nucleic acids can be directly targeted by small interfering RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNAs (tRNAs) for protection in some contexts. In this review, we summarize current knowledge of the antiviral functions of each of these small RNA types and consider their conceptual and mechanistic overlap with innate and adaptive protein-guided immunity, including mammalian antiviral cytokines, as well as the prokaryotic RNA-guided immune system, CRISPR. In light of recent successes in delivery of RNA for antiviral purposes, most notably for vaccination, we discuss the potential for development of small noncoding RNA–directed antiviral therapeutics and prophylactics. Viruses are all around us and are likely inside some of the reader’s cells at this moment. Organisms are accommodated to this reality and encode various immune systems to limit virus replication. In mammals, the best studied immune systems are directed by proteins that specifically recognize viruses. These include diverse antibodies and T cell receptors, which recognize viral proteins, and pattern recognition receptors, some of which can recognize viral nucleic acids. In other organisms, including bacteria, immune systems directed by small RNAs are also well known; spacer-derived guide RNAs in CRISPR/Cas immune systems are one prominent example. The small RNAs directing these systems derive their specificity via complementary base pairing with their targets, which include both host and viral nucleic acids. Rather than having “traded in” these systems for more advanced protein-directed systems, increasing evidence supports the perspective that small RNA–directed immune systems remain active in mammalian antiviral immunity in some contexts. Here, we review what is known so far about the emerging roles of mammalian siRNAs, miRNAs, piRNAs, and tRNAs in directing immunity to viruses.
Collapse
Affiliation(s)
- Tomoko Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
- * E-mail: (TT); (NFP)
| | - Steven M. Heaton
- Genome Immunobiology RIKEN Hakubi Research Team, Cluster for Pioneering Research, RIKEN, Yokohama, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, Cluster for Pioneering Research, RIKEN, Yokohama, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- * E-mail: (TT); (NFP)
| |
Collapse
|
36
|
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.
Collapse
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,
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
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.
Collapse
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.
| |
Collapse
|
39
|
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.
Collapse
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.
| |
Collapse
|
40
|
Ma X, Liu C, Cao X. Plant transfer RNA-derived fragments: Biogenesis and functions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1399-1409. [PMID: 34114725 DOI: 10.1111/jipb.13143] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/10/2021] [Indexed: 06/12/2023]
Abstract
Processing of mature transfer RNAs (tRNAs) produces complex populations of tRNA-derived fragments (tRFs). Emerging evidence shows that tRFs have important functions in bacteria, animals, and plants. Here, we review recent advances in understanding plant tRFs, focusing on their biological and cellular functions, such as regulating stress responses, mediating plant-pathogen interactions, and modulating post-transcriptional gene silencing and translation. We also review sequencing strategies and bioinformatics resources for studying tRFs in plants. Finally, we discuss future directions for plant tRF research, which will expand our knowledge of plant non-coding RNAs.
Collapse
Affiliation(s)
- Xuan Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
41
|
Yuan Y, Li J, He Z, Fan X, Mao X, Yang M, Yang D. tRNA-derived fragments as New Hallmarks of Aging and Age-related Diseases. Aging Dis 2021; 12:1304-1322. [PMID: 34341710 PMCID: PMC8279533 DOI: 10.14336/ad.2021.0115] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/15/2021] [Indexed: 01/02/2023] Open
Abstract
tRNA-derived fragments (tRFs), which are non-coding RNAs produced via tRNA cleavage with lengths of 14 to 50 nucleotides, originate from precursor tRNAs or mature tRNAs and exist in a wide range of organisms. tRFs are produced not by random fracture of tRNAs but by specific mechanisms. Considerable evidence shows that tRFs are detectable in model organisms of different ages and are associated with age-related diseases in humans, such as cancer and neurodegenerative diseases. In this literature review, the origin and classification of tRFs and the regulatory mechanisms of tRFs in aging and age-related diseases are summarized. We also describe the available tRF databases and research techniques and lay a foundation for the exploration of tRFs as biomarkers for the diagnosis and treatment of aging and age-related diseases.
Collapse
Affiliation(s)
- Ya Yuan
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jiamei Li
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zhi He
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaolan Fan
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xueping Mao
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingyao Yang
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Deying Yang
- 1Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| |
Collapse
|
42
|
Identification of transfer RNA-derived fragments and their potential roles in aortic dissection. Genomics 2021; 113:3039-3049. [PMID: 34214628 DOI: 10.1016/j.ygeno.2021.06.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/19/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022]
Abstract
Emerging evidence suggests that majority of the transfer RNA (tRNA)-derived small RNA, including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), play a significant role in the molecular mechanisms underlying some human diseases. However, expression of tRFs/tiRNAs and their potential roles in aortic dissection (AD) remain unclear. This study examined the expression characteristics and explored the functional roles of tRFs/tiRNAs in AD using RNA-sequencing, bioinformatics, real-time quantitative reverse transcription polymerase chain reaction, and loss- and gain-of-function analysis. Results revealed that a total of 41 tRFs/tiRNAs were dysregulated in the AD group compared to the control group. Among them, 12 were upregulated and 29 were downregulated (fold change≥1.5 and p < 0.05). RT-qPCR results revealed that expressions of tRF-1:30-chrM.Met-CAT was significantly upregulated, while that of tRF-54:71-chrM.Trp-TCA and tRF-1:32-chrM.Cys-GCA were notably downregulated; expression patterns were consistent with the RNA sequencing data. Bioinformatic analysis showed that a variety of related pathways might be involved in the pathogenesis of AD. Functionally, tRF-1:30-chrM.Met-CAT could facilitate proliferation, migration, and phenotype switching in vascular smooth muscle cells (VSMCs), which might serve as a significant regulator in the progression of AD. In summary, the study illustrated that tRFs/tiRNAs expressed in AD tissues have potential biological functions and may act as promising biomarkers or therapeutic targets for AD.
Collapse
|
43
|
Stenum TS, Kongstad M, Holmqvist E, Kallipolitis B, Svenningsen SL, Sørensen MA. Three Ribosomal Operons of Escherichia coli Contain Genes Encoding Small RNAs That Interact With Hfq and CsrA in vitro. Front Microbiol 2021; 12:625585. [PMID: 34046019 PMCID: PMC8144298 DOI: 10.3389/fmicb.2021.625585] [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: 11/04/2020] [Accepted: 04/09/2021] [Indexed: 01/08/2023] Open
Abstract
Three out of the seven ribosomal RNA operons in Escherichia coli end in dual terminator structures. Between the two terminators of each operon is a short sequence that we report here to be an sRNA gene, transcribed as part of the ribosomal RNA primary transcript by read-through of the first terminator. The sRNA genes (rrA, rrB and rrF) from the three operons (rrnA, rrnB and rrnD) are more than 98% identical, and pull-down experiments show that their transcripts interact with Hfq and CsrA. Deletion of rrA, B, F, as well as overexpression of rrB, only modestly affect known CsrA-regulated phenotypes like biofilm formation, pgaA translation and glgC translation, and the role of the sRNAs in vivo may not yet be fully understood. Since RrA, B, F are short-lived and transcribed along with the ribosomal RNA components, their concentration reflect growth-rate regulation at the ribosomal RNA promoters and they could function to fine-tune other growth-phase-dependent processes in the cell. The primary and secondary structure of these small RNAs are conserved among species belonging to different genera of Enterobacteriales.
Collapse
Affiliation(s)
| | - Mette Kongstad
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Erik Holmqvist
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Birgitte Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | | |
Collapse
|
44
|
Meseguer S. MicroRNAs and tRNA-Derived Small Fragments: Key Messengers in Nuclear-Mitochondrial Communication. Front Mol Biosci 2021; 8:643575. [PMID: 34026824 PMCID: PMC8138316 DOI: 10.3389/fmolb.2021.643575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondria are not only important as energy suppliers in cells but also participate in other biological processes essential for cell growth and survival. They arose from α-proteobacterial predecessors through endosymbiosis and evolved transferring a large part of their genome to the host cell nucleus. Such a symbiotic relationship has been reinforced over time through increasingly complex signaling mechanisms between the host cell and mitochondria. So far, we do not have a complete view of the mechanisms that allow the mitochondria to communicate their functional status to the nucleus and trigger adaptive and compensatory responses. Recent findings place two classes of small non-coding RNAs (sncRNAs), microRNAs (miRNAs), and tRNA-derived small fragments, in such a scenario, acting as key pieces in the mitochondria-nucleus cross-talk. This review highlights the emerging roles and the interrelation of these sncRNAs in different signaling pathways between mitochondria and the host cell. Moreover, we describe in what way alterations of these complex regulatory mechanisms involving sncRNAs lead to diseases associated with mitochondrial dysfunction. In turn, these discoveries provide novel prognostic biomarker candidates and/or potential therapeutic targets.
Collapse
Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| |
Collapse
|
45
|
Li J, Jin L, Gao Y, Gao P, Ma L, Zhu B, Yin X, Sui S, Chen S, Jiang Z, Zhu C. Low expression of tRF-Pro-CGG predicts poor prognosis in pancreatic ductal adenocarcinoma. J Clin Lab Anal 2021; 35:e23742. [PMID: 33675071 PMCID: PMC8128309 DOI: 10.1002/jcla.23742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/29/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND & AIMS tRFs (tRNA-derived RNA fragments) have been reported to facilitate cancer progression in multiple cancers. However, their role in pancreatic ductal adenocarcinoma (PDAC) remains to be determined. In this study, we mainly investigated the expression of tRF-Pro-CGG in pancreatic ductal adenocarcinoma and evaluated its relationship with the clinicopathology and survival time of patients. METHODS 37 cases of pancreatic ductal adenocarcinoma, and 15 cases of normal pancreatic tissues were collected which were resected by surgery from January 2017 to June 2020 from the Department of Hepatobiliary and Pancreatic surgery of Changzhou second people's Hospital. The expression of tRF-Pro-CGG in paraffin-embedded tissues was detected by fluorescence in situ hybridization (FISH). The clinical data including age, sex, tumor location, tumor diameter, tumor clinical stage (TNM stage), depth of invasion, regional lymph node metastasis, serum CA199, and serum CEA were collected and analyzed retrospectively, whether the expression tRF-Pro-CGG was correlation with the pathological parameters and clinical outcomes of patients. RESULTS The expression level of tRF-Pro-CGG was significantly downregulated in PDAC and associated with an advanced TNM stage (P=0.000) and the N stage (P=0.000) of patients. More importantly, low tRF-Pro-CGG expression predicted poor survival in PDAC patients (P=0.003). CONCLUSIONS TRF-Pro-CGG is under-expressed in PDAC and is associated with short clinical survival and poor prognosis. tRF-Pro-CGG is an independent prognostic factor, which highlights its role as a potential biomarker for PDAC progression and therapy.
Collapse
Affiliation(s)
- Jun Li
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Lei Jin
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Yuan Gao
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Peng Gao
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Le Ma
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Bei Zhu
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Xu Yin
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Shizhen Sui
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | - Shuai Chen
- Dalian Medical UniversityDalianChina
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| | | | - Chunfu Zhu
- Department of General SurgeryThe Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical UniversityChangzhouChina
| |
Collapse
|
46
|
Kayesh MEH, Hashem MA, Tsukiyama-Kohara K. Toll-Like Receptor and Cytokine Responses to Infection with Endogenous and Exogenous Koala Retrovirus, and Vaccination as a Control Strategy. Curr Issues Mol Biol 2021; 43:52-64. [PMID: 33946297 PMCID: PMC8928999 DOI: 10.3390/cimb43010005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
Koala populations are currently declining and under threat from koala retrovirus (KoRV) infection both in the wild and in captivity. KoRV is assumed to cause immunosuppression and neoplastic diseases, favoring chlamydiosis in koalas. Currently, 10 KoRV subtypes have been identified, including an endogenous subtype (KoRV-A) and nine exogenous subtypes (KoRV-B to KoRV-J). The host’s immune response acts as a safeguard against pathogens. Therefore, a proper understanding of the immune response mechanisms against infection is of great importance for the host’s survival, as well as for the development of therapeutic and prophylactic interventions. A vaccine is an important protective as well as being a therapeutic tool against infectious disease, and several studies have shown promise for the development of an effective vaccine against KoRV. Moreover, CRISPR/Cas9-based genome editing has opened a new window for gene therapy, and it appears to be a potential therapeutic tool in many viral infections, which could also be investigated for the treatment of KoRV infection. Here, we discuss the recent advances made in the understanding of the immune response in KoRV infection, as well as the progress towards vaccine development against KoRV infection in koalas.
Collapse
Affiliation(s)
- Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan; (M.E.H.K.); (M.A.H.)
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal 8210, Bangladesh
| | - Md Abul Hashem
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan; (M.E.H.K.); (M.A.H.)
- Department of Health, Chattogram City Corporation, Chattogram 4000, Bangladesh
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan; (M.E.H.K.); (M.A.H.)
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Correspondence: ; Tel.: +81-99-285-3589
| |
Collapse
|
47
|
Li HM, Tan X, Zhang S, Yao J, Li HG. Transfer- or 'transmission'-RNA fragments? The roles of tsRNAs in the reproductive system. Mol Hum Reprod 2021; 27:6218776. [PMID: 33837423 DOI: 10.1093/molehr/gaab026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
Transfer-RNAs (tRNAs) help ribosomes decode mRNAs and synthesize proteins; however, tRNA fragments produced under certain conditions, known as tRNA-derived small RNAs (tsRNAs), have been found to play important roles in pathophysiological processes. In the reproductive system, tsRNAs are abundant in gametes and embryos and at the maternal-fetal interface, as well as in microvesicles like epididymosomes, seminal plasma exosomes, and syncytiotrophoblast-derived extracellular vesicles. tsRNAs can affect gamete cell maturation, zygote activation, and early embryonic development. tsRNAs can transmit epigenetic information to later generations. In particular, exposure to environmental factors such as nutrition, isoproterenol, and poly(I:C) may allow tsRNAs to transfer information to the gametes or placenta to alter offspring phenotype. The underlying mechanisms of tsRNAs action include transposon silencing, translation regulation, and target mRNA degradation. Herein, we review the currently reported tsRNAs in the reproductive system, their validated functions, and potential roles. A better understanding of this field may help to provide useful recommendations or develop strategies to increase fertility and conception of healthy babies.
Collapse
Affiliation(s)
- Hui-Min Li
- Guilin Medical University, Guilin, P.R. China
| | - Xia Tan
- Center of Reproductive Medicine, Wuhan Union Hospital, Wuhan, P.R. China
| | - Shun Zhang
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Jun Yao
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Hong-Gang Li
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,Genetic Laboratory, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, P.R. China
| |
Collapse
|
48
|
Kim Y, Mensah GA, Al Sharif S, Pinto DO, Branscome H, Yelamanchili SV, Cowen M, Erickson J, Khatkar P, Mahieux R, Kashanchi F. Extracellular Vesicles from Infected Cells Are Released Prior to Virion Release. Cells 2021; 10:cells10040781. [PMID: 33916140 PMCID: PMC8066806 DOI: 10.3390/cells10040781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/29/2022] Open
Abstract
Here, we have attempted to address the timing of EV and virion release from virally infected cells. Uninfected (CEM), HIV-1-infected (J1.1), and human T cell leukemia virus-1 (HTLV-1)-infected (HUT102) cells were synchronized in G0. Viral latency was reversed by increasing gene expression with the addition of serum-rich media and inducers. Supernatants and cell pellets were collected post-induction at different timepoints and assayed for extracellular vesicle (EV) and autophagy markers; and for viral proteins and RNAs. Tetraspanins and autophagy-related proteins were found to be differentially secreted in HIV-1- and HTLV-1-infected cells when compared with uninfected controls. HIV-1 proteins were present at 6 h and their production increased up to 24 h. HTLV-1 proteins peaked at 6 h and plateaued. HIV-1 and HTLV-1 RNA production correlated with viral protein expression. Nanoparticle tracking analysis (NTA) showed increase of EV concentration over time in both uninfected and infected samples. Finally, the HIV-1 supernatant from the 6-h samples was found not to be infectious; however, the virus from the 24-h samples was successfully rescued and infectious. Overall, our data indicate that EV release may occur prior to viral release from infected cells, thereby implicating a potentially significant effect of EVs on uninfected recipient cells prior to subsequent viral infection and spread.
Collapse
Affiliation(s)
- Yuriy Kim
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Gifty A. Mensah
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Sarah Al Sharif
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Daniel O. Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Heather Branscome
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Sowmya V. Yelamanchili
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Pooja Khatkar
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
| | - Renaud Mahieux
- International Center for Research in Infectiology, Retroviral Oncogenesis Laboratory, INSERM U1111-Université Claude Bernard Lyon 1, Ecole Normale Superieure de Lyon, Université de Lyon, Fondation Pour La Recherche Médicale, Labex Ecofect, 69007 Lyon, France;
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (Y.K.); (G.A.M.); (S.A.S.); (D.O.P.); (H.B.); (M.C.); (J.E.); (P.K.)
- Correspondence: ; Tel.: +703-993-9160; Fax: +703-993-7022
| |
Collapse
|
49
|
Meng L, Jiang L, Chen J, Ren H, Gao Z, Wu F, Wen Y, Yang L. Transfer RNA-derived fragment tRF-28-QSZ34KRQ590K in plasma exosomes may be a potential biomarker for atopic dermatitis in pediatric patients. Exp Ther Med 2021; 21:489. [PMID: 33790998 DOI: 10.3892/etm.2021.9920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 01/28/2021] [Indexed: 12/31/2022] Open
Abstract
Atopic dermatitis (AD) is a common chronic relapsing inflammatory disease. There is substantial evidence suggesting that noncoding RNAs have indispensable roles in the pathogenesis of AD. Exosomal transfer RNA-derived fragments (tRFs) have been identified as potential biomarkers for various disorders. However, the role of tRFs in AD has remained to be elucidated, which was thus the aim of the present study. Plasma samples from 23 pediatric patients with AD and 23 healthy controls were collected. Exosomes were successfully isolated from plasma according to the manufacturer's protocol. Small RNA sequencing was performed in 3 patients with AD and 3 controls, and 135 significantly differentially expressed plasma exosomal tRFs were identified, including 36 upregulated and 99 downregulated tRFs. Using the miRanda and RNAhybrid databases, 58,227 target genes of these 135 differentially expressed tRFs were predicted. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggested that these target genes of tRFs are involved in multiple functions and pathways associated with AD. Downregulation of tRF-28-QSZ34KRQ590K and tRF-33-Q99P9P9NH57SD3 were validated in 20 patients with AD and 20 controls by reverse transcription-quantitative PCR and tRF-28-QSZ34KRQ590K exhibited significance in the receiver operating characteristic curve analysis. The present study was the first to provide a tRF profile in AD and implied that plasma exosomal tRF-28-QSZ34KRQ590K may be a potential biomarker for pediatric patients with AD. The present study enhanced the understanding of the pathogenesis of AD and provided a novel marker for the diagnosis and targeted treatment of AD.
Collapse
Affiliation(s)
- Li Meng
- Department of Dermatological Mycology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Long Jiang
- Department of Dermatological Surgery, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Jian Chen
- Department of Dermatological Mycology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Hongjin Ren
- Department of Dermatological Mycology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Zhiqin Gao
- Department of Dermatological Mycology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Fei Wu
- Department of Dermatological Pathology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Yiyang Wen
- Department of Dermatological Mycology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| | - Lianjuan Yang
- Department of Dermatological Mycology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, P.R. China
| |
Collapse
|
50
|
Huang P, Tu B, Liao HJ, Huang FZ, Li ZZ, Zhu KY, Dai F, Liu HZ, Zhang TY, Sun CZ. Elevation of plasma tRNA fragments as a promising biomarker for liver fibrosis in nonalcoholic fatty liver disease. Sci Rep 2021; 11:5886. [PMID: 33723340 PMCID: PMC7961013 DOI: 10.1038/s41598-021-85421-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Fibrotic tissue remodelling in nonalcoholic fatty liver disease (NAFLD) will probably emerge as the leading cause of end-stage liver disease in the coming decades, but the ability to diagnose liver fibrosis in NAFLD patients noninvasively is limited. The abnormal expression of tRNA-derived small RNA (tsRNA) in plasma provides a novel idea for noninvasive diagnosis of various diseases, however, the relationship between tsRNAs and NAFLD is still unknown. Here, we took advantage of small RNA-Seq technology to profile tsRNAs in NAFLD patients and found the ubiquitous presence of hepatic tsRNAs secreted into circulating blood. Verification in a cohort of 114 patients with NAFLD and 42 patients without NAFLD revealed that three tsRNAs (tRF-Val-CAC-005, tiRNA-His-GTG-001, and tRF-Ala-CGC-006) were significantly elevated in the plasma of NAFLD patients, and the expression level are associated with NAFLD activity score (calculated from 0 to 8) and fibrosis stage (scored from 0 to 4). In mouse models, we further found that increased plasma levels of these three tsRNAs were positively correlated with the degree of liver fibrosis. Our study potentially identifies a new class of NAFLD biomarkers and reveal the possible existence of tsRNAs in the blood that can be used to predict fibrogenesis risk in patients diagnosed with NAFLD.
Collapse
Affiliation(s)
- Peng Huang
- Department of General Surgery, Xiangya Hospital Central South University, No. 87 Xiangya Road, Changsha, 410008, Hunan, People's Republic of China
| | - Biao Tu
- Department of General Surgery, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Hui-Jun Liao
- Department of General Surgery, Chenzhou No. 1 People's Hospital, No. 102 Luojiajing Road, Chenzhou, 423000, Hunan, People's Republic of China
| | - Fei-Zhou Huang
- Department of General Surgery, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Zhen-Zhou Li
- Emergency Department, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Kuang-Ye Zhu
- Department of General Surgery, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Feng Dai
- Department of General Surgery, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Huai-Zheng Liu
- Emergency Department, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Tian-Yi Zhang
- Emergency Department, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Chuan-Zheng Sun
- Emergency Department, Central South University Third Xiangya Hospital, No. 138 Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| |
Collapse
|