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Zhang L, Liu J, Hou Y. Classification, function, and advances in tsRNA in non-neoplastic diseases. Cell Death Dis 2023; 14:748. [PMID: 37973899 PMCID: PMC10654580 DOI: 10.1038/s41419-023-06250-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
tRNA-derived small RNAs (tsRNAs) are non-coding small RNAs produced by specific endonucleases following the processing and splicing of precursor or mature tRNAs upon starvation, oxidative stress, hypoxia, and other adverse conditions. tRNAs are classified into two major categories, tRNA fragments (tRFs) and tRNA-derived stress-induced small RNAs (tiRNAs), based on differences in splice sites. With the development of high-throughput sequencing technologies in recent years, tsRNAs have been found to have important biological functions, including inhibition of apoptosis, epigenetic regulation, cell-cell communication, translation, and regulation of gene expression. Additionally, these molecules have been found to be aberrantly expressed in various diseases and to be involved in several pathological processes. In this article, the classification and nomenclature, biological functions, and potential use of tsRNAs as diagnostic biomarkers and therapeutic targets in non-neoplastic diseases are reviewed. Although tsRNA research is at its infancy, their potential in the treatment of non-tumor diseases warrants further investigation.
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Affiliation(s)
- Liou Zhang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jie Liu
- Translational Research Experiment Department, Science Experiment Center, China Medical University, Shenyang, China.
| | - Yang Hou
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Gong M, Deng Y, Xiang Y, Ye D. The role and mechanism of action of tRNA-derived fragments in the diagnosis and treatment of malignant tumors. Cell Commun Signal 2023; 21:62. [PMID: 36964534 PMCID: PMC10036988 DOI: 10.1186/s12964-023-01079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/13/2023] [Indexed: 03/26/2023] Open
Abstract
Cancer is a leading cause of morbidity and death worldwide. While various factors are established as causing malignant tumors, the mechanisms underlying cancer development remain poorly understood. Early diagnosis and the development of effective treatments for cancer are important research topics. Transfer RNA (tRNA), the most abundant class of RNA molecules in the human transcriptome, participates in both protein synthesis and cellular metabolic processes. tRNA-derived fragments (tRFs) are produced by specific cleavage of pre-tRNA and mature tRNA molecules, which are highly conserved and occur widely in various organisms. tRFs were initially thought to be random products with no physiological function, but have been redefined as novel functional small non-coding RNA molecules that help to regulate RNA stability, modulate translation, and influence target gene expression, as well as other biological processes. There is increasing evidence supporting roles for tRFs in tumorigenesis and cancer development, including the regulation of tumor cell proliferation, invasion, migration, and drug resistance. Understanding the regulatory mechanisms by which tRFs impact these processes has potential to inform malignant tumor diagnosis and treatment. Further, tRFs are expected to become new biological markers for early diagnosis and prognosis prediction in patients with tumors, as well as a targets for precision cancer therapies. Video abstract.
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Affiliation(s)
- Mengdan Gong
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yongqin Deng
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yizhen Xiang
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Dong Ye
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China.
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Chen S, Zhang X, Meng K, Sun Y, Shu R, Han Y, Feng Q, Li Z, Yang P, Liang J. Urinary exosome tsRNAs as novel markers for diagnosis and prediction of lupus nephritis. Front Immunol 2023; 14:1077645. [PMID: 36845141 PMCID: PMC9946979 DOI: 10.3389/fimmu.2023.1077645] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Objective Lupus nephritis (LN) is one of the most severe organ manifestations of systemic lupus erythematosus (SLE). Early identification of renal disease in SLE is important. Renal biopsy is currently recognized as the gold standard for diagnosing LN, however, it is invasive and inconvenient for dynamic monitoring. Urine has been considered more promising and valuable than blood in identifying inflamed kidney tissue. Here, we determine whether the signatures of tRNA-derived small noncoding RNA (tsRNA) in urinary exosomes can serve as novel biomarkers for the diagnosis of LN. Methods tsRNA sequencing was performed in exosome extracted from pooled urine of 20 LN patients and 20 SLE without LN, and the top 10 upregulated tsRNAs were screened as candidate markers of LN. The candidate urinary exosomal tsRNAs were primarily elected by TaqMan probe-based quantitative reverse transcription-PCR (RT-PCR) in 40 samples (20 LN and 20 SLE without LN) in the training phase. In the validation phase, selected tsRNAs from the training phase were further confirmed in a larger cohort (54 LN patients and 39 SLE without LN). Receiver operating characteristic curve (ROC) analysis was conducted to evaluate the diagnostic efficacy. Results Upregulated levels of tRF3-Ile-AAT-1 and tiRNA5-Lys-CTT-1 in the urinary exosomes were observed in LN compared with SLE without LN (P < 0.0001 and P < 0.001) and healthy controls (P < 0.01 and P < 0.01), with the area under the curve (AUC) of 0.777 (95% CI: 0.681-0.874, sensitivity 79.63%, specificity 66.69%) and 0.715 (95% CI: 0.610-0.820, sensitivity 66.96%, specificity 76.92%) for discriminating LN from SLE without LN patients. SLE patients with mild activity and moderate to severe activity had higher levels of urinary exosome derived tRF3-Ile AAT-1 (P = 0.035 and P < 0.001) and tiRNA5-Lys-CTT-1 (P = 0.021 and P < 0.001) compared with patients with no activity. Moreover, bioinformatics analysis revealed that both of the tsRNAs regulate the immune process by modulating metabolism and signal pathway. Conclusion In this study, we demonstrated that urinary exosome tsRNAs can be served as noninvasive biomarkers for the efficient diagnosis and prediction of nephritis in SLE.
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Affiliation(s)
- Shanshan Chen
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiaoshan Zhang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Kaifang Meng
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yifan Sun
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Ruilu Shu
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yan Han
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qingxiu Feng
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhiyang Li
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,*Correspondence: Jun Liang, ; Zhiyang Li, ; Ping Yang,
| | - Ping Yang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,*Correspondence: Jun Liang, ; Zhiyang Li, ; Ping Yang,
| | - Jun Liang
- Department of Rheumatology and Immunology, Affiliated Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China,*Correspondence: Jun Liang, ; Zhiyang Li, ; Ping Yang,
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Liang J, Xie F, Feng J, Huang C, Shen J, Han Z, Luo W, He J, Chen H. Progress in the application of body fluid and tissue level mRNAs-non-coding RNAs for the early diagnosis and prognostic evaluation of systemic lupus erythematosus. Front Immunol 2022; 13:1020891. [PMID: 36325322 PMCID: PMC9618628 DOI: 10.3389/fimmu.2022.1020891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
The diagnosis and differential classification of systemic lupus erythematosus (SLE) is difficult, especially in patients with early-onset SLE who are susceptible to systemic multi-organ damage and serious complications and have difficulties in individualized treatment. At present, diagnosis is based mainly on clinical manifestations and the detection of serological antinuclear antibodies. The pathogenesis of SLE involves multiple factors, is clinically heterogeneous, and lacks specific biomarkers. Therefore, it is necessary to identify new biomarkers for the diagnosis and subtype classification of SLE. Non-coding RNAs (ncRNAs) are composed of microRNAs, long non-coding RNAs, small nucleolar RNAs, circular RNAs, and transfer RNAs. They play an important role in the occurrence and development of diseases and are used widely in the early diagnosis and prognosis of autoimmune diseases. In this review, we focus on the research progress in the diagnosis and prognostic assessment of SLE using humoral to tissue level ncRNAs.
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Affiliation(s)
- Jiabin Liang
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
- Graduate School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fangmei Xie
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Jie Feng
- Radiology Department of Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chen Huang
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Jian Shen
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Zeping Han
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Wenfeng Luo
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Jinhua He
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
- *Correspondence: Hanwei Chen, ; Jinhua He,
| | - Hanwei Chen
- Central Laboratory of Guangzhou Panyu Central Hospital, Guangzhou, China
- Radiology Department of Panyu Health Management Center (Panyu Rehabilitation Hospital), Guangzhou, China
- *Correspondence: Hanwei Chen, ; Jinhua He,
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Shen J, Zhang M, Peng M. Progress of exosome research in systemic lupus erythematosus. Cytokine X 2022; 4:100066. [PMID: 35656386 PMCID: PMC9151726 DOI: 10.1016/j.cytox.2022.100066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/27/2022] [Accepted: 05/14/2022] [Indexed: 02/08/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a global chronic autoimmune disease that invades most organs of the body, with kidney injury being the most prominent feature. Exosomes are extracellular vesicles that carry a variety of proteins, lipids and genetic material, participate in the exchange of local and intersystem information, and play an important immunoregulatory role in a variety of autoimmune diseases. At the same time, the use of exosomes as disease biomarkers and drug delivery carriers also shows great application prospects. This article reviews current progress in the application of exosomes in the pathogenesis, diagnosis and treatment of SLE.
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Key Words
- CfDNA, Circulating free DNA
- Diagnostic role
- Exosomes
- HMGB1, High mobility group box 1
- Immunomodulation
- LN, Lupus nephritis
- MSC, Mesenchymal stem cells (MSC)
- MiRNAs, Microribonucleic acids
- Microribonucleic acid
- PAMPs, Pathogen-associated molecular patterns
- PDCs, Plasmacytoid dendritic cells
- SLE, Systemic lupus erythematosus
- Systemic lupus erythematosus
- TLR, Recombinant Toll Like Receptor
- Therapeutic potential
- Treg, Regulatory T cells
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Affiliation(s)
- Jie Shen
- Weifang Medical University, Weifang 261053, China
| | - Mengyu Zhang
- Weifang Medical University, Weifang 261053, China
| | - Meiyu Peng
- Weifang Medical University, Weifang 261053, China
- Department of Immunology, School of Basic Medical Sciences, Weifang Medical University, Weifang 261053, China
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tiRNAs: Insights into Their Biogenesis, Functions, and Future Applications in Livestock Research. Noncoding RNA 2022; 8:ncrna8030037. [PMID: 35736634 PMCID: PMC9231384 DOI: 10.3390/ncrna8030037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) belong to a group of transfer ribonucleic acid (tRNA)-derived fragments that have recently gained interest as molecules with specific biological functions. Their involvement in the regulation of physiological processes and pathological phenotypes suggests molecular roles similar to those of miRNAs. tsRNA biogenesis under specific physiological conditions will offer new perspectives in understanding diseases, and may provide new sources for biological marker design to determine and monitor the health status of farm animals. In this review, we focus on the latest discoveries about tsRNAs and give special attention to molecules initially thought to be mainly associated with tRNA-derived stress-induced RNAs (tiRNAs). We present an outline of their biological functions, offer a collection of useful databases, and discuss future research perspectives and applications in livestock basic and applied research.
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Zheng C, Xie L, Qin H, Liu X, Chen X, Lv F, Wang L, Zhu X, Xu J. The Role of Extracellular Vesicles in Systemic Lupus Erythematosus. Front Cell Dev Biol 2022; 10:835566. [PMID: 35309937 PMCID: PMC8924487 DOI: 10.3389/fcell.2022.835566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Extracellular Vesicles (EVs) are small vesicles that can be actively secreted by most cell types into the extracellular environment. Evidence indicates that EVs can carry microRNAs (miRNAs), long non-coding RNAs (lncRNAs), tRNA-derived small RNAs (tsRNAs), proteins, and lipids to target cells or tissue organizations. Latest studies show that EVs play a vital role in the immune modulation and may contribute to the pathogenesis of autoimmune diseases. Systemic lupus erythematosus (SLE) is a common autoimmune disease characterized by abnormal T cell activation and sustained production of autoantibodies against self-antigens, resulting in inflammation and damage to multiple systems. Pathogenic mechanisms of SLE, however, are still not well understood. In this review, we summarize the latest research advances on the functions and mechanisms of EVs, and its role in the pathogenesis, diagnosis, and treatment of SLE.
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Affiliation(s)
| | - Lin Xie
- *Correspondence: Lin Xie, ; Xiaohua Zhu, ; Jinhua Xu,
| | | | | | | | | | | | - Xiaohua Zhu
- *Correspondence: Lin Xie, ; Xiaohua Zhu, ; Jinhua Xu,
| | - Jinhua Xu
- *Correspondence: Lin Xie, ; Xiaohua Zhu, ; Jinhua Xu,
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Differential expression profiles and function prediction of tRNA-derived fragments in fibrous dysplasia. Arch Oral Biol 2022; 135:105347. [DOI: 10.1016/j.archoralbio.2022.105347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/05/2021] [Accepted: 01/05/2022] [Indexed: 01/01/2023]
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Liu B, Cao J, Wang X, Guo C, Liu Y, Wang T. Deciphering the tRNA-derived small RNAs: origin, development, and future. Cell Death Dis 2021; 13:24. [PMID: 34934044 PMCID: PMC8692627 DOI: 10.1038/s41419-021-04472-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 01/04/2023]
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs), a novel category of small noncoding RNAs, are enzymatically cleaved from tRNAs. Previous reports have shed some light on the roles of tsRNAs in the development of human diseases. However, our knowledge about tsRNAs is still relatively lacking. In this paper, we review the biogenesis, classification, subcellular localization as well as action mechanism of tsRNAs, and discuss the association between chemical modifications of tRNAs and the production and functions of tsRNAs. Furthermore, using immunity, metabolism, and malignancy as examples, we summarize the molecular mechanisms of tsRNAs in diseases and evaluate the potential of tsRNAs as new biomarkers and therapeutic targets. At the same time, we compile and introduce several resource databases that are currently publicly available for analyzing tsRNAs. Finally, we discuss the challenges associated with research in this field and future directions.
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Affiliation(s)
- Bowen Liu
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China.
| | - Jinling Cao
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China
| | - Xiangyun Wang
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China
| | - Chunlei Guo
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, Xinxiang Medical University, 453003, Xinxiang, Henan, PR China
| | - Yunxia Liu
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Tianjiao Wang
- State Key Laboratory of Medicinal Chemical Biology, Department of Biochemistry, College of Life Sciences, Nankai University, 300071, Tianjin, PR China
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Liang Y, Zhang J, Qiu W, Chen B, Zhou Y, Chen X, Shentu Y, Zhang H, Bai Y, Chen C. Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis. Lupus 2021; 30:2248-2255. [PMID: 34923866 DOI: 10.1177/09612033211061482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.
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Affiliation(s)
- Yan Liang
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Ji Zhang
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Wenxian Qiu
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Bo Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Ying Zhou
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Xiaoqian Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Yangping Shentu
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
| | - Yongheng Bai
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chaosheng Chen
- Department of Nephrology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Chronic Kidney Disease, Wenzhou Medical University, Wenzhou, China
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Dou R, Zhang X, Xu X, Wang P, Yan B. Mesenchymal stem cell exosomal tsRNA-21109 alleviate systemic lupus erythematosus by inhibiting macrophage M1 polarization. Mol Immunol 2021; 139:106-114. [PMID: 34464838 DOI: 10.1016/j.molimm.2021.08.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/09/2021] [Accepted: 08/22/2021] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with M1-type macrophage activation. Mesenchymal stem cells (MSCs) therapies have shown promise in models of pathologies relevant to SLE, while the function and mechanism of MSC-derived exosomes (MSC-exo) were still unclear. We aimed to interrogate the effect of MSC-exo on M1-type polarization of macrophage and investigate mechanisms underlying MSC-exo. Exosomes were isolated from MSC and the effect of MSC-exo on macrophage polarization was evaluated. The key tRNA-derived fragments (tRFs) carried by exosomes were identified by small RNA sequencing and verified in clinical samples. The effect of exosomal-tRFs on macrophage polarization was examined. In this study, MSC-exo dramatically suppressed expression of M1 markers, and reduced the levels of TNF-α and IL-1β, while increased M2 markers in macrophages. A total of 243 differently expressed tRFs (DEtRFs) were identified between MSC-exo treated and untreated macrophage, among which 103 DEtRFs were up-regulated in response to MSC-exo treatment, including tsRNA-21109. The target genes of tsRNA-21109 were mainly enriched in DNA transcription-related GO function, and mainly involved in inflammatory-related pathways, including Rap1, Ras, Hippo, Wnt, MAPK, TGF-beta signaling pathway. The tsRNA-21109 was lowly expressed in clinical samples and was associated with the patient data in SLE. Compared to the normal MSC-exo, the tsRNA-21109-privative MSC-exo up-regulated M1 marker (CD80, NOS2, MCP1) and down-regulated M2 marker (CD206, ARG1, MRC2), also increased the levels of TNF-α and IL-1β in macrophages. Western blot and immunofluorescence confirmed that the proportion of CD80/ARG-1 was increased in macrophages treated with tsRNA-21109-privatived MSC-exo compared to that with control MSC-exo. In conclusion, MSC-exo inhibited the M1-type polarization of macrophages, possibly through transferring tsRNA-21109, which may develop as a novel therapeutic target for SLE.
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Affiliation(s)
- Rui Dou
- Department of Blood Transfusion, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China.
| | - Xiulei Zhang
- Department of Microbiome Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China.
| | - Xiangdong Xu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
| | - Pei Wang
- Department of Rheumatology and Immunology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China.
| | - Beizhan Yan
- Department of Blood Transfusion, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, Henan Province, China.
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12
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Zhang J, Li L, Luo L, Yang X, Zhang J, Xie Y, Liang R, Wang W, Lu S. Screening and potential role of tRFs and tiRNAs derived from tRNAs in the carcinogenesis and development of lung adenocarcinoma. Oncol Lett 2021; 22:506. [PMID: 33986867 PMCID: PMC8114470 DOI: 10.3892/ol.2021.12767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Accumulating evidence has indicated that a group of novel molecules, known as transfer RNA (tRNA)-derived fragments (tRFs) and tRNA halves (tiRNAs), which are derived from tRNAs, serve an essential role in numerous types of human disease, in particular solid tumors. However, to the best of our knowledge, the underlying mechanisms of the effect of tRFs and tiRNAs in lung adenocarcinoma have not been reported. The present study aimed to determine the differential expression levels of tRFs and tiRNAs in lung adenocarcinoma and adjacent tissues using a NextSeq system, and further investigated their potential target genes via bioinformatics analysis. Kyoto Encyclopedia of Genes and Genomes signaling pathway and Gene Ontology functional term enrichment analyses were performed to investigate the function of these target genes in the occurrence and development of lung adenocarcinoma. In patients with lung adenocarcinoma, 338 types of tRFs and tiRNAs were detected via sequencing, 284 of which were not previously reported in the tRF database. Compared with the adjacent tissues, 17 types of tRFs and tiRNAs comprising 34 subtypes were found to be abnormally expressed in lung adenocarcinoma tissues, 20 of which were upregulated and 14 downregulated. Reverse transcription-quantitative PCR verification revealed that the expression levels of tiRNA-Lys-CTT-002, tRF-Val-CAC-010 and tRF-Val-CAC-011 were significantly upregulated, while those of tRF-Ser-TGA-005 were downregulated in lung adenocarcinoma tissues. Bioinformatics analysis identified that tRF-Ser-TGA-005 participated in the 'cellular response to transforming growth factor β stimulus' and tRF-Val-CAC-010 and tRF-Val-CAC-011 participated in the 'Hedgehog signaling pathway'. In conclusion, the results of the present study suggested that tRFs and tiRNAs may be closely associated with the pathogenesis and development of lung adenocarcinoma, providing a novel insight for further studies into lung adenocarcinoma.
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Affiliation(s)
- Jinhua Zhang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Linhui Li
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Lilin Luo
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Xuantao Yang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Juanjuan Zhang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Yuxin Xie
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Rui Liang
- Department of Pathology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Wanpu Wang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, P.R. China
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13
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Kuscu C, Kiran M, Mohammed A, Kuscu C, Satpathy S, Wolen A, Bardhi E, Bajwa A, Eason JD, Maluf D, Mas V, Akalin E. Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy. Int J Mol Sci 2021; 22:ijms22126218. [PMID: 34207555 PMCID: PMC8226568 DOI: 10.3390/ijms22126218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transplant glomerulopathy develops through multiple mechanisms, including donor-specific antibodies, T cells and innate immunity. This study investigates circulating small RNA profiles in serum samples of kidney transplant recipients with biopsy-proven transplant glomerulopathy. Among total small RNA population, miRNAs were the most abundant species in the serum of kidney transplant patients. In addition, fragments arising from mature tRNA and rRNA were detected. Most of the tRNA fragments were generated from 5′ ends of mature tRNA and mainly from two parental tRNAs: tRNA-Gly and tRNA-Glu. Moreover, transplant patients with transplant glomerulopathy displayed a novel tRNA fragments signature. Gene expression analysis from allograft tissues demonstrated changes in canonical pathways related to immune activation such as iCos-iCosL signaling pathway in T helper cells, Th1 and Th2 activation pathway, and dendritic cell maturation. mRNA targets of down-regulated miRNAs such as miR-1224-5p, miR-4508, miR-320, miR-378a from serum were globally upregulated in tissue. Integration of serum miRNA profiles with tissue gene expression showed that changes in serum miRNAs support the role of T-cell mediated mechanisms in ongoing allograft injury.
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Affiliation(s)
- Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
- Correspondence: ; Tel.: +1-901-448-3162
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Akram Mohammed
- Center for Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Sarthak Satpathy
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Aaron Wolen
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Elissa Bardhi
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - James D. Eason
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Daniel Maluf
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Valeria Mas
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Enver Akalin
- Montefiore Medical Center, Abdominal Transplant Program, Albert Einstein College of Medicine, Bronx, NY 10467, USA;
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14
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Li L, Liu P, Wang R, Huang Y, Luo J, Jiao L, Tao Z, Zheng Y, Fan J, Zhao H, Han Z, Luo Y. Pathophysiological Significance of Neutrophilic Transfer RNA-Derived Small RNAs in Asymptomatic Moyamoya Disease. Cells 2021; 10:1086. [PMID: 34062929 PMCID: PMC8147334 DOI: 10.3390/cells10051086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding asymptomatic moyamoya disease (aMMD), for which treatment options are currently limited, is key to the development of therapeutic strategies that will slow down the progression of this disease, as well as facilitate the discovery of therapeutic targets for symptomatic MMD. Newly found transfer RNA-derived small RNAs (tsRNAs) perform potential regulatory functions in neovascularization, which is a well-known pathological manifestation of MMD. In this study, the neutrophilic tsRNA transcriptome in aMMD was profiled using next-generation RNA sequencing in five patients and five matched healthy subjects. A negative binominal generalized log-linear regression was used to identify differentially expressed (DE)-tsRNAs in aMMD. Gene Ontology and functional pathway analyses were used to identify biological pathways involved with the targeted genes of the DE-tsRNAs. Four tsRNAs were selected and validated using quantitative reverse transcription polymerase chain reaction. In total, 186 tsRNAs were DE between the two groups. Pathophysiological events, including immune response, angiogenesis, axon guidance, and metabolism adjustment, were enriched for the DE-tsRNAs. The expression levels of the four DE-tsRNAs were consistent with those in the neutrophilic transcriptome. These aberrantly expressed tsRNAs and their targeted pathophysiological processes provide a basis for potential future interventions for aMMD.
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Affiliation(s)
- Lingzhi Li
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
| | - Ping Liu
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
| | - Rongliang Wang
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100000, China
| | - Yuyou Huang
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
| | - Jichang Luo
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (J.L.); (L.J.)
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (J.L.); (L.J.)
| | - Zhen Tao
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100000, China
| | - Yangmin Zheng
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
| | - Junfen Fan
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100000, China
| | - Haiping Zhao
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100000, China
| | - Ziping Han
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
| | - Yumin Luo
- Department of Neurology, Institute of Cerebrovascular Diseases Research, Xuanwu Hospital, Capital Medical University, Beijing 100000, China; (L.L.); (P.L.); (R.W.); (Y.H.); (Z.T.); (Y.Z.); (J.F.); (H.Z.)
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Diseases, Beijing 100000, China
- Beijing Institute for Brain Disorders, Beijing 100000, China
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15
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Xie Y, Yao L, Yu X, Ruan Y, Li Z, Guo J. Action mechanisms and research methods of tRNA-derived small RNAs. Signal Transduct Target Ther 2020; 5:109. [PMID: 32606362 PMCID: PMC7326991 DOI: 10.1038/s41392-020-00217-4] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023] Open
Abstract
tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.
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Affiliation(s)
- Yaoyao Xie
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Lipeng Yao
- Ningbo College of Health Sciences, Ningbo, 315000, Zhejiang, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Yao Ruan
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Zhe Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, 315211, Ningbo, China.
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