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Li HM, Che X, Tong Z, Wei W, Teng C. A Novel Role for Protein Tyrosine Phosphatase 1B in Alleviating Chondrocyte Senescence. ACS OMEGA 2024; 9:27017-27029. [PMID: 38947824 PMCID: PMC11209688 DOI: 10.1021/acsomega.3c10313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/10/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024]
Abstract
Osteoarthritis (OA) is a kind of arthritis that impairs movement and causes joint discomfort. Recent research has demonstrated a connection between cellular senescence and the degenerative processes of OA chondrocytes. In yeast and human cells, protein tyrosine phosphatase 1B (PTP1B) knockdown prolongs longevity; however, the function of PTP1B in chondrocyte senescence has not been investigated. The goal of the current investigation was to evaluate PTP1B's contribution to human OA chondrocyte senescence. The function of PTP1B and cellular senescence in the onset of OA was investigated and confirmed by using a combination of bioinformatics techniques, clinical samples, and in vitro experimental procedures. The RNA sequencing data pertinent to the OA were obtained using the Gene Expression Omnibus database. Function enrichment analysis, protein-protein correlation analysis, the construction of the correlation regulatory network, and an investigation into possible connections between PTP1B and cellular senescence in OA were all carried out using various bioinformatic techniques. Compared with healthy cartilage, PTP1B expression was increased in OA cartilage. According to a Pearson correlation study, cellular senescence-related genes, including MAP2K1 and ABL1, were highly correlated with PTP1B expression levels in senescent chondrocytes. Furthermore, in vitro tests confirmed that PTP1B knockdown slowed cartilage degradation and prevented chondrocyte senescence in OA. In conclusion, we showed that PTP1B knockdown prevented the senescence of chondrocytes and prevented cartilage degradation in OA. These findings offer a fresh perspective on the pathophysiology of OA, opening up new avenues for OA clinical diagnosis and targeted treatment.
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Affiliation(s)
- Hui-Min Li
- Department
of Orthopedics, the Fourth Affiliated Hospital of School of Medicine,
and International School of Medicine, International Institutes of
Medicine, Zhejiang University, Yiwu, Zhejiang 322000, PR China
| | - Xianda Che
- Department
of Orthopedics, The Second Hospital of Shanxi
Medical University, Taiyuan, Shanxi 030001, PR China
| | - Zhicheng Tong
- Department
of Orthopedics, the Fourth Affiliated Hospital of School of Medicine,
and International School of Medicine, International Institutes of
Medicine, Zhejiang University, Yiwu, Zhejiang 322000, PR China
| | - Wei Wei
- Department
of Orthopedics, the Fourth Affiliated Hospital of School of Medicine,
and International School of Medicine, International Institutes of
Medicine, Zhejiang University, Yiwu, Zhejiang 322000, PR China
- Key
Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang
Province, Zhejiang University School of
Medicine, Hangzhou, Zhejiang 310000, PR China
| | - Chong Teng
- Department
of Orthopedics, the Fourth Affiliated Hospital of School of Medicine,
and International School of Medicine, International Institutes of
Medicine, Zhejiang University, Yiwu, Zhejiang 322000, PR China
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2
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Liu W, Li HM, Bai G. Integrated bioinformatics analysis of ferroptosis-related gene signature in inflammation and immunity in intervertebral disc degeneration. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-21. [PMID: 38531048 DOI: 10.1080/15257770.2024.2332403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
Ferroptosis has recently been shown to play a significant role in the progression of intervertebral disk degeneration (IDD), although the underlying mechanism is still unknown. The objective of this work was to use stringent bioinformatic techniques to clarify the crucial roles played by genes associated with ferroptosis in the emergence of IDD. For additional study, the microarray data pertinent to the IDD were acquired from the Gene Expression Omnibus database. The ferroptosis-related and IDD-related genes (FIDDRGs) were identified using a variety of bioinformatic techniques, which were also used to carry out function enrichment analysis, protein-protein correlation analysis, build the correlation regulatory network, and examine the potential connections between ferroptosis and immune abnormalities and inflammatory responses in IDD. A total of 16 FIDDRGs were eliminated for the further function enrichment analysis, and 10 hub FIDDRGs were chosen to build the correlation regulatory network. Hub FIDDRGs were shown to be highly associated with M2 macrophages and hub inflammatory response-related genes in IDD. When seen as a whole, our findings can give fresh perspectives on the mechanistic studies of ferroptosis in the emergence of IDD and new prospective targets for the therapeutic approaches.
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Affiliation(s)
- Wei Liu
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, PR China
| | - Hui-Min Li
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, PR China
| | - Guangchao Bai
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, PR China
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Zhang Q, Zhao X, Sun M, Dong D. Novel insights into transfer RNA-derived small RNA (tsRNA) in cardio-metabolic diseases. Life Sci 2024; 341:122475. [PMID: 38309576 DOI: 10.1016/j.lfs.2024.122475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Cardio-metabolic diseases, including a cluster of metabolic disorders and their secondary affections on cardiovascular physiology, are gradually brought to the forefront by researchers due to their high prevalence and mortality, as well as an unidentified pathogenesis. tRNA-derived small RNAs (tsRNAs), cleaved by several specific enzymes and once considered as some "metabolic junks" in the past, have been proved to possess numerous functions in human bodies. More interestingly, such a potential also seems to influence the progression of cardio-metabolic diseases to some extent. In this review, the biogenesis, classification and mechanisms of tsRNAs will be discussed based on some latest studies, and their relations with several cardio-metabolic diseases will be highlighted in sequence. Lastly, some future prospects, such as their clinical applications as biomarkers and therapeutic targets will also be mentioned, in order to provide researchers with a comprehensive understanding of the research status of tsRNAs as well as its association with cardio-metabolic diseases, thus presenting as a beacon to indicate directions for the next stage of study.
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Affiliation(s)
- Qingya Zhang
- Innovation Institute, China Medical University, Shenyang 110122, Liaoning, China
| | - Xiaopeng Zhao
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Mingli Sun
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Dan Dong
- College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning, China.
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Zhou Y, Wang Z, Zhou H, Tan W, Liu J, Cai Y, Huang Q, Li B, He Y, Yoshida S, Li Y. Identification and clinical significance of tsRNAs and miRNAs in PBMCs of treatment-requiring retinopathy of prematurity. Exp Eye Res 2023; 232:109518. [PMID: 37257714 DOI: 10.1016/j.exer.2023.109518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/23/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023]
Abstract
The aim of the study is to reveal the expression profiling and clinical significance of peripheral blood mononuclear cell (PBMC) tRNA-derived small RNAs (tsRNAs) and microRNAs (miRNAs) of premature infants with treatment-requiring retinopathy of prematurity (ROP). Significantly altered tsRNAs and miRNAs were screened using small RNA sequencing. RT-qPCR was used to verify the altered RNAs identified by small RNA transcriptomics. The target genes, their enriched functions, and possibly involved signaling pathways were identified by bioinformatics analyses. According to the small RNA sequencing, 125 tsRNAs and 205 miRNAs were significantly altered in PBMCs obtained from infants with treatment-requiring ROP compared with the premature controls without retinopathy. We preliminarily validated the significant alterations of 6 tsRNAs and 9 miRNAs. The target genes for those tsRNAs were enriched for cellular macromolecule metabolic process, intracellular anatomical structure, transcription regulatory region nucleic acid binding, and Th17 cell differentiation; those of the altered miRNAs were enriched for the developmental process, cell junction, DNA-binding transcription activator activity, and FoxO signaling pathway. By verification with the extended sample size, we identified tsRNAs and miRNAs that could be potential biomarkers with clinical values. The study recognized the alterations and clinical significance of changed tsRNA/miRNA profiles in PBMCs from premature infants with ROP. These significantly altered tsRNAs and miRNAs might be useful as potential diagnostic biomarkers and molecular targets for treatment-requiring ROP.
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Affiliation(s)
- Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Zicong Wang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Haixiang Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Jie Liu
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Yuting Cai
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Qian Huang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Bingyan Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Yan He
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China
| | - Shigeo Yoshida
- Department of Ophthalmology, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yun Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, 410011, China.
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5
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Wu J, Cai X, Lu Y, Shen Y, Shen Z, Lyv Q. Plasma tRF-16-79MP9PD and tRF-28-OB1690PQR304 as potential biomarkers for 4- to 7-year-old children with obstructive sleep apnea-hypopnea syndrome. Front Pediatr 2023; 11:1141348. [PMID: 37325347 PMCID: PMC10267831 DOI: 10.3389/fped.2023.1141348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023] Open
Abstract
Background We investigated the expression and the potential value of plasma transfer RNA-derived fragments (tRFs) of children with obstructive sleep apnea-hypopnea syndrome (OSAHS) as screening biomarkers. Methods At first, we randomly selected five plasma samples from the case group and the control group for high-throughput RNA sequencing. Secondly, we screened two tRFs with different expression between the two groups, amplified it by quantitative reverse transcription-PCR (qRT-PCR) on all samples. Then we analyzed the diagnostic value of the tRFs and their correlation with the clinical data. Results A total of 50 OSAHS children and 38 healthy controls were included. Our results demonstrated that the plasma levels of tRF-16-79MP9PD and tRF-28-OB1690PQR304 were significantly down-regulated in OSAHS children. Receiver operating characteristic curve (ROC) showed that the area under the curve (AUC) of tRF-16-79MP9PD and tRF-28-OB1690PQR304 was 0.7945 and 0.8276. In addition, the AUC of the combination reached 0.8303 with 73.46% and 76.42% sensitivity and specificity. Correlation analysis showed that the degree of tonsil enlargement, hemoglobin (Hb) and triglyceride (TG). were related to the expression levels of tRF-16-79MP9PD and tRF-28-OB1690PQR304. Multivariable linear regression analysis showed that degree of tonsil enlargement, Hb and TG related to tRF-16-79MP9PD while degree of tonsil enlargement and Hb related to tRF-28-OB1690PQR304. Conclusions The expression levels of tRF-16-79MP9PD and tRF-28-OB1690PQR304 in the plasma of OSAHS children decreased significantly which were closely related to the degree of tonsil enlargement, Hb and TG, may become novel biomarkers for the diagnosis of pediatric OSAHS.
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Affiliation(s)
- Junhua Wu
- School of Medicine, Ningbo University, Ningbo, China
- Department of Pediatric, Ningbo Women and Children's Hospital, Ningbo, China
| | - Xiaohong Cai
- School of Medicine, Ningbo University, Ningbo, China
| | - Yanbo Lu
- School of Medicine, Ningbo University, Ningbo, China
| | - Yijing Shen
- Department of Pediatric, Ningbo Women and Children's Hospital, Ningbo, China
| | - Zhisen Shen
- Department of Otorhinolaryngology, Lihuili Hospital of Ningbo University, Ningbo, China
| | - Qin Lyv
- Department of Pediatric, Ningbo Women and Children's Hospital, Ningbo, China
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Tyczewska A, Rzepczak A, Sobańska D, Grzywacz K. The emerging roles of tRNAs and tRNA-derived fragments during aging: Lessons from studies on model organisms. Ageing Res Rev 2023; 85:101863. [PMID: 36707034 DOI: 10.1016/j.arr.2023.101863] [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: 10/26/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
Aging is a gradual decline of various functions of organisms resulting in diminished abilities to protect against the environmental damage and reinforce the physiological harmony. Age-related functional declines have been thought to be passive and not regulated. However, studies on numerous model organisms, from yeast to mammals, exposed that the mechanisms of lifespan regulation are remarkably conserved throughout the evolution. Following the pioneering genetic studies in C. elegans, it has been shown that the genes related to the longevity are conserved in yeast, flies and mice. For a long time, tRNAs have been only considered as molecules transporting amino acids to the ribosome during translation. Nonetheless, it has become apparent from many biological studies that tRNAs are entangled in a variety of physiological and pathological processes. This review focuses on the emerging roles of tRNA-associated processes in aging and lifespan of model organisms. More specificaly, we present a summary on the importance of tRNA metabolism, epitranscriptome and possible roles of tRNA-derived fragments in aging and lifespan regulation. Better understanding of the basic mechanisms of aging could lead to the development of new diagnostics and treatments for aging-related diseases.
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Affiliation(s)
- Agata Tyczewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Alicja Rzepczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Daria Sobańska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Kamilla Grzywacz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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7
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Zhang XT, Mao ZY, Jin XY, Wang YG, Dong YQ, Zhang C. Identification of a tsRNA Contributor to Impaired Diabetic Wound Healing via High Glucose-Induced Endothelial Dysfunction. Diabetes Metab Syndr Obes 2023; 16:285-298. [PMID: 36760596 PMCID: PMC9899021 DOI: 10.2147/dmso.s379473] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/21/2022] [Indexed: 01/31/2023] Open
Abstract
PURPOSE Delayed skin healing in diabetic wounds is a major clinical problem. The tRNA-derived small RNAs (tsRNAs) were reported to be associated with diabetes. However, the role of tsRNAs in diabetic wound healing is unclear. Our study was designed to explore the tsRNA expression profile and mine key potential tsRNAs and their mechanism in diabetic wounds. METHODS Skin tissues of patients with diabetic foot ulcers and healthy controls were subjected to small RNA sequencing. The role of candidate tsRNA was explored by loss- and gain-of-function experiments in HUVECs. RESULTS A total of 55 differentially expressed tsRNAs were identified, including 12 upregulated and 43 downregulated in the diabetes group compared with the control group. These tsRNAs were mainly concentrated in intercellular interactions and neural function regulation in GO terms and enriched in MAPK, insulin, FoxO, calcium, Ras, ErbB, Wnt, T cell receptor, and cGMP-PKG signaling pathways. tRF-Gly-CCC-039 expression was upregulated in vivo and in vitro in the diabetic model. High glucose disturbed endothelial function in HUVECs, and tRF-Gly-CCC-039 mimics further harmed HUVECs function, characterized by the suppression of proliferation, migration, tube formation, and the expression of Coll1a1, Coll4a2, and MMP9. Conversely, the tRF-Gly-CCC-039 inhibitor could attenuate high-glucose-induced endothelial injury to HUVECs. CONCLUSION We investigated the tsRNAs expression profile in diabetic foot ulcers and defined the impairment role of tRF-Gly-CCC-039 in endothelial function in HUVECs. This study may provide novel insights into accelerating diabetic skin wound healing.
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Affiliation(s)
- Xiao-Tian Zhang
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Zhen-Yang Mao
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Xiang-Yun Jin
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yu-Gang Wang
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Yu-Qi Dong
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Chao Zhang
- Department of Orthopedics, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Correspondence: Chao Zhang; Yu-Qi Dong, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160, Pujian Road, Pudong New Area, Shanghai, People’s Republic of China, Tel +86-13817307997; +86-13331873590, Email ;
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8
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Zhang G, Kang L, Li P, Ran Q, Chen X, Ji M, Guan H. Genome-wide repertoire of transfer RNA-derived fragments in a mouse model of age-related cataract. Curr Eye Res 2022; 47:1397-1404. [PMID: 35930684 DOI: 10.1080/02713683.2022.2110263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Purpose To investigate the roles of tRNA-derived small RNAs (tsRNAs) containing transfer RNA-derived fragments (tRFs) and tRNA halves in age-related cataract (ARC). Methods: Lens capsule tissue from Emory mice at 3 months and 8 months of age were dissected for integrated tsRNA and gene transcriptome sequencing. Quantitative real-time PCR assay (qRT-PCR) was perform for validating sequencing results. Bioinformatics analysis was constructed to reveal the roles of tsRNAs. Results: A total of 422 DE tsRNAs were changed, in which 156 were elevated while 266 were declined in 8-month-old mice. Subsequently, the gene sequencing data exhibited 375 upregulated and 456 downregulated DE genes. Validation by qRT-PCR in 5 selected upregulated tRFs was consistent with tsRNAs sequencing results. Moreover, bioinformatics analysis identified 25 downregulated target genes of the 5 validated tRFs. Furthermore, GO analysis revealed that these target genes were mainly enriched in camera-type eye development, sensory organ development and so on. Conclusion: Our study provide a novel perspective for the role of tsRNAs in pathogenesis of ARC, and thus therapeutic potential targets for ARC.
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Affiliation(s)
- Guowei Zhang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Lihua Kang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Pengfei Li
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Qiliang Ran
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xiang Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Min Ji
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Huaijin Guan
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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Yue Z, Tong F, Zeng C, Wei R. Identification of tRNA-Related Fragments and Their Potential Regulatory Effects in Thyroid-Associated Ophthalmopathy. Front Genet 2022; 13:878405. [PMID: 35444685 PMCID: PMC9013859 DOI: 10.3389/fgene.2022.878405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, the potential role of tRNA-related fragments (tRFs) in ophthalmic diseases has been extensively researched. However, systematic studies on the potential regulatory effects of tRFs in thyroid-associated ophthalmopathy (TAO) are lacking. We used high-throughput sequencing techniques to measure expression levels of mRNAs and tRFs in patients with TAO, and the results were verified by real-time quantitative reverse transcription polymerase chain reaction (q-PCR). Next, the potential biological regulatory effect of differentially expressed tRFs was analyzed, and potential downstream target RNAs of differentially expressed tRFs were predicted to explore the potential role of tRFs as therapeutic targets and biomarkers of TAO. A total of 50 tRFs and 361 mRNAs were dysregulated in the TAO group, and tRF5-GluCTC, PMAIP1, HSD17B2 and ATF3 were verified to be significantly differentially expressed in TAO. Our research reveals that several associated pathways likely play a role in the pathogenesis of TAO. By targeting ATF3, HSD17B2 and PMAIP1, tRF5-GluCTC may play a potential role in regulating the orbital fibroblast adipogenic response and fibrotic hyperplasia in patients with TAO.
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Affiliation(s)
| | | | | | - Ruili Wei
- Department of Ophthalmology, Changzheng Hospital of Navy Military Medical University, Shanghai, China
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Zhao Y, Wang R, Qin Q, Yu J, Che H, Wang L. Differentially expressed tRNA-derived fragments and their roles in primary cardiomyocytes stimulated by high glucose. Front Endocrinol (Lausanne) 2022; 13:1049251. [PMID: 36714586 PMCID: PMC9880064 DOI: 10.3389/fendo.2022.1049251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 01/15/2023] Open
Abstract
Diabetic cardiomyopathy (DCM) is a serious complication of diabetes mellitus that can cause malignant arrhythmia and sudden death and is associated with cardiomyocyte dysfunction induced by hyperglycemia. Emerging evidence has revealed that transfer RNA-derived fragments (tRFs), a novel class of noncoding RNAs, play a crucial role in a variety of pathophysiologic processes, including cell death, cell growth and proliferation. However, it remains unknown whether and how tRFs are involved in cardiomyocyte dysfunction during the progression of DCM. In this study, we found that cardiomyocyte abnormalities were induced by high glucose (HG) treatment, as demonstrated by a decrease in cell viability and autophagy activation as well as an increase in cell death and proinflammatory cytokine release. Moreover, HG treatment resulted in differential expression of tRFs in cardiomyocytes, of which 4 upregulated and 1 downregulated tRFs were observed compared with the control group. The differential expression of 4 upregulated tRFs was primarily involved in cardiac dysfunction-related processes, such as autophagy, AGE-RAGE signaling pathway in diabetic complications, MAPK signaling pathway, insulin signaling pathway, FoxO signaling pathway, insulin resistance and peroxisome pathways based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Furthermore, we found that tRF-5014a, the most significantly upregulated tRF among all tested tRFs, negatively regulated the expression of the autophagy-related protein ATG5. Importantly, inhibition of tRF-5014a not only abolished autophagy inactivation but also attenuated the decrease in cell viability and increase in cell death as well as proinflammatory cytokine release under HG conditions. These findings suggest that tRFs may contribute to HG-induced cardiomyocyte injury during DCM progression.
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Affiliation(s)
- Yongting Zhao
- Department of Endocrinology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ruxin Wang
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Qi Qin
- Innovation Center for Neurological Disorders, Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jiaojiao Yu
- Department of Endocrinology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hui Che
- Department of Endocrinology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Lihong Wang, ; Hui Che,
| | - Lihong Wang
- Department of Endocrinology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Endocrinology and Metabolism, First Affiliated Hospital of Jinan University, Guangzhou, China
- *Correspondence: Lihong Wang, ; Hui Che,
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11
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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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12
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Zeng L, Peng H, Yu H, Wang W, Duan C, Fang C, Wu Y. Expression profiles of tRNA-derived small RNA and their potential roles in oral submucous fibrosis. J Oral Pathol Med 2021; 50:1057-1066. [PMID: 34558114 DOI: 10.1111/jop.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Although transfer RNA (tRNA) has been found to be the main source of a rich class of noncoding RNA, the tRNA-derived small RNA (tsRNA) has been proved to play an irreplaceable role in the human body, and its dynamic imbalance could affect the progress of the disease. However, the research on tsRNA in oral submucous fibrosis (OSF) is still scarce. METHODS We sequenced the OSF and validated it by PCR. We found that there were significant differences in their expression levels in OSF. Furthermore, bioinformatic analysis was performed to explore the roles of these fragments in oral submucous fibrosis. RESULTS Of 126 tsRNAs in OSF were dysregulated, including 73 upregulated tsRNAs and 53 downregulated tsRNAs. The downregulated tiRNA-Val-CAC-002, tRF-Asn-GTT-005, tRF-Trp-CCA-007 and upregulated tRF-Gly-TCC-016, tRF-Pro-TGG-009 showed significant differences by qRT-PCR validation, which were consistent with the results of RNA sequencing. Gene ontology and pathway analysis revealed that tRF-Gly-TCC-016 would possibly promote the formation and progress of OSF through cytokine-cytokine receptor interaction and cAMP signal pathway, while tiRNA-Val-CAC-002 could be primarily concerned with the transition from OSF to oral squamous cell carcinoma (OSCC). CONCLUSION tRNA-derived fragments are dysregulated and could be involved in the pathogenesis of oral submucous fibrosis. tRF-Gly-TCC-016 and tiRNA-Val-CAC-002 may be new regulatory molecules that could affect the process of OSF by regulating signal pathways through interacting with multiple genes.
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Affiliation(s)
- Liujun Zeng
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Hui Peng
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Huiqiao Yu
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Weiming Wang
- Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University.,Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Changyun Fang
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
| | - Yingfang Wu
- Centre of Stomatology, Xiangya Hospital, Central South University, Changsha, China.,Research Center of Oral and Maxillofacial Tumor, Xiangya Hospital, Central South University, Changsha, China.,Institute of Oral Cancer and Precancerous Lesions, Central South University
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13
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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.
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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
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