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Liang X, Zhang C, Shen L, Ding L, Guo H. Role of non‑coding RNAs in UV‑induced radiation effects (Review). Exp Ther Med 2024; 27:262. [PMID: 38756908 PMCID: PMC11097301 DOI: 10.3892/etm.2024.12550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
Ultraviolet (UV) is divided into UVA (long-wave, 320-400 nm), UVB (middle-wave, 280-320 nm) and UVC (short-wave, 100-280 nm) based on wavelength. UV radiation (UVR) from sunlight (UVA + UVB) is a major cause of skin photodamage including skin inflammation, aging and pigmentation. Accidental exposure to UVC burns the skin and induces skin cancer. In addition to the skin, UV radiation can also impair visual function. Non-coding RNAs (ncRNAs) are a class of functional RNAs that do not have coding activity but can control cellular processes at the post-transcriptional level, including microRNA (miRNA), long non-coding RNA (lncRNA) and circulatory RNA (circRNA). Through a review of the literature, it was determined that UVR can affect the expression of various ncRNAs, and that this regulation may be wavelength specific. Functionally, ncRNAs participate in the regulation of photodamage through various pathways and play pathogenic or protective regulatory roles. In addition, ncRNAs that are upregulated or downregulated by UVR can serve as biomarkers for UV-induced diseases, aiding in diagnosis and prognosis assessment. Therapeutic strategies targeting ncRNAs, including the use of natural drugs and their extracts, have shown protective effects against UV-induced photodamage. In the present review, an extensive summarization of previous studies was performed and the role and mechanism of ncRNAs in UV-induced radiation effects was reviewed to aid in the diagnosis and treatment of UV-related diseases.
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Affiliation(s)
- Xiaofei Liang
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
| | - Chao Zhang
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
| | - Lijuan Shen
- Department of Laboratory Medicine, Qiqihar MingZhu Hospital, Qiqihar, Heilongjiang 161000, P.R. China
| | - Ling Ding
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
| | - Haipeng Guo
- Department of Laboratory Medicine, The First Hospital of Qiqihar, Qiqihar, Heilongjiang 161000, P.R. China
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Wang Q, Huang Q, Ying X, Shen J, Duan S. Unveiling the role of tRNA-derived small RNAs in MAPK signaling pathway: implications for cancer and beyond. Front Genet 2024; 15:1346852. [PMID: 38596214 PMCID: PMC11002130 DOI: 10.3389/fgene.2024.1346852] [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: 11/30/2023] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are novel small non-coding RNAs originating from mature or precursor tRNAs (pre-tRNA), typically spanning 14 to 30 nt. The Mitogen-activated protein kinases (MAPK) pathway orchestrates cellular responses, influencing proliferation, differentiation, apoptosis, and transformation. tsRNAs influence the expression of the MAPK signaling pathway by targeting specific proteins within the pathway. Presently, four MAPK-linked tsRNAs have implications in gastric cancer (GC) and high-grade serous ovarian cancer (HGSOC). Notably, tRF-Glu-TTC-027 and tRF-Val-CAC-016 modulate MAPK-related protein expression, encompassing p38, Myc, ERK, CyclinD1, CyclinB, and c-Myc, hindering GC progression via MAPK pathway inhibition. Moreover, tRF-24-V29K9UV3IU and tRF-03357 remain unexplored in specific mechanisms. KEGG analysis posits varied tsRNAs in MAPK pathway modulation for diverse non-cancer maladies. Notably, high tRF-36-F900BY4D84KRIME and tRF-23-87R8WP9IY expression relates to varicose vein (VV) risk. Elevated tiRNA-Gly-GCC-001, tRF-Gly-GCC-012, tRF-Gly-GCC-013, and tRF-Gly-GCC-016 target spinal cord injury (SCI)-related brain-derived neurotrophic factor (BDNF), influencing MAPK expression. tRF-Gly-CCC-039 associates with diabetes foot sustained healing, while tRF-5014a inhibits autophagy-linked ATG5 in diabetic cardiomyopathy (DCM). Additionally, tsRNA-14783 influences keloid formation by regulating M2 macrophage polarization. Upregulation of tRF-Arg-ACG-007 and downregulation of tRF-Ser-GCT-008 are associated with diabetes. tsRNA-04002 alleviates Intervertebral disk degeneration (IDD) by targeting PRKCA. tsRNA-21109 alleviates Systemic lupus erythematosus (SLE) by inhibiting macrophage M1 polarization. The upregulated tiNA-Gly-GCC-002 and the downregulated tRF-Ala-AGC-010, tRF-Gln-CTG-005 and tRF-Leu-AAG-001 may be involved in the pathogenesis of Lupus nephritis (LN) by affecting the expression of MAPK pathway. Downregulation of tsRNA-1018, tsRNA-3045b, tsRNA-5021a and tsRNA-1020 affected the expression of MAPK pathway, thereby improving Acute lung injury (ALI). This review comprehensively dissects tsRNA roles in MAPK signaling across cancers and other diseases, illuminating a novel avenue for translational medical exploration.
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Affiliation(s)
- Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qinyuan Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xiaowei Ying
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
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He Y, Zheng X, Hu Y, Deng L, Xu J, Wu S. Proteomics analysis to investigate the potential mechanism of theacrine against UV-induced skin photodamage. PHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE 2023; 39:620-632. [PMID: 37641574 DOI: 10.1111/phpp.12908] [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: 05/25/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
AIM This study aimed to explore the underlying mechanism of theacrine treatment of UV-induced skin photodamage. MATERIALS AND METHODS Tandem Mass Tag (TMT) relative quantitative proteomics analysis was used to characterize the proteins and pathways associated with the ability of theacrine to combat photodamage in mouse skin by modeling UV irradiation of the backs of ICR mice. RESULTS Apoptosis-related proteins and signaling pathways play a key role in the ability of theacrine to protect against skin photodamage, according to proteomic and bioinformatics analysis; molecular docking and Western blotting further revealed that theacrine was associated with apoptosis-related proteins (p53, Bcl-2, Bax, caspase-3, and cleaved-caspase-3) with strong binding affinity, which can significantly reduce skin cell apoptosis induced by UV exposure. CONCLUSION The findings revealed that theacrine can reduce UVB-induced epidermal damage by controlling the apoptosis signaling pathway, implying that theacrine could be a useful anti-UVB damage agent.
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Affiliation(s)
- Yong He
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, China
| | - Xinkai Zheng
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, China
| | - Yunfeng Hu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, China
| | - Liehua Deng
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, China
| | - Jin Xu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, China
| | - Shi Wu
- Department of Dermatology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province, China
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Ni Y, Wu A, Li J, Zhang W, Wang Y. Evaluation of the serum tRNA-derived fragment tRF-5022B as a potential biomarker for the diagnosis of osteoarthritis. J Orthop Surg Res 2023; 18:800. [PMID: 37880787 PMCID: PMC10601305 DOI: 10.1186/s13018-023-04273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
Osteoarthritis (OA) is a degenerative disease. It is common in middle-aged and elderly people and is one of the main causes of disability. Currently, the etiology of OA is unclear, and no specific biomarkers for the diagnosis of OA have been identified. Therefore, finding a highly sensitive biomarker is essential for a proper diagnosis.TRNA-derived fragments (tRFs) and tRNA-derived stress-induced RNAs (tiRNAs) are newly discovered classes of noncoding RNAs. tRF has been proven in several studies to have significant associations with tumor diagnosis, making it a promising biomarker in cancer research. However, the diagnostic utility of tRF in OA patients and the correlation between OA progression and trf differential expression have yet to be elaborated. The purpose of this research was to identify tRFs with differential expression in OA to assess their potential as OA biomarkers. To determine the tRF-5022B expression level in this research, real-time fluorescence quantitative PCR has been employed. Agarose gel electrophoresis, Sanger sequencing, and other investigations have been employed for evaluating tRF-5022B's molecular properties. Receiver operating characteristic curve analysis has been utilized for assessing the diagnostic effectiveness of the tRF-5022B. The findings demonstrated that tRF-5022B expression was considerably lower in OA serum. The Kellgren-Lawrence grading scale was shown to correspond with serum expression levels. The ROC curve confirmed that tRF-5022B serum expression levels might differentiate OA cases from healthy individuals and RA patients. According to the aforementioned findings, tRF-5022B may be employed as a novel biomarker for OA diagnosis due to its excellent diagnostic value.
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Affiliation(s)
- Yingchen Ni
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Anqi Wu
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Jianxin Li
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Weidong Zhang
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong, 226001, China.
| | - Youhua Wang
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong, 226001, China.
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Wei D, Niu B, Zhai B, Liu XB, Yao YL, Liang CC, Wang P. Expression profiles and function prediction of tRNA-derived fragments in glioma. BMC Cancer 2023; 23:1015. [PMID: 37864150 PMCID: PMC10588164 DOI: 10.1186/s12885-023-11532-8] [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: 03/27/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most aggressive malignant primary brain tumor. The transfer RNA-derived fragments (tRFs) are a new group of small noncoding RNAs, which are dysregulated in many cancers. Until now, the expression and function of tRFs in glioma remain unknown. METHODS The expression profiles of tRF subtypes were analyzed using the Cancer Genome Atlas (TCGA)-low-grade gliomas (LGG)/GBM dataset. The target genes of tRFs were subjected to Gene Ontology, Kyoto Encyclopedia and Gene set enrichment analysis of Genes and Genomes pathway enrichment analysis. The protein-protein interaction enrichment analysis was performed by STRING. QRT-PCR was performed to detect the expressions of tRFs in human glioma cell lines U87, U373, U251, and human astrocyte cell line SVG p12. Western blot assay was used to detect to the expression of S100A11. The interaction between tRF-19-R118LOJX and S100A11 mRNA 3'UTR was detected by dual-luciferase reporter assay. The effects of tRF-19-R118LOJX, tRF-19-6SM83OJX and S100A11 on the glioma cell proliferation, migration and in vitro vasculogenic mimicry formation ability were examined by CCK-8 proliferation assay, EdU assay, HoloMonitor cell migration assay and tube formation assay, respectively. RESULTS tRF-19-R118LOJX and tRF-19-6SM83OJX are the most differentially expressed tRFs between LGG and GBM groups. The functional enrichment analysis showed that the target genes of tRF-19-R118LOJX and tRF-19-6SM83OJX are enriched in regulating blood vessel development. The upregulated target genes are linked to adverse survival outcomes in glioma patients. tRF-19-R118LOJX and tRF-19-6SM83OJX were identified to suppress glioma cell proliferation, migration, and in vitro vasculogenic mimicry formation. The mechanism of tRF-19-R118LOJX might be related to its function as an RNA silencer by targeting the S100A11 mRNA 3'UTR. CONCLUSION tRFs would become novel diagnostic biomarkers and therapeutic targets of glioma, and the mechanism might be related to its post-transcriptionally regulation of gene expression by targeting mRNA 3'UTR.
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Affiliation(s)
- Deng Wei
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Ben Niu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Bei Zhai
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiao-Bai Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yi-Long Yao
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Chan-Chan Liang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.
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Zhao M, Tian C, Di X, Cong S, Cao Y, Zhou X, Wang K. Systematic and Comprehensive Analysis of tRNA-Derived Small RNAs Reveals Their Potential Regulatory Roles and Clinical Relevance in Sarcoidosis. J Inflamm Res 2023; 16:2357-2374. [PMID: 37284703 PMCID: PMC10241215 DOI: 10.2147/jir.s406484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction The pathogenesis of sarcoidosis, which involves several systems, is unclear, and its pathological type is non-caseating epithelioid granulomas. tRNA-derived small RNA (tsRNA) is a novel class of short non-coding RNAs with potential regulatory functions. However, whether tsRNA contributes to sarcoidosis pathogenesis remains unclear. Methods Deep sequencing technology was used to identify alterations in tsRNA relative abundance profiles between patients with sarcoidosis and healthy controls and quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate. The clinical parameters were analysis to evaluate the clinical feature correlations initially. Target prediction and bioinformatics analysis of validated tsRNA were conducted to explore the mechanisms of tsRNAs in sarcoidosis pathogenesis. Results A total of 360 tsRNAs were identified for exact matches. Among them, the relative abundance of three tRNAs (tiRNA-Glu-TTC-001, tiRNA-Lys-CTT-003, and tRF-Ser-TGA-007) was markedly regulated in sarcoidosis. The levels of various tsRNAs were significantly correlated with age, the number of affected systems, and calcium levels in the blood. Additionally, target prediction and bioinformatics analyses revealed that these tsRNAs may play roles in chemokine, cAMP, cGMP-PKG, retrograde endorphin, and FoxO signalling pathways. The related genes, APP, PRKACB, ARRB2, and NR5A1 finding may participate in the occurrence and development of sarcoidosis through immune inflammation. Conclusion This study provides novel insights to explore tsRNA as a novel and efficacious pathogenic target of sarcoidosis.
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Affiliation(s)
- Min Zhao
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Chang Tian
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Xin Di
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Shan Cong
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Yingshu Cao
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Xijia Zhou
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
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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.
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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.)
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Macvanin MT, Zafirovic S, Obradovic M, Isenovic ER. Editorial: Non-coding RNA in diabetes and cardiovascular diseases. Front Endocrinol (Lausanne) 2023; 14:1149857. [PMID: 36814579 PMCID: PMC9939813 DOI: 10.3389/fendo.2023.1149857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
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Wang X, Hu Z. tRNA derived fragment tsRNA-14783 promotes M2 polarization of macrophages in keloid. Biochem Biophys Res Commun 2022; 636:119-127. [DOI: 10.1016/j.bbrc.2022.10.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/02/2022]
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George S, Rafi M, Aldarmaki M, ElSiddig M, Al Nuaimi M, Amiri KMA. tRNA derived small RNAs—Small players with big roles. Front Genet 2022; 13:997780. [PMID: 36199575 PMCID: PMC9527309 DOI: 10.3389/fgene.2022.997780] [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: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022] Open
Abstract
In the past 2 decades, small non-coding RNAs derived from tRNA (tsRNAs or tRNA derived fragments; tRFs) have emerged as new powerful players in the field of small RNA mediated regulation of gene expression, translation, and epigenetic control. tRFs have been identified from evolutionarily divergent organisms from Archaea, the higher plants, to humans. Recent studies have confirmed their roles in cancers and other metabolic disorders in humans and experimental models. They have been implicated in biotic and abiotic stress responses in plants as well. In this review, we summarize the current knowledge on tRFs including types of tRFs, their biogenesis, and mechanisms of action. The review also highlights recent studies involving differential expression profiling of tRFs and elucidation of specific functions of individual tRFs from various species. We also discuss potential considerations while designing experiments involving tRFs identification and characterization and list the available bioinformatics tools for this purpose.
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Affiliation(s)
- Suja George
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohamed ElSiddig
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mariam Al Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- *Correspondence: Khaled M. A. Amiri,
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TRFs and tiRNAs sequence in acute rejection for vascularized composite allotransplantation. Sci Data 2022; 9:544. [PMID: 36071069 PMCID: PMC9452673 DOI: 10.1038/s41597-022-01577-y] [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: 03/18/2022] [Accepted: 07/20/2022] [Indexed: 12/13/2022] Open
Abstract
Illumina tRFs & tiRNAs-seq analysis was used to characterize the whole transcriptomes of acute rejection caused by vascularized composite allotransplantation (VCA). tRFs & tiRNAs-seq information for muscle samples with VCA was obtained and compared with similar information for same age- and sex-matched healthy control subjects. The expression of 16 tRFs and tiRNAs, including 5 up-regulated target genes and 11 down-regulated target genes, were significantly different. According to bioinformatics analysis and reverse transcription quantitative polymerase chain reaction, we speculate that tiRNA-1-34-Glu-CTC-1 plays an important role in VCA-induced acute rejection by regulating the CACNA1D gene in the MAPK signaling pathway The findings provide the whole-transcriptome signatures of acute rejection for VCA, allowing further exploration of gene expression patterns/signatures associated with the various clinical symptoms of acute rejection for VCA. Measurement(s) | gene expression | Technology Type(s) | RNA sequence | Factor Type(s) | RNA | Sample Characteristic - Organism | rn6 | Sample Characteristic - Location | China |
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Qin C, Chen ZH, Cao R, Shi MJ, Tian Y. Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population. Genes (Basel) 2022; 13:genes13040601. [PMID: 35456407 PMCID: PMC9030102 DOI: 10.3390/genes13040601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have not yet been identified. Here, RNA sequencing, bioinformatics, and quantitative reverse transcription- polymerase chain reaction (qRT-PCR) were used to screen the expression profiles and predict the potential roles of tsRNAs in MIBC. Of 406 tsRNAs differentially expressed in MIBC tissues, 91 tsRNAs were significantly differentially expressed. Then, four candidate tsRNAs, tiRNA-1:34-Val-CAC-2, tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1, were selected. Next, a bioinformatics analysis showed the potential target genes and tsRNA–mRNA network. The most significant and meaningful terms of gene ontology were the positive regulation of the phosphate metabolic process, lamellipodium, and protein-cysteine S-acyltransferase activity in the biological process, cellular component, and molecular function, respectively. In addition, the top four pathways were predicted by the Kyoto Encyclopedia of Genes and Genomes database (KEGG). Finally, qRT-PCR demonstrated a similar expression pattern compared to sequencing data for the candidate tsRNAs. In short, we find differential expression profiles and predict that tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1 are very likely to engage in the pathophysiological process of MIBC via regulating the target genes in the key pathways.
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Affiliation(s)
| | | | | | | | - Ye Tian
- Correspondence: ; Tel.: +86-010-63138377
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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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