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Xi X, Wang B, Zhang R, Ling C. Serum exosome tRFs as a promising biomarker for active tuberculosis and latent tuberculosis infection. J Microbiol Methods 2024; 222:106944. [PMID: 38705210 DOI: 10.1016/j.mimet.2024.106944] [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: 12/05/2023] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To analyse the expression profiles of serum exosome tRFs/tiRNAs and to explore their diagnostic value in tuberculosis (TB) activity. METHODS The serum exosome tRF/tiRNA profile was analysed using high-throughput sequencing technology in 5 active tuberculosis (ATB) patients, 5 latent tuberculosis infection (LTBI) patients and 5 healthy controls (HCs). Then, serum exosome tRFs/tiRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR), and their diagnostic value was evaluated by receiver operating characteristic curve (ROC) and area under the curve (AUC). Finally, bioinformatics analysis was performed to explore and identify the potential biological pathways induced by tRFs/tiRNAs. RESULTS The sequencing results revealed that serum exosome tRF/tiRNA expression profiles were different among ATB patients, LTBI patients and HCs. Three tRFs (tRF-56:75-Trp-CCA-4, tRF-1:22-chrM.Ser-GCT and tRF-56:76-Val-TAC-1-M2) were selected for qRT-PCR validation. The results demonstrated that the expression level of tRF-1-22-chrM.Ser-GCT was upregulated in ATB patients, while tRF-56-75-Trp-CCA-4 was downregulated, which was consistent with the sequencing data. The AUCs of tRF-56:75-Trp-CCA-4 and tRF-1:22-chrM. Ser-GCT were 0.824 and 1.000, respectively, which have significant values in the diagnosis of ATB patients. Moreover, the expression levels of tRF-56:75-Trp-CCA-4 and tRF-1:22-chrM.Ser-GCT and tRF-56:76-Val-TAC-1-M2 in ATB patients and LTBI were different, which indicated that these three tRFs could effectively distinguish ATB patients and LTBI patients. CONCLUSION Our findings indicate that serum exosome tRFs can be used as potential markers for the diagnosis of ATB and LTBI.
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Affiliation(s)
- Xiangyu Xi
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; Xuzhou Infectious Disease Hospital, Xuzhou, Jiangsu, China
| | - Binghua Wang
- Department of Epidemiology, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ruimei Zhang
- Xuzhou Infectious Disease Hospital, Xuzhou, Jiangsu, China
| | - Chunhua Ling
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
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Tian H, Gao S, Xu M, Yang M, Shen M, Liu J, Li G, Zhuang D, Hu Z, Wang C. tiRNA-Gly-GCC-001 in major depressive disorder: Promising diagnostic and therapeutic biomarker. Br J Pharmacol 2024; 181:1952-1972. [PMID: 38439581 DOI: 10.1111/bph.16319] [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: 06/07/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND AND PURPOSE In major depressive disorder (MDD), exploration of biomarkers will be helpful in diagnosing the disorder as well as in choosing a treatment and predicting the treatment response. Currently, tRNA-derived small ribonucleic acids (tsRNAs) have been established as promising non-invasive biomarker candidates that may enable a more reliable diagnosis or monitoring of various diseases. Herein, we aimed to explore tsRNA expression together with functional activities in MDD development. EXPERIMENTAL APPROACH Serum samples were obtained from patients with MDD and healthy controls, and small RNA sequencing (RNA-Seq) was used to profile tsRNA expression. Dysregulated tsRNAs in MDD were validated by quantitative real-time polymerase chain reaction (qRT-PCR). The diagnostic utility of specific tsRNAs and the expression of these tsRNAs after antidepressant treatment were analysed. KEY RESULTS In total, 38 tsRNAs were significantly differentially expressed in MDD samples relative to healthy individuals (34 up-regulated and 4 down-regulated). qRT-PCR was used to validate the expression of six tsRNAs that were up-regulated in MDD (tiRNA-1:20-chrM.Ser-GCT, tiRNA-1:33-Gly-GCC-1, tRF-1:22-chrM.Ser-GCT, tRF-1:31-Ala-AGC-4-M6, tRF-1:31-Pro-TGG-2 and tRF-1:32-chrM.Gln-TTG). Interestingly, serum tiRNA-Gly-GCC-001 levels exhibited an area under the ROC curve of 0.844. Moreover, tiRNA-Gly-GCC-001 is predicted to suppress brain-derived neurotrophic factor (BDNF) expression. Furthermore, significant tiRNA-Gly-GCC-001 down-regulation was evident following an 8-week treatment course and served as a promising baseline predictor of patient response to antidepressant therapy. CONCLUSION AND IMPLICATIONS Our current work reports for the first time that tiRNA-Gly-GCC-001 is a promising MDD biomarker candidate that can predict patient responses to antidepressant therapy.
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Affiliation(s)
- Haihua Tian
- Zhejiang Key Laboratory of Pathophysiology, Health Center, Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Shugui Gao
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Miaomiao Xu
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Mei Yang
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Mengyuan Shen
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Jimeng Liu
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Guangxue Li
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Dingding Zhuang
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Zhenyu Hu
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Chuang Wang
- Zhejiang Key Laboratory of Pathophysiology, Health Center, Ningbo University, Ningbo, Zhejiang, China
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3
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Lu J, Zhu P, Zhang X, Zeng L, Xu B, Zhou P. tRNA-derived fragments: Unveiling new roles and molecular mechanisms in cancer progression. Int J Cancer 2024. [PMID: 38867475 DOI: 10.1002/ijc.35041] [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: 11/09/2023] [Revised: 04/17/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
tRNA-derived fragments (tRFs) are novel small noncoding RNAs (sncRNAs) that range from approximately 14 to 50 nt. They are generated by the cleavage of mature tRNAs or precursor tRNAs (pre-tRNAs) at specific sites. Based on their origin and length, tRFs can be classified into three categories: (1) tRF-1 s; (2) tRF-3 s, tRF-5 s, and internal tRFs (i-tRFs); and (3) tRNA halves. They play important roles in stress response, signal transduction, and gene expression processes. Recent studies have identified differential expression of tRFs in various tumors. Aberrantly expressed tRFs have critical clinical value and show promise as new biomarkers for tumor diagnosis and prognosis and as therapeutic targets. tRFs regulate the malignant progression of tumors via various mechanisms, primarily including modulation of noncoding RNA biogenesis, global chromatin organization, gene expression regulation, modulation of protein translation, regulation of epigenetic modification, and alternative splicing regulation. In conclusion, tRF-mediated regulatory pathways could present new avenues for tumor treatment, and tRFs could serve as promising therapeutic targets for cancer therapy.
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Affiliation(s)
- Jingjing Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong, China
| | - Ping Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiufen Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Linzi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Bujie Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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4
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Gotte G. Effects of Pathogenic Mutants of the Neuroprotective RNase 5-Angiogenin in Amyotrophic Lateral Sclerosis (ALS). Genes (Basel) 2024; 15:738. [PMID: 38927674 PMCID: PMC11202570 DOI: 10.3390/genes15060738] [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: 05/01/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the motoneurons. More than 40 genes are related with ALS, and amyloidogenic proteins like SOD1 and/or TDP-43 mutants are directly involved in the onset of ALS through the formation of polymorphic fibrillogenic aggregates. However, efficacious therapeutic approaches are still lacking. Notably, heterozygous missense mutations affecting the gene coding for RNase 5, an enzyme also called angiogenin (ANG), were found to favor ALS onset. This is also true for the less-studied but angiogenic RNase 4. This review reports the substrate targets and illustrates the neuroprotective role of native ANG in the neo-vascularization of motoneurons. Then, it discusses the molecular determinants of many pathogenic ANG mutants, which almost always cause loss of function related to ALS, resulting in failures in angiogenesis and motoneuron protection. In addition, ANG mutations are sometimes combined with variants of other factors, thereby potentiating ALS effects. However, the activity of the native ANG enzyme should be finely balanced, and not excessive, to avoid possible harmful effects. Considering the interplay of these angiogenic RNases in many cellular processes, this review aims to stimulate further investigations to better elucidate the consequences of mutations in ANG and/or RNase 4 genes, in order to achieve early diagnosis and, possibly, successful therapies against ALS.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
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5
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Qiao YY, Ji JL, Hou WL, Qu GT, Li SW, Li XY, Jin R, Li YF, Shi HM, Zhang AQ. tRF3-IleAAT reduced extracellular matrix synthesis in diabetic kidney disease mice by targeting ZNF281 and inhibiting ferroptosis. Acta Pharmacol Sin 2024; 45:1032-1043. [PMID: 38286833 PMCID: PMC11053026 DOI: 10.1038/s41401-024-01228-5] [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: 08/26/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
It is well established that the synthesis of extracellular matrix (ECM) in mesangial cells is a major determinant of diabetic kidney disease (DKD). Elucidating the major players in ECM synthesis may be helpful to provide promising candidates for protecting against DKD progression. tRF3-IleAAT is a tRNA-derived fragment (tRF) produced by nucleases at tRNA-specific sites, which is differentially expressed in the sera of patients with diabetes mellitus and DKD. In this study we investigated the potential roles of tRFs in DKD. Db/db mice at 12 weeks were adapted as a DKD model. The mice displayed marked renal dysfunction accompanied by significantly reduced expression of tRF3-IleAAT and increased ferroptosis and ECM synthesis in the kidney tissues. The reduced expression of tRF3-IleAAT was also observed in high glucose-treated mouse glomerular mesangial cells. We administered ferrostatin-1 (1 mg/kg, once every two days, i.p.) to the mice from the age of 12 weeks for 8 weeks, and found that inhibition of the onset of ferroptosis significantly improved renal function, attenuated renal fibrosis and reduced collagen deposition. Overexpression of tRF3-IleAAT by a single injection of AAV carrying tRF3-IleAAT via caudal vein significantly inhibited ferroptosis and ECM synthesis in DKD model mice. Furthermore, we found that the expression of zinc finger protein 281 (ZNF281), a downstream target gene of tRF3-IleAAT, was significantly elevated in DKD models but negatively regulated by tRF3-IleAAT. In high glucose-treated mesangial cells, knockdown of ZNF281 exerted an inhibitory effect on ferroptosis and ECM synthesis. We demonstrated the targeted binding of tRF3-IleAAT to the 3'UTR of ZNF281. In conclusion, tRF3-IleAAT inhibits ferroptosis by targeting ZNF281, resulting in the mitigation of ECM synthesis in DKD models, suggesting that tRF3-IleAAT may be an attractive therapeutic target for DKD.
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Affiliation(s)
- Yun-Yang Qiao
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China
| | - Jia-Ling Ji
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China
| | - Wei-Ling Hou
- Department of Science and Education, the Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 211199, China
| | - Gao-Ting Qu
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Shan-Wen Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Xing-Yue Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Ran Jin
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Yin-Fang Li
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China
| | - Hui-Min Shi
- Department of Pediatric Nephrology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, China.
| | - Ai-Qing Zhang
- Department of Pediatrics, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China.
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Padhiar NH, Katneni U, Komar AA, Motorin Y, Kimchi-Sarfaty C. Advances in methods for tRNA sequencing and quantification. Trends Genet 2024; 40:276-290. [PMID: 38123442 DOI: 10.1016/j.tig.2023.11.001] [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: 08/18/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023]
Abstract
In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.
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Affiliation(s)
- Nigam H Padhiar
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Anton A Komar
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR 2008, IBSLor UMR 7365 IMoPA, Nancy, France.
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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Song B, Qian J, Fu J. Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine. Int J Legal Med 2024; 138:329-350. [PMID: 37770641 DOI: 10.1007/s00414-023-03091-1] [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: 05/18/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.
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Affiliation(s)
- Binghui Song
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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8
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Weidong L, Liuting C, Xiangcong C, Jianhong P, Xueying Y. Analysis of the relationship of refractory gout between potential biomarkers and diet structure and lifestyle based on 1H-NMR. J Orthop Surg Res 2024; 19:78. [PMID: 38243298 PMCID: PMC10797800 DOI: 10.1186/s13018-024-04540-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/06/2024] [Indexed: 01/21/2024] Open
Abstract
OBJECTIVE We investigated the different life styles among the diet structures and exercise patterns of 100 patients with refractory gout and 79 healthy volunteers; of these, we selected 39 patients and 20 healthy volunteers for serum proton magnetic resonance (1H-NMR) metabolic network detection. We determined the potential biomarkers of refractory gout and attempted to explore the relation between potential biomarkers and diet structures and exercise patterns. METHODS The study employed a questionnaire survey to analyze diet structures and exercise patterns from 100 patients of refractory gout and 79 healthy volunteers. At the same time, using 1H-NMR metabolic technology to analyze the metabolites present in the serum samples obtained from 39 patients of refractory gout (group B) and 20 healthy subjects (group A). Employing MestReNova (Version 8.0.1) to analyze the metabolites maps, collecting the NMR results, further importing into SIMCA-P+ 14.0 software (Umetrics, Sweden) for principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA) statistical analysis. Combining patterns recognition and multivariate statistics, potential biomarkers were searched. Other experimental data, including creatinine and adiponectin, were counted by the SPSS21.0. The measurement data were expressed by X ± S and t test. The counting data were expressed in percent and performed by X2 test. RESULTS Our results revealed that patients with gout tended to be obese, and there were differences in their lifestyle with exercise, sleep, and smoking, as well as in their preference for fructose drinks, alcohol, and total and structural distribution of meat, milk, eggs, and so on when compared with the healthy volunteers. Importantly, we found the adiponectin in the gout group was lower as compared to the healthy group. Further, metabolomics in combination with KEGG analysis revealed that the biosynthesis of aminoacyl tRNA, biosynthesis of valine, leucine, and isoleucine, metabolism of alanine, aspartic, and glutamate, metabolism of glycine, serine, and threonine, phenylalanine, glycolysis/gluconeogenesis, ketone body synthesis and degradation, metabolism of D-glutamine, citric acid cycle (TCA cycle), triglyceride metabolism, and others could be used as specific biomarkers of this disease. CONCLUSION Recurrent refractory gout and formation of tophus may be related to the diet structures and lifestyles between the patients and the healthy people, and their abnormal metabolic network may be related to the disorder of mitochondrial energy metabolism, which further results in abnormal metabolism of glucose, lipids, amino acids, and deposition of uric acid in joints, peripheral connective tissue, and kidney, inducing an inflammatory response.
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Affiliation(s)
- Liang Weidong
- Department of Rheumatology, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, 523200, China
| | - Chen Liuting
- Department of Rheumatology, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, 523200, China
| | - Cheng Xiangcong
- Dongguan Hospital of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Peng Jianhong
- Department of Rheumatology, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, 523200, China.
| | - Ye Xueying
- Department of Rheumatology, Dongguan Hospital of Traditional Chinese Medicine, Dongguan, 523200, China
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9
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Li N, Yao S, Yu G, Lu L, Wang Z. tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. Nucleic Acids Res 2024; 52:D345-D350. [PMID: 37811890 PMCID: PMC10767876 DOI: 10.1093/nar/gkad815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/22/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
tRFtarget 1.0 (http://trftarget.net/) is a platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments (tRFs) and target genes (or transcripts) across multiple organisms. Here, we introduce a newly released version of tRFtarget 2.0, in which we integrated 6 additional tRF sources, resulting in a comprehensive collection of 2614 high-quality tRF sequences spanning across 9 species, including 1944 Homo sapiens tRFs and one newly incorporated species Rattus norvegicus. We also expanded target genes by including ribosomal RNAs, long non-coding RNAs, and coding genes >50 kb in length. The predicted binding sites have surged up to approximately 6 billion, a 20.5-fold increase than that in tRFtarget 1.0. The manually curated publications relevant to tRF targets have increased to 400 and the gene-level experimental evidence has risen to 232. tRFtarget 2.0 introduces several new features, including a web-based tool that identifies potential binding sites of tRFs in user's own datasets, integration of standardized tRF IDs, and inclusion of external links to contents within the database. Additionally, we enhanced website framework and user interface. With these improvements, tRFtarget 2.0 is more user-friendly, providing researchers a streamlined and comprehensive platform to accelerate their research progress.
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Affiliation(s)
- Ningshan Li
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong 518172, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Siqiong Yao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- SJTU-Yale Joint Center of Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangjun Yu
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of Shenzhen, Shenzhen, Guangdong 518172, China
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
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10
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Shi Y, Feng Y, Wang Q, Dong G, Xia W, Jiang F. The Role of tRNA-Centered Translational Regulatory Mechanisms in Cancer. Cancers (Basel) 2023; 16:77. [PMID: 38201505 PMCID: PMC10778012 DOI: 10.3390/cancers16010077] [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: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. While numerous factors have been identified as contributing to the development of malignancy, our understanding of the mechanisms involved remains limited. Early cancer detection and the development of effective treatments are therefore critical areas of research. One class of molecules that play a crucial role in the transmission of genetic information are transfer RNAs (tRNAs), which are the most abundant RNA molecules in the human transcriptome. Dysregulated synthesis of tRNAs directly results in translation disorders and diseases, including cancer. Moreover, various types of tRNA modifications and the enzymes responsible for these modifications have been implicated in tumor biology. Furthermore, alterations in tRNA modification can impact tRNA stability, and impaired stability can prompt the cleavage of tRNAs into smaller fragments known as tRNA fragments (tRFs). Initially believed to be random byproducts lacking any physiological function, tRFs have now been redefined as non-coding RNA molecules with distinct roles in regulating RNA stability, translation, target gene expression, and other biological processes. In this review, we present recent findings on translational regulatory models centered around tRNAs in tumors, providing a deeper understanding of tumorigenesis and suggesting new directions for cancer treatment.
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Affiliation(s)
- Yuanjian Shi
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Qinglin Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
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11
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Zhang C, Ye W, Zhao M, Xia D, Fan Z. tRNA-derived small RNA changes in bone marrow stem cells under hypoxia and osteogenic conduction. J Oral Rehabil 2023; 50:1487-1497. [PMID: 37574812 DOI: 10.1111/joor.13566] [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: 02/15/2023] [Revised: 04/04/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND Tissue engineering using bone mesenchymal stem cells (BMSCs) transplantation is a promising therapeutic for bone regeneration. However, the effect of bone regeneration remains unsatisfactory due to the BMSCs' functional abnormality influenced by hypoxia. In this study, we attempt to explore the mechanism of osteogenic differentiation of BMSCs under hypoxic conditions from the perspective of non-coding RNA regulation. METHODS The study employed BMSCs obtained from healthy donors and simulated hypoxia using CoCl2 stimulation. High-throughput sequencing technique was used to identify differential expression profiles of tRNA-derived small RNA (tsRNA) in three experimental groups: BMSCs-0d, BMSCs-7d and BMSCs-0d-CoCl2 . TargetScan and miRanda algorithms were used to determine tsRNA target genes, while Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were employed for the prediction of biological functions. Real-time reverse transcriptase-polymerase chain reaction (Real-time RT-PCR) was carried out on four selected differentially expressed tsRNAs. RESULTS After the osteogenic induction and CoCl2 stimulated separately, there were 19 tsRNAs differentially expressed in BMSCs, including 14 upregulated and five downregulated. According to the analysis of biological information, these tsRNAs may regulate 311 potential target genes and mainly enrich the pathways such as metabolic pathways, Wnt signalling pathway, osteoclast differentiation, cellular senescence and mTOR signalling pathway. The results of Real-time RT-PCR for 3'tiRNA-41-GlnTTG-6, 3'tiRNA-42-LysTTT-8, 5'tiRNA-35-CysACA-1 and tRF3a-AsnGTT-9 were consistent with small RNA sequencing data. CONCLUSION We discovered the tsRNA that changes the process of osteogenesis and hypoxia, which provides new targets for promoting survival and regeneration functions after BMSCs transplantation.
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Affiliation(s)
- Chen Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
- Department of Dental Emergency, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Weilong Ye
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Mengyao Zhao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Dengsheng Xia
- Department of Dental Emergency, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, China
- Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
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12
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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13
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Pinzaru AM, Tavazoie SF. Transfer RNAs as dynamic and critical regulators of cancer progression. Nat Rev Cancer 2023; 23:746-761. [PMID: 37814109 DOI: 10.1038/s41568-023-00611-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 10/11/2023]
Abstract
Transfer RNAs (tRNAs) have been historically viewed as non-dynamic adaptors that decode the genetic code into proteins. Recent work has uncovered dynamic regulatory roles for these fascinating molecules. Advances in tRNA detection methods have revealed that specific tRNAs can become modulated upon DNA copy number and chromatin alterations and can also be perturbed by oncogenic signalling and transcriptional regulators in cancer cells or the tumour microenvironment. Such alterations in the levels of specific tRNAs have been shown to causally impact cancer progression, including metastasis. Moreover, sequencing methods have identified tRNA-derived small RNAs that influence various aspects of cancer progression, such as cell proliferation and invasion, and could serve as diagnostic and prognostic biomarkers or putative therapeutic targets in various cancers. Finally, there is accumulating evidence, including from genetic models, that specific tRNA synthetases - the enzymes responsible for charging tRNAs with amino acids - can either promote or suppress tumour formation. In this Review, we provide an overview of how deregulation of tRNAs influences cancer formation and progression.
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Affiliation(s)
- Alexandra M Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
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14
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Zhang J, Xi Y, Fei Q, Xu J, Hu J. Identification of tRNA-derived RNAs in adipose tissue from overweight type 2 diabetes mellitus patients and their potential biological functions. Front Endocrinol (Lausanne) 2023; 14:1139157. [PMID: 37484941 PMCID: PMC10358832 DOI: 10.3389/fendo.2023.1139157] [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: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Background Type 2 diabetes mellitus (T2DM)causes a huge public health burden worldwide, especially for those who are overweight or obese, the pain is often greater. And search for effective targets in overweight T2DM could help improve patient quality of life and prognosis. tRNA-derived RNAs (tsRNAs) are multifunctional regulators that are currently receiving much attention, but there is still a lack of knowledge about tsRNAs in overweight T2DM. Methods T2DM patients with BMI ≥ 25 (Overweight group) and BMI< 25 (Control group) were subjected to tsRNA sequencing; differentially expressed tsRNAs in the two groups were analyzed and their expression was verified using qRT-PCR. The biological function of downstream target genes was also evaluated by enrichment analysis. Results qRT-PCR evaluation identified a tsRNA with up-regulated expression (tRF-1-28-Glu-TTC-3-M2) and a tsRNA with down-regulated expression (tRF-1-31-His-GTG-1), both of which may be involved in metabolic and energy-related processes. Conclusion Dysregulation of tsRNA expression in overweight patients with T2DM suggests a potential role for tsRNA in the development of T2DM.
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15
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Yang M, Mo Y, Ren D, Liu S, Zeng Z, Xiong W. Transfer RNA-derived small RNAs in tumor microenvironment. Mol Cancer 2023; 22:32. [PMID: 36797764 PMCID: PMC9933334 DOI: 10.1186/s12943-023-01742-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Transfer RNAs (tRNAs) are a class of non-coding RNAs responsible for amino acid translocation during protein synthesis and are ubiquitously found in organisms. With certain modifications and under specific conditions, tRNAs can be sheared and fragmented into small non-coding RNAs, also known as tRNA-derived small RNAs (tDRs). With the development of high-throughput sequencing technologies and bioinformatic strategies, more and more tDRs have been identified and their functions in organisms have been characterized. tRNA and it derived tDRs, have been shown to be essential not only for transcription and translation, but also for regulating cell proliferation, apoptosis, metastasis, and immunity. Aberrant expression of tDRs is associated with a wide range of human diseases, especially with tumorigenesis and tumor progression. The tumor microenvironment (TME) is a complex ecosystem consisting of various cellular and cell-free components that are mutually compatible with the tumor. It has been shown that tDRs regulate the TME by regulating cancer stem cells, immunity, energy metabolism, epithelial mesenchymal transition, and extracellular matrix remodeling, playing a pro-tumor or tumor suppressor role. In this review, the biogenesis, classification, and function of tDRs, as well as their effects on the TME and the clinical application prospects will be summarized and discussed based on up to date available knowledge.
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Affiliation(s)
- Mei Yang
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yongzhen Mo
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Daixi Ren
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Shun Liu
- grid.452708.c0000 0004 1803 0208Department of Cardiovascular Medicine, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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16
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Fu M, Gu J, Wang M, Zhang J, Chen Y, Jiang P, Zhu T, Zhang X. Emerging roles of tRNA-derived fragments in cancer. Mol Cancer 2023; 22:30. [PMID: 36782290 PMCID: PMC9926655 DOI: 10.1186/s12943-023-01739-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.
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Affiliation(s)
- Min Fu
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China ,grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jianmei Gu
- grid.260483.b0000 0000 9530 8833Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226361 Jiangsu China
| | - Maoye Wang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jiahui Zhang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Yanke Chen
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Pengcheng Jiang
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China
| | - Taofeng Zhu
- Department of Pulmonary and Critical Care Medicine, Yixing Hospital Affiliated to Jiangsu University, Yixing, 214200, Jiangsu, China.
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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17
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Mathew BA, Katta M, Ludhiadch A, Singh P, Munshi A. Role of tRNA-Derived Fragments in Neurological Disorders: a Review. Mol Neurobiol 2023; 60:655-671. [PMID: 36348262 DOI: 10.1007/s12035-022-03078-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022]
Abstract
tRFs are small tRNA derived fragments that are emerging as novel therapeutic targets and regulatory molecules in the pathophysiology of various neurological disorders. These are derived from precursor or mature tRNA, forming different subtypes that have been reported to be involved in neurological disorders like stroke, Alzheimer's, epilepsy, Parkinson's, MELAS, autism, and Huntington's disorder. tRFs were earlier believed to be random degradation debris of tRNAs. The significant variation in the expression level of tRFs in disease conditions indicates their salient role as key players in regulation of these disorders. Various animal studies are being carried out to decipher their exact role; however, more inputs are required to transform this research knowledge into clinical application. Future investigations also call for high-throughput technologies that could help to bring out the other hidden aspects of these entities. However, studies on tRFs require further research efforts to overcome the challenges posed in quantifying tRFs, their interactions with other molecules, and the exact mechanism of function. In this review, we are abridging the current understanding of tRFs, including their biogenesis, function, relevance in clinical therapies, and potential as diagnostic and prognostic biomarkers of these neurological disorders.
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Affiliation(s)
- Blessy Aksa Mathew
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Madhumitha Katta
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Abhilash Ludhiadch
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Paramdeep Singh
- Department of Radiology, All India Institute of Medical Sciences, Bathinda, Punjab, India, 151001
| | - Anjana Munshi
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401.
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18
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Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines. Comput Struct Biotechnol J 2022; 21:401-417. [PMID: 36618980 PMCID: PMC9798144 DOI: 10.1016/j.csbj.2022.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m5C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m3C), 7-methylguanosine (m7G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.
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19
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Hou J, Li Q, Wang J, Lu W. tRFs and tRNA Halves: Novel Cellular Defenders in Multiple Biological Processes. Curr Issues Mol Biol 2022; 44:5949-5962. [PMID: 36547066 PMCID: PMC9777342 DOI: 10.3390/cimb44120405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA transcripts rather than via random degradation. tRFs and tRNA halves are highly involved in regulating transcription and translation in a canonical or non-canonical manner in response to cellular stress. In this review, we summarize the biogenesis and types of tRFs and tRNA halves, clarify the biological functions and molecular mechanisms of tRNA fragments in both physiological and pathological processes with a particular focus on their cytoprotective roles in defending against oxidation and apoptosis, and highlight their potential application as biomarkers in determining cell fate.
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Affiliation(s)
- Jiani Hou
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qianqing Li
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jun Wang
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
| | - Wenfa Lu
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
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20
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Expression profiles of tRNA‑derived fragments in high glucose‑treated tubular epithelial cells. Exp Ther Med 2022; 25:26. [PMID: 36561608 PMCID: PMC9748664 DOI: 10.3892/etm.2022.11725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA-derived fragments (tRFs), a novel class of small non-coding RNA produced by the cleavage of pre- and mature tRNAs, are involved in various diseases. Renal tubulointerstitial fibrosis is a common final pathway in diabetic nephropathy (DN) in which hyperglycemia-induced tubular extracellular matrix (ECM) accumulation serves a vital role. The present study aimed to detect and investigate the role of tRFs in the accumulation of tubular ECM. Differentially expressed tRFs were analysed with high-throughput sequencing in primary mouse tubular epithelial cells treated with high glucose (HG). The Gene Ontology (GO) was used to analyze the potential molecular functions of these differentially expressed tRFs, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the associated signaling pathways involved in these differentially expressed tRFs. tRF-1:30-Gln-CTG-4 was overexpressed using tRF-1:30-Gln-CTG-4 mimic, followed by HG treatment. A total of 554 distinct tRFs were detected and 64 differentially expressed tRFs (fold change >2; P<0.05) were identified in tubular epithelial cells following high glucose (HG) treatment, among which 27 were upregulated and 37 were downregulated. Ten selected tRFs with the greatest difference (fold change >2; P<0.05) were verified to be consistent with small RNA-sequencing data, of which tRF-1:30-Gln-CTG-4 showed the most pronounced difference in expression and was significantly decreased in response to HG. GO analysis indicated that the differentially expressed tRFs were associated with 'cellular process', 'biological regulation' and 'metabolic process'. An analysis of the KEGG database suggested that these differentially expressed tRFs were involved in 'autophagy' and signaling pathways for 'forkhead box O', 'the mammalian target of rapamycin' and 'mitogen-activated protein kinase'. Finally, the overexpression of tRF-1:30-Gln-CTG-4 ameliorated HG-induced ECM accumulation in tubular epithelial cells. Therefore, the present study demonstrated that there may be a significant association between tRFs and HG-induced ECM accumulation in tubular epithelial cells; these differentially expressed tRFs warrant further study to explore the pathogenesis of DN.
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21
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Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Front Cell Neurosci 2022; 16:852002. [PMID: 35846567 PMCID: PMC9279898 DOI: 10.3389/fncel.2022.852002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.
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Affiliation(s)
- Xiaoling Li
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Xiaoling Li
| | - Guanghui Cao
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Xiaokang Liu
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Caixia Guo
- Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- *Correspondence: Caixia Guo
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Hongmei Liu
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22
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Role of the Ribonuclease ONCONASE in miRNA Biogenesis and tRNA Processing: Focus on Cancer and Viral Infections. Int J Mol Sci 2022; 23:ijms23126556. [PMID: 35742999 PMCID: PMC9223570 DOI: 10.3390/ijms23126556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 12/23/2022] Open
Abstract
The majority of transcribed RNAs do not codify for proteins, nevertheless they display crucial regulatory functions by affecting the cellular protein expression profile. MicroRNAs (miRNAs) and transfer RNA-derived small RNAs (tsRNAs) are effectors of interfering mechanisms, so that their biogenesis is a tightly regulated process. Onconase (ONC) is an amphibian ribonuclease known for cytotoxicity against tumors and antiviral activity. Additionally, ONC administration in patients resulted in clinical effectiveness and in a well-tolerated feature, at least for lung carcinoma and malignant mesothelioma. Moreover, the ONC therapeutic effects are actually potentiated by cotreatment with many conventional antitumor drugs. This review not only aims to describe the ONC activity occurring either in different tumors or in viral infections but also to analyze the molecular mechanisms underlying ONC pleiotropic and cellular-specific effects. In cancer, data suggest that ONC affects malignant phenotypes by generating tRNA fragments and miRNAs able to downregulate oncogenes expression and upregulate tumor-suppressor proteins. In cells infected by viruses, ONC hampers viral spread by digesting the primer tRNAs necessary for viral DNA replication. In this scenario, new therapeutic tools might be developed by exploiting the action of ONC-elicited RNA derivatives.
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23
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Xu W, Zheng J, Wang X, Zhou B, Chen H, Li G, Yan F. tRF-Val-CAC-016 modulates the transduction of CACNA1d-mediated MAPK signaling pathways to suppress the proliferation of gastric carcinoma. Cell Commun Signal 2022; 20:68. [PMID: 35590368 PMCID: PMC9118711 DOI: 10.1186/s12964-022-00857-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 03/04/2022] [Indexed: 11/25/2022] Open
Abstract
Background As a new kind of non-coding RNAs (ncRNAs), tRNA derivatives play an important role in gastric carcinoma (GC). Nevertheless, the underlying mechanism tRNA derivatives were involved in was rarely illustrated. Methods We screened out the tRNA derivative, tRF-Val-CAC-016, based on the tsRNA sequencing and demonstrated the effect tRF-Val-CAC-016 exerted on GC proliferation in vitro and in vivo. We applied Dual-luciferase reporter assay, RIP assay, and bioinformatic analysis to discover the downstream target of tRF-Val-CAC-016. Then CACNA1d was selected, and the oncogenic characteristics were verified. Subsequently, we detected the possible regulation of the canonical MAPK signaling pathway to further explore the downstream mechanism of tRF-Val-CAC-016. Results As a result, we found that tRF-Val-CAC-016 was low-expressed in GC, and upregulation of tRF-Val-CAC-016 could significantly suppress the proliferation of GC cell lines. Meanwhile, tRF-Val-CAC-016 regulated the canonical MAPK signaling pathway by targeting CACNA1d. Conclusions tRF-Val-CAC-016 modulates the transduction of CACNA1d-mediated MAPK signaling pathways to suppress the proliferation of gastric carcinoma. This study discussed the function and mechanism of tRF-Val-CAC-016 in GC for the first time. The pioneering work has contributed to our present understanding of tRNA derivative, which might provide an alternative mean for the targeted therapy of GC. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00857-9.
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Affiliation(s)
- Weiguo Xu
- Department of General Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Junyu Zheng
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China
| | - Xiao Wang
- Department of Radiology, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Bin Zhou
- Department of Gastric Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China
| | - Huanqiu Chen
- Department of Gastric Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China.
| | - Gang Li
- Department of Gastric Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China.
| | - Feng Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China.
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24
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A 5’-tiRNA fragment that inhibits proliferation and migration of laryngeal squamous cell carcinoma by targeting PIK3CD. Genomics 2022; 114:110392. [DOI: 10.1016/j.ygeno.2022.110392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/24/2022] [Accepted: 05/22/2022] [Indexed: 12/24/2022]
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25
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Wilson B, Dutta A. Function and Therapeutic Implications of tRNA Derived Small RNAs. Front Mol Biosci 2022; 9:888424. [PMID: 35495621 PMCID: PMC9043108 DOI: 10.3389/fmolb.2022.888424] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022] Open
Abstract
tRNA derived small RNAs are mainly composed of tRNA fragments (tRFs) and tRNA halves (tiRs). Several functions have been attributed to tRFs and tiRs since their initial characterizations, spanning all aspects of regulation of the Central Dogma: from nascent RNA silencing, to post-transcriptional gene silencing, and finally, to translational regulation. The length distribution, sequence diversity, and multifaceted functions of tRFs and tiRs positions them as attractive new models for small RNA therapeutics. In this review, we will discuss the principles of tRF biogenesis and function in order to highlight their therapeutic potential.
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Affiliation(s)
- Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Anindya Dutta
- Department of Genetics, University of Alabama, Birmingham, AL, United States
- *Correspondence: Anindya Dutta,
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26
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Zhang W, Foo M, Eren AM, Pan T. tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Mol Cell 2022; 82:891-906. [PMID: 35032425 PMCID: PMC8897278 DOI: 10.1016/j.molcel.2021.12.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/17/2022]
Abstract
tRNA is the most extensively modified RNA in cells. On average, a bacterial tRNA contains 8 modifications per molecule and a eukaryotic tRNA contains 13 modifications per molecule. Recent studies reveal that tRNA modifications are highly dynamic and respond extensively to environmental conditions. Functions of tRNA modification dynamics include enhanced, on-demand decoding of specific codons in response genes and regulation of tRNA fragment biogenesis. This review summarizes recent advances in the studies of tRNA modification dynamics in biological processes, tRNA modification erasers, and human-associated bacteria. Furthermore, we use the term "metaepitranscriptomics" to describe the potential and approach of tRNA modification studies in natural biological communities such as microbiomes. tRNA is highly modified in cells, and tRNA modifications respond extensively to environmental conditions to enhance translation of specific genes and produce tRNA fragments on demand. We review recent advances in tRNA sequencing methods, tRNA modification dynamics in biological processes, and tRNA modification studies in natural communities such as the microbiomes.
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Affiliation(s)
- Wen Zhang
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Marcus Foo
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - A. Murat Eren
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA;,Department of Medicine, University of Chicago, Chicago, IL 60637, USA;,Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
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27
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Penning A, Tosoni G, Abiega O, Bielefeld P, Gasperini C, De Pietri Tonelli D, Fitzsimons CP, Salta E. Adult Neural Stem Cell Regulation by Small Non-coding RNAs: Physiological Significance and Pathological Implications. Front Cell Neurosci 2022; 15:781434. [PMID: 35058752 PMCID: PMC8764185 DOI: 10.3389/fncel.2021.781434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/09/2021] [Indexed: 01/11/2023] Open
Abstract
The adult neurogenic niches are complex multicellular systems, receiving regulatory input from a multitude of intracellular, juxtacrine, and paracrine signals and biological pathways. Within the niches, adult neural stem cells (aNSCs) generate astrocytic and neuronal progeny, with the latter predominating in physiological conditions. The new neurons generated from this neurogenic process are functionally linked to memory, cognition, and mood regulation, while much less is known about the functional contribution of aNSC-derived newborn astrocytes and adult-born oligodendrocytes. Accumulating evidence suggests that the deregulation of aNSCs and their progeny can impact, or can be impacted by, aging and several brain pathologies, including neurodevelopmental and mood disorders, neurodegenerative diseases, and also by insults, such as epileptic seizures, stroke, or traumatic brain injury. Hence, understanding the regulatory underpinnings of aNSC activation, differentiation, and fate commitment could help identify novel therapeutic avenues for a series of pathological conditions. Over the last two decades, small non-coding RNAs (sncRNAs) have emerged as key regulators of NSC fate determination in the adult neurogenic niches. In this review, we synthesize prior knowledge on how sncRNAs, such as microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), may impact NSC fate determination in the adult brain and we critically assess the functional significance of these events. We discuss the concepts that emerge from these examples and how they could be used to provide a framework for considering aNSC (de)regulation in the pathogenesis and treatment of neurological diseases.
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Affiliation(s)
- Amber Penning
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
| | - Giorgia Tosoni
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
| | - Oihane Abiega
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Pascal Bielefeld
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
| | - Caterina Gasperini
- Neurobiology of miRNAs Lab, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Carlos P. Fitzsimons
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Carlos Fitzsimons Evgenia Salta
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Amsterdam, Netherlands
- *Correspondence: Carlos Fitzsimons Evgenia Salta
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