101
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Kaymak E, Rando OJ. Staying together after the breakup: tRNA halves in extracellular fluids. Proc Natl Acad Sci U S A 2023; 120:e2300300120. [PMID: 36780520 PMCID: PMC9974496 DOI: 10.1073/pnas.2300300120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Affiliation(s)
- Ebru Kaymak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01605
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA01605
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102
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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] [MESH Headings] [Grants] [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
- 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
| | - Yongzhen Mo
- 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
| | - Daixi Ren
- 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
| | - Shun Liu
- Department 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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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: 35] [Impact Index Per Article: 35.0] [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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104
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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: 3] [Impact Index Per Article: 3.0] [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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105
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Long KLP, Muroy SE, Sorooshyari SK, Ko MJ, Jaques Y, Sudmant P, Kaufer D. Transcriptomic profiles of stress susceptibility and resilience in the amygdala and hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527777. [PMID: 36798395 PMCID: PMC9934702 DOI: 10.1101/2023.02.08.527777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
A single, severe episode of stress can bring about myriad responses amongst individuals, ranging from cognitive enhancement to debilitating and persistent anxiety; however, the biological mechanisms that contribute to resilience versus susceptibility to stress are poorly understood. The dentate gyrus (DG) of the hippocampus and the basolateral nucleus of the amygdala (BLA) are key limbic regions that are susceptible to the neural and hormonal effects of stress. Previous work has also shown that these regions contribute to individual variability in stress responses; however, the molecular mechanisms underlying the role of these regions in susceptibility and resilience are unknown. In this study, we profiled the transcriptomic signatures of the DG and BLA of rats with divergent behavioral outcomes after a single, severe stressor. We subjected rats to three hours of immobilization with exposure to fox urine and conducted a behavioral battery one week after stress to identify animals that showed persistent, high anxiety-like behavior. We then conducted bulk RNA sequencing of the DG and BLA from susceptible, resilient, and unexposed control rats. Differential gene expression analyses revealed that the molecular signatures separating each of the three groups were distinct and non-overlapping between the DG and BLA. In the amygdala, key genes associated with insulin and hormonal signaling corresponded with vulnerability. Specifically, Inhbb, Rab31 , and Ncoa3 were upregulated in the amygdala of stress-susceptible animals compared to resilient animals. In the hippocampus, increased expression of Cartpt - which encodes a key neuropeptide involved in reward, reinforcement, and stress responses - was strongly correlated with vulnerability to anxiety-like behavior. However, few other genes distinguished stress-susceptible animals from control animals, while a larger number of genes separated stress-resilient animals from control and stress-susceptible animals. Of these, Rnf112, Tbx19 , and UBALD1 distinguished resilient animals from both control and susceptible animals and were downregulated in resilience, suggesting that an active molecular response in the hippocampus facilitates protection from the long-term consequences of severe stress. These results provide novel insight into the mechanisms that bring about individual variability in the behavioral responses to stress and provide new targets for the advancement of therapies for stress-induced neuropsychiatric disorders.
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106
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 01/05/2024] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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107
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Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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108
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Ha SG, Lee SJV. The role of tRNA-derived small RNAs in aging. BMB Rep 2023; 56:49-55. [PMID: 36646437 PMCID: PMC9978369 DOI: 10.5483/bmbrep.2022-0199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/18/2022] [Accepted: 01/17/2023] [Indexed: 10/15/2023] Open
Abstract
Aging is characterized by a gradual decline in biological functions, leading to the increased probability of diseases and deaths in organisms. Previous studies have identified biological factors that modulate aging and lifespan, including non-coding RNAs (ncRNAs). Here, we review the relationship between aging and tRNA-derived small RNAs (tsRNAs), ncRNAs that are generated from the cleavage of tRNAs. We describe age-dependent changes in tsRNA levels and their functions in age-related diseases, such as cancer and neurodegenerative diseases. We also discuss the association of tsRNAs with aging-regulating processes, including mitochondrial respiration and reduced mRNA translation. We cover recent findings regarding the potential roles of tsRNAs in cellular senescence, a major cause of organismal aging. Overall, our review will provide useful information for understanding the roles of tsRNAs in aging and age-associated diseases. [BMB Reports 2023; 56(2): 49-55].
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Affiliation(s)
- Seokjun G. Ha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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109
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Ha SG, Lee SJV. The role of tRNA-derived small RNAs in aging. BMB Rep 2023; 56:49-55. [PMID: 36646437 PMCID: PMC9978369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/18/2022] [Accepted: 01/17/2023] [Indexed: 01/18/2023] Open
Abstract
Aging is characterized by a gradual decline in biological functions, leading to the increased probability of diseases and deaths in organisms. Previous studies have identified biological factors that modulate aging and lifespan, including non-coding RNAs (ncRNAs). Here, we review the relationship between aging and tRNA-derived small RNAs (tsRNAs), ncRNAs that are generated from the cleavage of tRNAs. We describe age-dependent changes in tsRNA levels and their functions in age-related diseases, such as cancer and neurodegenerative diseases. We also discuss the association of tsRNAs with aging-regulating processes, including mitochondrial respiration and reduced mRNA translation. We cover recent findings regarding the potential roles of tsRNAs in cellular senescence, a major cause of organismal aging. Overall, our review will provide useful information for understanding the roles of tsRNAs in aging and age-associated diseases. [BMB Reports 2023; 56(2): 49-55].
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Affiliation(s)
- Seokjun G. Ha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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110
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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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111
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Chen F, Song C, Meng F, Zhu Y, Chen X, Fang X, Ma D, Wang Y, Zhang C. 5'-tRF-GlyGCC promotes breast cancer metastasis by increasing fat mass and obesity-associated protein demethylase activity. Int J Biol Macromol 2023; 226:397-409. [PMID: 36464183 DOI: 10.1016/j.ijbiomac.2022.11.295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/19/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
tRNA-derived fragments (tRFs) are a class of regulatory non-coding RNAs that play essential biological functions in cancer and stress-induced diseases. Several lines of evidence suggest that 5'-tRF-GlyGCC participates in tumor progression; however, its molecular mechanisms remain unclear. In this study, we explored the function of 5'-tRF-GlyGCC in breast cancer (BC) progression and studied the related potential molecular mechanisms. 5'-tRF-GlyGCC expression increased in human BC, and it promoted the proliferation, migration, and invasion of BC cells in vitro and tumor growth and metastasis in vivo. 5'-tRF-GlyGCC was found for the first time to bind directly to fat mass and obesity-associated proteins, and increase the activity of FTO demethylase, reducing eIF4G1 methylation, inhibiting autophagy, and promoting BC proliferation and metastasis. These findings suggest that 5'-tRF-GlyGCC might be a therapeutic target for treating BC.
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Affiliation(s)
- Fang Chen
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Chengchuang Song
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China; Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Fantong Meng
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Yuhua Zhu
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China; Laboratory Animal Center, Xuzhou Medical University, Xuzhou 221004, Jiangsu Province, China
| | - Xi Chen
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China; Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Xingtang Fang
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China; Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China
| | - Daifu Ma
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture, Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221004, Jiangsu Province, China
| | - Yanhong Wang
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China; Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China.
| | - Chunlei Zhang
- Institute of Cellular and Molecular Biology, College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China; Laboratory of Phylogenomics and Comparative Genomics, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, China.
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112
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Wang C, Chen W, Aili M, Zhu L, Chen Y. tRNA-derived small RNAs in plant response to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1131977. [PMID: 36798699 PMCID: PMC9928184 DOI: 10.3389/fpls.2023.1131977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
tRNA-derived small RNAs (tsRNAs) represent a novel category of small non-coding RNAs and serve as a new regulator of gene expression at both transcriptional and post-transcriptional levels. Growing evidence indicates that tsRNAs can be induced by diverse stimuli and regulate stress-responsive target genes, allowing plants to adapt to unfavorable environments. Here, we discuss the latest developments about the biogenesis and classification of tsRNAs and highlight the expression regulation and potential function of tsRNAs in plant biotic and abiotic stress responses. Of note, we also collect useful bioinformatics tools and resources for tsRNAs study in plants. Finally, we propose current limitations and future directions for plant tsRNAs research. These recent discoveries have refined our understanding of whether and how tsRNAs enhance plant stress tolerance.
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Affiliation(s)
- Chaojun Wang
- Institute of Education Science, Leshan Normal University, Leshan, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Xinjiang Institute of Traditional Uyghur Medicine, Urumqi, China
| | - Maimaiti Aili
- Xinjiang Institute of Traditional Uyghur Medicine, Urumqi, China
| | - Lei Zhu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Chen
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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113
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Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids. Proc Natl Acad Sci U S A 2023; 120:e2216330120. [PMID: 36652478 PMCID: PMC9942843 DOI: 10.1073/pnas.2216330120] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Nonvesicular extracellular RNAs (nv-exRNAs) constitute the majority of the extracellular RNAome, but little is known about their stability, function, and potential use as disease biomarkers. Herein, we measured the stability of several naked RNAs when incubated in human serum, urine, and cerebrospinal fluid (CSF). We identified extracellularly produced tRNA-derived small RNAs (tDRs) with half-lives of several hours in CSF. Contrary to widespread assumptions, these intrinsically stable small RNAs are full-length tRNAs containing broken phosphodiester bonds (i.e., nicked tRNAs). Standard molecular biology protocols, including phenol-based RNA extraction and heat, induce the artifactual denaturation of nicked tRNAs and the consequent in vitro production of tDRs. Broken bonds are roadblocks for reverse transcriptases, preventing amplification and/or sequencing of nicked tRNAs in their native state. To solve this, we performed enzymatic repair of nicked tRNAs purified under native conditions, harnessing the intrinsic activity of phage and bacterial tRNA repair systems. Enzymatic repair regenerated an RNase R-resistant tRNA-sized band in northern blot and enabled RT-PCR amplification of full-length tRNAs. We also separated nicked tRNAs from tDRs by chromatographic methods under native conditions, identifying nicked tRNAs inside stressed cells and in vesicle-depleted human biofluids. Dissociation of nicked tRNAs produces single-stranded tDRs that can be spontaneously taken up by human epithelial cells, positioning stable nv-exRNAs as potentially relevant players in intercellular communication pathways.
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Liu W, Yu M, Cheng S, Zhou X, Li J, Lu Y, Liu P, Ding S. tRNA-Derived RNA Fragments Are Novel Biomarkers for Diagnosis, Prognosis, and Tumor Subtypes in Prostate Cancer. Curr Oncol 2023; 30:981-999. [PMID: 36661724 PMCID: PMC9857875 DOI: 10.3390/curroncol30010075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND tRNA-derived RNA fragments (tRFs) are a novel class of small ncRNA that are derived from precursor or mature tRNAs. Recently, the general relevance of their roles and clinical values in tumorigenesis, metastasis, and recurrence have been increasingly highlighted. However, there has been no specific systematic study to elucidate any potential clinical significance for these tRFs in prostate adenocarcinoma (PRAD), one of the most common and malignant cancers that threatens male health worldwide. Here, we investigate the clinical value of 5'-tRFs in PRAD. METHODS Small RNA sequencing data were analyzed to discover new 5'-tRFs biomarkers for PRAD. Machine learning algorithms were used to identify 5'-tRF classifiers to distinguish PRAD tumors from normal tissues. LASSO and Cox regression analyses were used to construct 5'-tRF prognostic predictive models. NMF and consensus clustering analyses were performed on 5'-tRF profiles to identify molecular subtypes of PRAD. RESULTS The overall levels of 5'-tRFs were significantly upregulated in the PRAD tumor samples compared to their adjacent normal samples. tRF classifiers composed of 13 5'-tRFs achieved AUC values as high as 0.963, showing high sensitivity and specificity in distinguishing PRAD tumors from normal samples. Multiple 5'-tRFs were identified as being associated with the PRAD prognosis. The tRF score, defined by a set of eight 5'-tRFs, was highly predictive of survival in PRAD patients. The combination of tRF and Gleason scores showed a significantly better performance than the Gleason score alone, suggesting that 5'-tRFs can offer PRAD patients additional and improved prognostic information. Four molecular subtypes of the PRAD tumor were identified based on their 5'-tRF expression profiles. Genetically, these 5'-tRFs PRAD tumor subtypes exhibited distinct genomic landscapes in tumor cells. Clinically, they showed marked differences in survival and clinicopathological features. CONCLUSIONS 5'-tRFs are potential clinical biomarkers for the diagnosis, prognosis, and classification of tumor subtypes on a molecular level. These can help clinicians formulate personalized treatment plans for PRAD patients and may have similar potential applications for other disease types.
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Affiliation(s)
- Weigang Liu
- Department of Cell Biology, The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengqian Yu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Sheng Cheng
- Department of Urology, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xiaoxu Zhou
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Department of Gynecologic Oncology, Women’s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Jia Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Yan Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Department of Gynecologic Oncology, Women’s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310006, China
- Cancer Center, Zhejiang University, Hangzhou 310013, China
| | - Pengyuan Liu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310016, China
- Cancer Center, Zhejiang University, Hangzhou 310013, China
- Department of Physiology and Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shiping Ding
- Department of Cell Biology, The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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Guan L, Grigoriev A. tatDB: a database of Ago1-mediated targets of transfer RNA fragments. Nucleic Acids Res 2023; 51:D297-D305. [PMID: 36350638 PMCID: PMC9825446 DOI: 10.1093/nar/gkac1018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/16/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
tRNA-derived fragments (tRFs) are a class of emerging post-transcriptional regulators of gene expression likely binding to the transcripts of target genes. However, only a few tRFs targets have been experimentally validated, making it hard to extrapolate the functions or binding mechanisms of tRFs. The paucity of resources supporting the identification of the targets of tRFs creates a bottleneck in the fast-developing field. We have previously analyzed chimeric reads in crosslinked Argonaute1-RNA complexes to help infer the guide-target pairs and binding mechanisms of multiple tRFs based on experimental data in human HEK293 cells. To efficiently disseminate these results to the research community, we designed a web-based database tatDB (targets of tRFs DataBase) populated with close to 250 000 experimentally determined guide-target pairs with ∼23 000 tRF isoforms. tatDB has a user-friendly interface with flexible query options/filters allowing one to obtain comprehensive information on given tRFs (or targets). Modes of interactions are supported by secondary structures of potential guide-target hybrids and binding motifs, essential for understanding the targeting mechanisms of tRFs. Further, we illustrate the value of the database on an example of hypothesis-building for a tRFs potentially involved in the lifecycle of the SARS-CoV-2 virus. tatDB is freely accessible at https://grigoriev-lab.camden.rutgers.edu/tatdb.
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Affiliation(s)
- Lingyu Guan
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
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Xia L, Guo H, Wu X, Xu Y, Zhao P, Yan B, Zeng Y, He Y, Chen D, Gale RP, Zhang Y, Zhang X. Human circulating small non-coding RNA signature as a non-invasive biomarker in clinical diagnosis of acute myeloid leukaemia. Theranostics 2023; 13:1289-1301. [PMID: 36923527 PMCID: PMC10008735 DOI: 10.7150/thno.80054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Background: Acute myeloid leukaemia (AML) is the most common acute leukaemia in adults; AML is highly heterogeneous and involves abnormalities at multiple omics levels. Small non-coding RNAs (sncRNAs) present in body fluids are important regulatory molecules and considered promising non-invasive clinical diagnostic biomarkers for disease. However, the signature of sncRNA profile alteration in AML patient serum and bone marrow supernatant is still under exploration. Methods: We examined data for blood and bone marrow samples from 80 consecutive, newly-diagnosed patients with AML and 12 healthy controls for high throughput small RNA-sequencing. Differentially expressed sncRNAs were analysed to reveal distinct patterns between AML patients and controls. Machine learning methods were used to evaluate the efficiency of specific sncRNAs in discriminating individuals with AML from controls. The altered expression level of individual sncRNAs was evaluated by RT-PCR, Q-PCR, and northern blot. Correlation analysis was employed to assess sncRNA patterns between serum and bone marrow supernatant. Results: We identified over 20 types of sncRNA categories beyond miRNAs in both serum and bone marrow supernatant, with highly coordinated expression patterns between them. Non-classical sncRNAs, including rsRNA (62.86%), ysRNA (14.97%), and tsRNA (4.22%), dominated among serum sncRNAs and showed sensitive alteration patterns in AML patients. According to machine learning-based algorithms, the tsRNA-based signature robustly discriminated subjects with AML from controls and was more reliable than that comprising miRNAs. Our data also showed that serum tsRNAs to be closely associated with AML prognosis, suggesting the potential application of serum tsRNAs as biomarkers to assist in AML diagnosis. Conclusions: We comprehensively characterized the expression pattern of circulating sncRNAs in blood and bone marrow and their alteration signature between healthy controls and AML patients. This study enriches research of sncRNAs in the regulation of AML, and provides insights into the role of sncRNAs in AML.
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Affiliation(s)
- Lin Xia
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Huanping Guo
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Xiao Wu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Yinying Xu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Pan Zhao
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Bingbing Yan
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Yunjing Zeng
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Yundi He
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Dan Chen
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Robert Peter Gale
- Haematology Centre, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China.,Jinfeng Laboratory, Chongqing, China
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Xu F, Yan J, Peng Z, Liu J, Li Z. Comprehensive analysis of a glycolysis and cholesterol synthesis-related genes signature for predicting prognosis and immune landscape in osteosarcoma. Front Immunol 2022; 13:1096009. [PMID: 36618348 PMCID: PMC9822727 DOI: 10.3389/fimmu.2022.1096009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Glycolysis and cholesterol synthesis are crucial in cancer metabolic reprogramming. The aim of this study was to identify a glycolysis and cholesterol synthesis-related genes (GCSRGs) signature for effective prognostic assessments of osteosarcoma patients. Methods Gene expression data and clinical information were obtained from GSE21257 and TARGET-OS datasets. Consistent clustering method was used to identify the GCSRGs-related subtypes. Univariate Cox regression and LASSO Cox regression analyses were used to construct the GCSRGs signature. The ssGSEA method was used to analyze the differences in immune cells infiltration. The pRRophetic R package was utilized to assess the drug sensitivity of different groups. Western blotting, cell viability assay, scratch assay and Transwell assay were used to perform cytological validation. Results Through bioinformatics analysis, patients diagnosed with osteosarcoma were classified into one of 4 subtypes (quiescent, glycolysis, cholesterol, and mixed subtypes), which differed significantly in terms of prognosis and tumor microenvironment. Weighted gene co-expression network analysis revealed that the modules strongly correlated with glycolysis and cholesterol synthesis were the midnight blue and the yellow modules, respectively. Both univariate and LASSO Cox regression analyses were conducted on screened module genes to identify 5 GCSRGs (RPS28, MCAM, EN1, TRAM2, and VEGFA) constituting a prognostic signature for osteosarcoma patients. The signature was an effective prognostic predictor, independent of clinical characteristics, as verified further via Kaplan-Meier analysis, ROC curve analysis, univariate and multivariate Cox regression analysis. Additionally, GCSRGs signature had strong correlation with drug sensitivity, immune checkpoints and immune cells infiltration. In cytological experiments, we selected TRAM2 as a representative gene to validate the validity of GCSRGs signature, which found that TRAM2 promoted the progression of osteosarcoma cells. Finally, at the pan-cancer level, TRAM2 had been correlated with overall survival, progression free survival, disease specific survival, tumor mutational burden, microsatellite instability, immune checkpoints and immune cells infiltration. Conclusion Therefore, we constructed a GCSRGs signature that efficiently predicted osteosarcoma patient prognosis and guided therapy.
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Affiliation(s)
- Fangxing Xu
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinglong Yan
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Jinglong Yan,
| | - Zhibin Peng
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jingsong Liu
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zecheng Li
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Pichot F, Hogg MC, Marchand V, Bourguignon V, Jirström E, Farrell C, Gibriel HA, Prehn JH, Motorin Y, Helm M. 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: 8] [Impact Index Per Article: 4.0] [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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Affiliation(s)
- Florian Pichot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Marion C. Hogg
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valérie Bourguignon
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Elisabeth Jirström
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Cliona Farrell
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Hesham A. Gibriel
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Jochen H.M. Prehn
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs. Animals (Basel) 2022; 12:ani12243561. [PMID: 36552481 PMCID: PMC9774726 DOI: 10.3390/ani12243561] [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: 11/24/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Epigenetic factors, including non-coding RNA regulation, play a vital role in the development of obesity and have been well researched. Transfer RNA-derived small RNA (tsRNA) is a class of non-coding RNA proven to be involved in various aspects of mammalian biology. Here we take pigs as a model for obesity research and use tsRNA-seq to investigate the difference in tsRNA expression in the subcutaneous adipose tissue of obese and lean pigs to elucidate the role of tsRNA in obesity development. A total of 482 tsRNAs were identified in pig adipose tissue, of which 123 were significantly differentially accumulated tsRNAs compared with the control group. The tRF-5c was the main type of these tsRNAs. The largest number of tsRNAs produced was the Gly-carrying tRNA, which produced 81 tsRNAs. Functional enrichment analysis revealed that differential tsRNAs indirectly participated in MAPK, AMPK, insulin resistance, the TNF signaling pathway, adipocytokine signaling pathway, and other signaling pathways by interacting with target genes. These are involved in bioenergetic metabolic regulatory processes, suggesting that tsRNAs may influence these pathways to mediate the regulation of energy metabolism in porcine adipocytes to promote lipid deposition, thus contributing to obesity. Our findings suggest a potential function of tsRNA in regulating obesity development.
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Yang X, Chen D, Zheng S, Yi M, Liu Z, Liu Y, Yang D, Liu Y, Tang L, Zhu C, Huang Y. BmHen1 is essential for eupyrene sperm development in Bombyx mori but PIWI proteins are not. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103874. [PMID: 36375757 DOI: 10.1016/j.ibmb.2022.103874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/02/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
In lepidopteran insects, sperm dimorphism is a remarkable feature, in which males exhibit two different types of sperms. Both sperm morphs are essential for fertilization: Eupyrene sperm carry DNA and fertilize eggs, whereas apyrene sperm, which do not have nuclei, are necessary for transport of eupyrene sperm into eggs. In this study, we showed that the gene BmHen1, which encodes a methyltransferase that modifies piRNAs, is necessary for eupyrene sperm development in the lepidopteran model insect, Bombyx mori. Loss-of-function mutants of BmHen1 of both sexes were sterile. BmHen1 female mutants laid fewer eggs than wild-type females, and the eggs laid had morphological defects. Immunofluorescence analysis of BmHen1 male mutants revealed that nuclei formation in the eupyrene sperm was defective, whereas apyrene sperm were normal. In mice, worms, and flies, the components in piRNA biogenesis pathway play an important role in gonad development; therefore, we constructed mutations in genes encoding core elements in the piRNA biogenesis pathway, Siwi, and BmAgo3. To our surprise, no obvious phenotypes were observed in the male reproduction system in the Siwi and BmAgo3 mutants, which demonstrated that sperm development in B. mori does not depend on piRNAs. As the sperm development phenotype in BmHen1 mutants mimics the phenotype of the BmPnldc1 mutants, we then performed RNA sequencing analysis of sperm bundles from both mutants. We found that the defects in eupyrene sperm resulted from dysregulation of the expression of genes involved in energy metabolism. Taken together, our findings demonstrate the crucial functions of BmHen1 in the development of eupyrene sperm and provide evidence that spermatogenesis in B. mori is PIWI-independent. Our results suggest potential targets for lepidopteran pest control and broaden our knowledge of the reproduction in this order of insects.
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Affiliation(s)
- Xu Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dongbin Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Shirui Zheng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Meiyan Yi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Zulian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongjian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dehong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yujia Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linmeng Tang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chenxu Zhu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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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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Zou L, Yang Y, Zhou B, Li W, Liu K, Li G, Miao H, Song X, Yang J, Geng Y, Li M, Bao R, Liu Y. tRF-3013b inhibits gallbladder cancer proliferation by targeting TPRG1L. Cell Mol Biol Lett 2022; 27:99. [PMID: 36401185 PMCID: PMC9673407 DOI: 10.1186/s11658-022-00398-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND tRNA-derived fragments (tRFs) are newly discovered noncoding RNAs and regulate tumor progression via diverse molecular mechanisms. However, the expression and biofunction of tRFs in gallbladder cancer (GBC) have not been reported yet. METHODS The expression of tRFs in GBC was detected by tRF and tiRNA sequencing in GBC tissues and adjacent tissues. The biological function of tRFs was investigated by cell proliferation assay, clonal formation assay, cell cycle assay, and xenotransplantation model in GBC cell lines. The molecular mechanism was discovered and verified by transcriptome sequencing, fluorescence in situ hybridization (FISH), target gene site prediction, and RNA binding protein immunoprecipitation (RIP). RESULTS tRF-3013b was significantly downregulated in GBC compared with para-cancer tissues. Decreased expression of tRF-3013b in GBC patients was correlated with poor overall survival. Dicer regulated the production of tRF-3013b, and its expression was positively correlated with tRF-3013b in GBC tissues. Functional experiments demonstrated that tRF-3013b inhibited GBC cell proliferation and induced cell-cycle arrest. Mechanically, tRF-3013b exerted RNA silencing effect on TPRG1L by binding to AGO3, and then inhibited NF-κB. TPRG1L overexpression could rescue the effects of tRF-3013b on GBC cell proliferation. CONCLUSIONS This study indicated that Dicer-induced tRF-3013b inhibited GBC proliferation by targeting TPRG1L and repressed NF-κB, pointing to tRF-3013b as a novel potential therapeutic target of GBC.
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Affiliation(s)
- Lu Zou
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Yang Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Biyu Zhou
- Department of Plastic and Reconstructive Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Weijian Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Ke Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Guoqiang Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Huijie Miao
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Xiaoling Song
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665, Kongjiang Road, Shanghai, 200092, China
| | - Jiahua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Yajun Geng
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China
| | - Maolan Li
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China.
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
| | - Runfa Bao
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China.
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 1665, Kongjiang Road, Shanghai, 200092, China.
| | - Yingbin Liu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China.
- Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, 200092, China.
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200032, China.
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Bhadsavle SS, Golding MC. Paternal epigenetic influences on placental health and their impacts on offspring development and disease. Front Genet 2022; 13:1068408. [PMID: 36468017 PMCID: PMC9716072 DOI: 10.3389/fgene.2022.1068408] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 07/25/2023] Open
Abstract
Our efforts to understand the developmental origins of birth defects and disease have primarily focused on maternal exposures and intrauterine stressors. Recently, research into non-genomic mechanisms of inheritance has led to the recognition that epigenetic factors carried in sperm also significantly impact the health of future generations. However, although researchers have described a range of potential epigenetic signals transmitted through sperm, we have yet to obtain a mechanistic understanding of how these paternally-inherited factors influence offspring development and modify life-long health. In this endeavor, the emerging influence of the paternal epigenetic program on placental development, patterning, and function may help explain how a diverse range of male exposures induce comparable intergenerational effects on offspring health. During pregnancy, the placenta serves as the dynamic interface between mother and fetus, regulating nutrient, oxygen, and waste exchange and coordinating fetal growth and maturation. Studies examining intrauterine maternal stressors routinely describe alterations in placental growth, histological organization, and glycogen content, which correlate with well-described influences on infant health and adult onset of disease. Significantly, the emergence of similar phenotypes in models examining preconception male exposures indicates that paternal stressors transmit an epigenetic memory to their offspring that also negatively impacts placental function. Like maternal models, paternally programmed placental dysfunction exerts life-long consequences on offspring health, particularly metabolic function. Here, focusing primarily on rodent models, we review the literature and discuss the influences of preconception male health and exposure history on placental growth and patterning. We emphasize the emergence of common placental phenotypes shared between models examining preconception male and intrauterine stressors but note that the direction of change frequently differs between maternal and paternal exposures. We posit that alterations in placental growth, histological organization, and glycogen content broadly serve as reliable markers of altered paternal developmental programming, predicting the emergence of structural and metabolic defects in the offspring. Finally, we suggest the existence of an unrecognized developmental axis between the male germline and the extraembryonic lineages that may have evolved to enhance fetal adaptation.
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Affiliation(s)
| | - Michael C. Golding
- Department of Veterinary Physiology and Pharmacology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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Wang L, Liu Y, Yan W, Huang C, Ding Z, Yang J, Jiang S, Sun L. Clinical Significance of High Expression of tRF-Glu-TTC-2 in Prostate Carcinoma and its Effect on Growth. Am J Mens Health 2022; 16:15579883221135970. [PMID: 36377736 PMCID: PMC9673532 DOI: 10.1177/15579883221135970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The tRNA-derived fragments (tRFs) are a new class of regulatory noncoding RNAs and have different biological functions in cancer. This article investigated the expression and clinicopathological significance of tRF-Glu-TTC-2 in prostate carcinoma (PCa), and its effect on tumor growth. Expression profiles of tRFs and tiRNAs were analyzed by tRF and tiRNAs microarray in PCa samples, and then the expression was confirmed by qRT-PCR; RNA in situ hybridization was used to detect the positive expression of tRF-Glu-TTC-2 and to analyze the correlation between the expression level of tRF-Glu-TTC-2 and clinicopathological parameters. CCK-8 experiment was used to detect the effect of tRF-Glu-TTC-2 on the proliferation of PCa cells, and nude mice subcutaneous tumor model was used to detect the effect of tRF-Glu-TTC-2 on the growth of PCa cells. The results showed that tRF-Glu-TTC-2 was mainly positive and its expression level increased in PCa. The high expression was closely related to the tumor size (p < .05). Overexpression of tRF-Glu-TTC-2 promoted the proliferation of PCa cells, and decreased expression of tRF-Glu-TTC-2 inhibited the proliferation of PCa cells (p < .05). The results of subcutaneous tumor transplantation in nude mice showed that the tumor volume and weight of the knockdown group were smaller than those of the control group(all ps < .05). Ki-67 staining showed that the proportion of Ki-67-positive cells in the reduced tRF-Glu-TTC-2 group was lower than that in the control group (p < .05). The tRF-Glu-TTC-2 may be a new oncogene that can promote growth and proliferation of PCa. It provides a new idea for the treatment of PCa.
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Affiliation(s)
- Lei Wang
- Department of Pathology and Forensic Medicine, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yaxin Liu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Wenqing Yan
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Caihong Huang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Zhiyan Ding
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Jiajia Yang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Shuwan Jiang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Lei Sun
- Department of Pathology and Forensic Medicine, College of Basic Medical Sciences, Dalian Medical University, Dalian, China,Prof. Lei Sun, Department of Pathology and Forensic Medicine, College of Basic Medical Sciences, Dalian Medical University, No. 9, west section of Lushun South Road, Dalian, Liaoning 116044, China.
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Ren J, Wu X, Shang FF, Qi Y, Tang Z, Wen C, Cao W, Cheng Q, Tan L, Chen H, Zhou HH, Zou H. The tRNA-Cys-GCA Derived tsRNAs Suppress Tumor Progression of Gliomas via Regulating VAV2. DISEASE MARKERS 2022; 2022:8708312. [PMID: 36426134 PMCID: PMC9681550 DOI: 10.1155/2022/8708312] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/29/2022] [Indexed: 02/03/2024]
Abstract
The tsRNAs (tRNA-derived small RNAs) are new types of small noncoding RNAs derived from tRNAs. Gliomas are well-known malignant brain tumors. The study focused on tsRNA characterizations within gliomas. Datasets processing, bioinformatics analyses, and visualizations were performed with the packages of Python and R. Cell proliferations were demonstrated via CCK8 assays and colony formation assays, and in vivo xenograft experiments. Dual-luciferase reporter assay was performed to confirm the binding of tsRNA with its targets. Via using bioinformatics approaches, the hundreds of tsRNAs with available expression abundance were identified in gliomas dataset, most of them derived from D-loop or T-loop fragments of tRNAs. Among tsRNAs derived from tRNA-Cys-GCA, tRFdb-3003a and tRFdb-3003b (tRFdb-3003a/b) were remarkably down-regulated in gliomas. The survival outcome of gliomas patients with low tRFdb-3003a/b expressions was notably worse than that of high-expression patients. In glioma cells, tRFdb-3003a could suppress cells proliferation and colony formation ability. In vivo, tRFdb-3003a suppressed the tumor growth of xenograft gliomas. Enrichment analyses displayed the tRFdb-3003a-related mRNAs were enriched in the specific GO terms, spliceosome and autophagy pathways, and three GSEA molecular signatures. Mechanically, 3'-UTR regions of VAV2 mRNA were predicted to contain the binding positions of tRFdb-3003a/b, tRFdb-3003a and tRFdb-3003b was effective to reduce the relative luciferase activity of cells with VAV2 wild-type reporter. Overexpression of tRFdb-3003a/b could down-regulated the expression levels of VAV2 protein and mRNA in glioma cells. The tRNA-Cys-GCA derived tRFdb-3003a and tRFdb-3003b might act as key player in tumor progressions of gliomas; tRFdb-3003a/b might directly bind to VAV2 and regulate VAV2 expressions in gliomas.
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Affiliation(s)
- Jian Ren
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
- Department of Neurology, The Affiliated Hospital of Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Xiaoling Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
- Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Fei-Fei Shang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yingqiang Qi
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Zhurong Tang
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Chunjie Wen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Weiguo Cao
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Quan Cheng
- Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China
| | - Lihong Tan
- Department of Neurology, The Affiliated Hospital of Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Huan Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Hong-Hao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
- Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China
| | - Hecun Zou
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
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Xiong Q, Zhang Y, Li J, Zhu Q. Small Non-Coding RNAs in Human Cancer. Genes (Basel) 2022; 13:genes13112072. [PMID: 36360311 PMCID: PMC9690286 DOI: 10.3390/genes13112072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Small non-coding RNAs are widespread in the biological world and have been extensively explored over the past decades. Their fundamental roles in human health and disease are increasingly appreciated. Furthermore, a growing number of studies have investigated the functions of small non-coding RNAs in cancer initiation and progression. In this review, we provide an overview of the biogenesis of small non-coding RNAs with a focus on microRNAs, PIWI-interacting RNAs, and a new class of tRNA-derived small RNAs. We discuss their biological functions in human cancer and highlight their clinical application as molecular biomarkers or therapeutic targets.
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Affiliation(s)
- Qunli Xiong
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junjun Li
- Department of Radiation Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Qing Zhu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
- Correspondence:
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127
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Mueth NA, Hulbert SH. Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction. Genomics 2022; 114:110526. [PMID: 36427746 DOI: 10.1016/j.ygeno.2022.110526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The wheat stripe rust fungus (Puccinia striiformis f.sp. tritici) threatens global wheat production. Small RNAs (sRNAs) modulate plant defense induction, and RNA exchange between host and microbe causes cross-kingdom gene silencing, but few examples are known in rust fungi. This study combined sRNA, parallel analysis of RNA ends, and gene expression data to discover sRNA-target pairs on each side of the interaction. Specific wheat 24 nt sRNAs were suppressed, while particular 35 nt fragments were strongly induced upon infection. Wheat sRNAs cleaved fungal transcripts coding for a ribosomal protein and a glycosyl hydrolase effector. Fungal microRNA-like and phased 21 nt sRNAs originated from long inverted repeats near protein coding genes. Fungal sRNAs targeted native transcripts: transposons and kinases; and cross-kingdom transcripts: a wheat nucleotide-binding domain leucine-rich repeat receptor (NLR) and multiple defense-related transcription factor families. This work sheds light on host-microbe coevolution and delivers prospects for developing pathogen control biotechnology.
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Affiliation(s)
- Nicholas A Mueth
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA.
| | - Scot H Hulbert
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
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Yoshida T, Latt KZ, Rosenberg AZ, Shrivastav S, Heymann J, Halushka MK, Winkler CA, Kopp JB. Transcriptomic Analysis of Human Podocytes In Vitro: Effects of Differentiation and APOL1 Genotype. Kidney Int Rep 2022; 8:164-178. [PMID: 36644347 PMCID: PMC9831945 DOI: 10.1016/j.ekir.2022.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction The mechanisms in podocytes that mediate the pathologic effects of the APOL1 high-risk (HR) variants remain incompletely understood, although various molecular and cellular mechanisms have been proposed. We previously established conditionally immortalized human urine-derived podocyte-like epithelial cell (HUPEC) lines to investigate APOL1 HR variant-induced podocytopathy. Methods We conducted comprehensive transcriptomic analysis, including mRNA, microRNA (miRNA), and transfer RNA fragments (tRFs), to characterize the transcriptional profiles in undifferentiated and differentiated HUPEC with APOL1 HR (G1/G2, 2 cell lines) and APOL1 low-risk (LR) (G0/G0, 2 cell lines) genotypes. We reanalyzed single-cell RNA-seq data from urinary podocytes from focal segmental glomerulosclerosis (FSGS) subjects to characterize the effect of APOL1 genotypes on podocyte transcriptomes. Results Differential expression analysis showed that the ribosomal pathway was one of the most enriched pathways, suggesting that altered function of the translation initiation machinery may contribute to APOL1 variant-induced podocyte injury. Expression of genes related to the elongation initiation factor 2 pathway was also enriched in the APOL1 HR urinary podocytes from single-cell RNA-seq, supporting a prior report on the role of this pathway in APOL1-associated cell injury. Expression of microRNA and tRFs were analyzed, and the profile of small RNAs differed by both differentiation status and APOL1 genotype. Conclusion We have profiled the transcriptomic landscape of human podocytes, including mRNA, miRNA, and tRF, to characterize the effects of differentiation and of different APOL1 genotypes. The candidate pathways, miRNAs, and tRFs described here expand understanding of APOL1-associated podocytopathies.
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Affiliation(s)
- Teruhiko Yoshida
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA,Correspondence: Teruhiko Yoshida, Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, 3N104, Bethesda, Maryland 20892-1268, USA.
| | - Khun Zaw Latt
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Shashi Shrivastav
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jurgen Heymann
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Cheryl A. Winkler
- Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Jeffrey B. Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Zeng X, Li J, Yang F, Xia R. The effect of narcotics on ferroptosis-related molecular mechanisms and signalling pathways. Front Pharmacol 2022; 13:1020447. [PMID: 36313359 PMCID: PMC9606818 DOI: 10.3389/fphar.2022.1020447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2022] Open
Abstract
Ferroptosis is a novel programmed cell death form characterized by iron-mediated reactive oxygen species-induced lipid peroxidation and subsequent cell damage that is distinct from apoptosis, necroptosis, pyroptosis, and autophagy. Most studies on ferroptosis are based on its function and mechanism, but there have been relatively few studies on the effects of drugs, especially anaesthetics, on ferroptosis. Therefore, we summarized the recent literature on the effects of anaesthetics on ferroptosis to understand the underlying mechanism. In particular, we focused on the targets of various anaesthetics in different mechanisms of ferroptosis and the effects of ferroptosis induction or inhibition by narcotics on various diseases. The aims of this review are to provide a relatively reasonable drug regimen for clinicians, to explore potential ferroptosis protection drugs and targets, to reduce perioperative complications and to improve the postoperative performance of patients, especially those who are critically ill.
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Affiliation(s)
- Xiaoqin Zeng
- Department of Anaesthesiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Jingda Li
- College of Life Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Fuyuan Yang
- School of Basic Medicine, Yangtze University Health Science Center, Jingzhou, Hubei, China
- *Correspondence: Fuyuan Yang, ; Rui Xia,
| | - Rui Xia
- Department of Anaesthesiology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
- *Correspondence: Fuyuan Yang, ; Rui Xia,
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130
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Xu D, Qiao D, Lei Y, Zhang C, Bu Y, Zhang Y. Transfer RNA-derived small RNAs (tsRNAs): Versatile regulators in cancer. Cancer Lett 2022; 546:215842. [PMID: 35964819 DOI: 10.1016/j.canlet.2022.215842] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/02/2022]
Abstract
tRNA-derived small RNAs (tsRNAs) represent a novel class of regulatory small non-coding RNAs (sncRNAs), produced by the specific cleavage of transfer RNAs (tRNAs). In recent years, pilot studies one after the other have uncovered the critical roles of tsRNAs in various fundamental biological processes as well as in the development of human diseases including cancer. Based on the newly updated hallmarks of cancer, we provide a comprehensive review regarding the dysregulation, functional implications and complicated molecular mechanisms of tsRNAs in cancer. In addition, the potential technical challenges and future prospects in the fields of tsRNA research are discussed in this review.
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Affiliation(s)
- Dandan Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Deqian Qiao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yunlong Lei
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Chundong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China.
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China.
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Liu D, Wu C, Wang J, Zhang L, Sun Z, Chen S, Ding Y, Wang W. Transfer RNA-derived fragment 5'tRF-Gly promotes the development of hepatocellular carcinoma by direct targeting of carcinoembryonic antigen-related cell adhesion molecule 1. Cancer Sci 2022; 113:3476-3488. [PMID: 35879647 PMCID: PMC9530880 DOI: 10.1111/cas.15505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
Transfer RNA-derived fragments are a group of small noncoding single-stranded RNA that play essential roles in multiple diseases. However, their biological functions in carcinogenesis are not well understood. In this study, 5'tRF-Gly was found to have significantly high expression in hepatocellular carcinoma (HCC), and the upregulation of 5'tRF-Gly was positively correlated with tumor size and tumor metastasis. Overexpression of 5'tRF-Gly induced increased growth rate and metastasis in HCC cells in vitro and in nude mice, while knockdown showed the opposite effect. Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) was confirmed to be a direct target of 5'tRF-Gly in HCC. In addition, the cytological effect of CEACAM1 knockdown proved to be similar to the overexpression of 5'tRF-Gly. Moreover, attenuation of CEACAM1 expression rescued the 5'tRF-Gly-mediated promoting effects on HCC cells. These data show that 5'tRF-Gly is a new tumor-promoting factor and could be a potential diagnostic biomarker or new therapeutic target for HCC.
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Affiliation(s)
- Dekai Liu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Chengdong Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Jingjie Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Lufei Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Zhongquan Sun
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Shihong Chen
- Department of Clinical MedicineWenzhou Medical CollegeWenzhouChina
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang ProvinceHangzhouChina
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang ProvinceHangzhouChina
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang UniversityHangzhouChina
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang ProvinceHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
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132
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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: 11] [Impact Index Per Article: 5.5] [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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133
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Khanbabaei H, Ebrahimi S, García-Rodríguez JL, Ghasemi Z, Pourghadamyari H, Mohammadi M, Kristensen LS. Non-coding RNAs and epithelial mesenchymal transition in cancer: molecular mechanisms and clinical implications. J Exp Clin Cancer Res 2022; 41:278. [PMID: 36114510 PMCID: PMC9479306 DOI: 10.1186/s13046-022-02488-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a fundamental process for embryonic development during which epithelial cells acquire mesenchymal characteristics, and the underlying mechanisms confer malignant features to carcinoma cells such as dissemination throughout the organism and resistance to anticancer treatments. During the past decades, an entire class of molecules, called non-coding RNA (ncRNA), has been characterized as a key regulator of almost every cellular process, including EMT. Like protein-coding genes, ncRNAs can be deregulated in cancer, acting as oncogenes or tumor suppressors. The various forms of ncRNAs, including microRNAs, PIWI-interacting RNAs, small nucleolar RNAs, transfer RNA-derived RNA fragments, long non-coding RNAs, and circular RNAs can orchestrate the complex regulatory networks of EMT at multiple levels. Understanding the molecular mechanism underlying ncRNAs in EMT can provide fundamental insights into cancer metastasis and may lead to novel therapeutic approaches. In this review, we describe recent advances in the understanding of ncRNAs in EMT and provide an overview of recent ncRNA applications in the clinic.
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134
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Characteristics of tRNA-Derived Small RNAs and microRNAs Associated with Immunocompromise in an Intrauterine Growth-Restricted Pig Model. Animals (Basel) 2022; 12:ani12162102. [PMID: 36009692 PMCID: PMC9404909 DOI: 10.3390/ani12162102] [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: 07/26/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Intrauterine growth restriction (IUGR) refers to the slow growth and development of an embryo or fetus in the uterus of mammals. IUGR newborns commonly present with slow growth and the development of the body and organs accompany increased risks of infection during the early life period. IUGR remains a significant global public health issue, particularly in developing countries. In this work, we investigated the transfer RNA-derived small RNA and microRNA expression profiles in the spleen using pigs as an IUGR model. These results uncover an important potential regulator network involved in immunocompromise caused by IUGR. The present studies provide a novel perspective on the molecular regulatory mechanism of IUGR and a reference for prevention and treatment. Abstract Intrauterine growth restriction (IUGR) is an important cause of newborn morbidity and mortality in mammals. Transfer RNA-derived small RNA (tsRNA) has become an emerging non-coding RNA in recent years. tsRNA and microRNAs (miRNAs) share similar mechanisms, which are involved in various biological processes. In this study, the pig was used as a model of IUGR, and the tsRNA and miRNA expression profile in the spleen was characterized by RNA sequencing. A total of 361 miRNAs and 620 tsRNAs were identified, of which 22 were differentially expressed miRNA (DEM) and 25 differentially expressed tsRNA (DET). tRF-5c were the primary tsRNA type making up more than 90%, and the most abundantly expressed tsRNAs are from tRNA-Gly-GCC. Functional enrichment analysis found that those DETs and DEMs have been implicated in the immune system process. Protein–protein interaction (PPI) network analysis revealed ssc-miR-370, ssc-miR-206, tiRNA-Ser-TGA-001 and tRF-Val-AAC-034 could be major regulators. TNF, TLR4, CD44, MAPK1 and STAT1 were predicted hub target genes. Those DETs and DEMs may regulate the T-cell receptor signaling pathway and Toll-like receptor signaling pathway to mediate the immunocompromise caused by IUGR. The results discussed in this article uncover the potential role of tsRNAs and miRNAs in IUGR porcine spleen.
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135
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Sommerauer C, Kutter C. Noncoding RNAs in liver physiology and metabolic diseases. Am J Physiol Cell Physiol 2022; 323:C1003-C1017. [PMID: 35968891 DOI: 10.1152/ajpcell.00232.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The liver holds central roles in detoxification, energy metabolism and whole-body homeostasis but can develop malignant phenotypes when being chronically overwhelmed with fatty acids and glucose. The global rise of metabolic-associated fatty liver disease (MAFLD) is already affecting a quarter of the global population. Pharmaceutical treatment options against different stages of MAFLD do not yet exist and several clinical trials against hepatic transcription factors and other proteins have failed. However, emerging roles of noncoding RNAs, including long (lncRNA) and short noncoding RNAs (sRNA), in various cellular processes pose exciting new avenues for treatment interventions. Actions of noncoding RNAs mostly rely on interactions with proteins, whereby the noncoding RNA fine-tunes protein function in a process termed riboregulation. The developmental stage-, disease stage- and cell type-specific nature of noncoding RNAs harbors enormous potential to precisely target certain cellular pathways in a spatio-temporally defined manner. Proteins interacting with RNAs can be categorized into canonical or non-canonical RNA binding proteins (RBPs) depending on the existence of classical RNA binding domains. Both, RNA- and RBP-centric methods have generated new knowledge of the RNA-RBP interface and added an additional regulatory layer. In this review, we summarize recent advances of how of RBP-lncRNA interactions and various sRNAs shape cellular physiology and the development of liver diseases such as MAFLD and hepatocellular carcinoma.
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Affiliation(s)
- Christian Sommerauer
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, grid.4714.6Karolinska Institute, Stockholm, Sweden
| | - Claudia Kutter
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, grid.4714.6Karolinska Institute, Stockholm, Sweden
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136
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A miR-34a-guided, tRNA iMet-derived, piR_019752-like fragment (tRiMetF31) suppresses migration and angiogenesis of breast cancer cells via targeting PFKFB3. Cell Death Dis 2022; 8:355. [PMID: 35961977 PMCID: PMC9374763 DOI: 10.1038/s41420-022-01054-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/12/2022] [Accepted: 05/03/2022] [Indexed: 12/01/2022]
Abstract
Although we recently demonstrated that miR-34a directly targets tRNAiMet precursors via Argonaute 2 (AGO2)-mediated cleavage, consequently attenuating the proliferation of breast cancer cells, whether tRNAiMet fragments derived from this cleavage influence breast tumor angiogenesis remains unknown. Here, using small-RNA-Seq, we identified a tRNAiMet-derived, piR_019752-like 31-nt fragment tRiMetF31 in breast cancer cells expressing miR-34a. Bioinformatic analysis predicted 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) as a potential target of tRiMrtF31, which was validated by luciferase assay. tRiMetF31 was downregulated, whereas PFKFB3 was overexpressed in cancer cell lines. Overexpression of tRiMetF31 profoundly inhibited the migration and angiogenesis of two breast cancer cell lines while slightly inducing apoptosis. Conversely, knockdown of tRiMetF31 restored PFKFB3-driven angiogenesis. miR-34a was downregulated, whereas tRNAiMet and PFKFB3 were upregulated in breast cancer, and elevated PFKFB3 significantly correlated with metastasis. Our findings demonstrate that tRiMetF31 profoundly suppresses angiogenesis by silencing PFKFB3, presenting a novel target for therapeutic intervention in breast cancer.
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137
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Kohansal M, Ghanbarisad A, Tabrizi R, Daraei A, Kashfi M, Tang H, Song C, Chen Y. tRNA-derived fragments in gastric cancer: Biomarkers and functions. J Cell Mol Med 2022; 26:4768-4780. [PMID: 35957621 PMCID: PMC9465185 DOI: 10.1111/jcmm.17511] [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: 03/11/2022] [Revised: 06/14/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
tRNA‐derived fragments (tRFs), non‐coding RNAs that regulate protein expression after transcription, have recently been identified as potential biomarkers. We identified differentially expressed tRFs in gastric cancer (GC) and the biological properties of tRFs in predicting the malignancy status of GCs as possible biomarkers. Until 15 February 2022, two independent reviewers did a thorough search in electronic databases of Scopus, EMBASE and PubMed. The QUADAS scale was used for quality assessment of the included studies. Ten articles investigating the clinical significance of tRFs, including 928 patients, were analysed. In 10 GC studies, seven tRFs were considerably upregulated and five tRFs were significantly downregulated when compared to controls. Risk of bias was rated low for index test, and flow as well as timing domains in relation to the review question. The applicability of the index test, flow and timing and patient selection for 10 studies was deemed low. In this study, we review the advances in the study of tRFs in GC and describe their functions in gene expression regulation, such as suppression of translation, cell differentiation, proliferation and the related signal transduction pathways associated with them. Our findings may offer researchers new ideas for cancer treatment as well as potential biomarkers for further research in GC.
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Affiliation(s)
- Maryam Kohansal
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran.,Department of biology, Payame Noor University, Tehran, Iran
| | - Ali Ghanbarisad
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran.,Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Reza Tabrizi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolreza Daraei
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mojtaba Kashfi
- Departmen of Microbiology, School of Medicine, Shahid Beheshti Univercity of Medical Sciences, Tehran, Iran
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cailu Song
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongming Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
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138
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Xu B, Liang J, Zou H, Wang J, Xiong Y, Pei J. Identification of Novel tRNA-Leu-CAA-Derived tsRNAs for the Diagnosis and Prognosis of Diffuse Gliomas. Cancer Manag Res 2022; 14:2609-2623. [PMID: 36072386 PMCID: PMC9441585 DOI: 10.2147/cmar.s367020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/27/2022] [Indexed: 12/26/2022] Open
Abstract
Purpose tsRNA is a type of small non-coding RNA derived from tRNA. Diffuse gliomas are the most common brain tumors. This investigation focused on tsRNA identification and characterization within gliomas. Methods The sequences of human tRNA and tsRNAs were taken from GtRNAdb, tRFdb and tRFexplorer databases. Data processing and bioinformatic analysis were performed with R or Python software. The expression of tsRNAs in glioma tissues was analyzed by qRT-PCR assay. Results With computational approaches, we identified hundreds of tsRNAs with available expression abundance in the glioma datasets, most of them derived from the 3′ end or 5′ end of mature tRNA. Among the tsRNAs derived from tRNA-Leu-CAA, ts-26, tRFdb-3012a, and tRFdb-3012b (tRFdb-3012a/b) were significantly decreased in diffuse gliomas. The clinical survivals of glioma patients with low tsRNA (ts-26, tRFdb-3012a, and tRFdb-3012b) expression were remarkably worse than that of those with high expression. Expression of tRFdb-3012a/b was correlated with IDH mutant status and MGMT promoter mutation in gliomas, and tRFdb-3012a/b and ts-23 tended to be highly expressed in patients with the IDH mutant. The enrichment analysis showed that some tRFdb-3012a/b-related genes were enriched in RNA splicing and processing, the spliceosome pathway and astrocyte molecular signatures. Moreover, the 3′ untranslated region of the RBM43 gene was predicted to contain putative binding sites of tRFdb-3012a/b, ts-26 may directly bind to the 3′ untranslated region of the HOXA13 gene, and the expressions of both RBM43 and HOXA13 were up-regulated in diffuse gliomas. High RBM43 and HOXA13 expressions were significantly associated with poor survival outcome of glioma patients. Conclusion These results suggest that tRNA-Leu-CAA-derived tsRNAs (ts-26, tRFdb-3012a, and tRFdb-3012b) could be explored as diagnostic and prognostic biomarkers for diffuse gliomas, and tRFdb-3012a/b and ts-26 may play an important role in the progression of gliomas, through binding RBM43 and HOXA13, respectively.
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Affiliation(s)
- Bing Xu
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, 441021, People’s Republic of China
| | - Jian Liang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, 441021, People’s Republic of China
| | - Hecun Zou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Jingwen Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yubo Xiong
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, 441021, People’s Republic of China
- Department of Neurosurgery, General Hospital of the Yangtze River Shipping, Wuhan Brain Hospital, Wuhan, Hubei, 430010, People’s Republic of China
| | - Jiao Pei
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, 441021, People’s Republic of China
- Correspondence: Jiao Pei; Yubo Xiong, Email ;
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139
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Wu H, Wei M, Li Y, Ma Q, Zhang H. Research Progress on the Regulation Mechanism of Key Signal Pathways Affecting the Prognosis of Glioma. Front Mol Neurosci 2022; 15. [DOI: https:/doi.org/10.3389/fnmol.2022.910543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Abstract
As is known to all, glioma, a global difficult problem, has a high malignant degree, high recurrence rate and poor prognosis. We analyzed and summarized signal pathway of the Hippo/YAP, PI3K/AKT/mTOR, miRNA, WNT/β-catenin, Notch, Hedgehog, TGF-β, TCS/mTORC1 signal pathway, JAK/STAT signal pathway, MAPK signaling pathway, the relationship between BBB and signal pathways and the mechanism of key enzymes in glioma. It is concluded that Yap1 inhibitor may become an effective target for the treatment of glioma in the near future through efforts of generation after generation. Inhibiting PI3K/Akt/mTOR, Shh, Wnt/β-Catenin, and HIF-1α can reduce the migration ability and drug resistance of tumor cells to improve the prognosis of glioma. The analysis shows that Notch1 and Sox2 have a positive feedback regulation mechanism, and Notch4 predicts the malignant degree of glioma. In this way, notch cannot only be treated for glioma stem cells in clinic, but also be used as an evaluation index to evaluate the prognosis, and provide an exploratory attempt for the direction of glioma treatment. MiRNA plays an important role in diagnosis, and in the treatment of glioma, VPS25, KCNQ1OT1, KB-1460A1.5, and CKAP4 are promising prognostic indicators and a potential therapeutic targets for glioma, meanwhile, Rheb is also a potent activator of Signaling cross-talk etc. It is believed that these studies will help us to have a deeper understanding of glioma, so that we will find new and better treatment schemes to gradually conquer the problem of glioma.
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140
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Wu H, Wei M, Li Y, Ma Q, Zhang H. Research Progress on the Regulation Mechanism of Key Signal Pathways Affecting the Prognosis of Glioma. Front Mol Neurosci 2022; 15:910543. [PMID: 35935338 PMCID: PMC9354928 DOI: 10.3389/fnmol.2022.910543] [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: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
As is known to all, glioma, a global difficult problem, has a high malignant degree, high recurrence rate and poor prognosis. We analyzed and summarized signal pathway of the Hippo/YAP, PI3K/AKT/mTOR, miRNA, WNT/β-catenin, Notch, Hedgehog, TGF-β, TCS/mTORC1 signal pathway, JAK/STAT signal pathway, MAPK signaling pathway, the relationship between BBB and signal pathways and the mechanism of key enzymes in glioma. It is concluded that Yap1 inhibitor may become an effective target for the treatment of glioma in the near future through efforts of generation after generation. Inhibiting PI3K/Akt/mTOR, Shh, Wnt/β-Catenin, and HIF-1α can reduce the migration ability and drug resistance of tumor cells to improve the prognosis of glioma. The analysis shows that Notch1 and Sox2 have a positive feedback regulation mechanism, and Notch4 predicts the malignant degree of glioma. In this way, notch cannot only be treated for glioma stem cells in clinic, but also be used as an evaluation index to evaluate the prognosis, and provide an exploratory attempt for the direction of glioma treatment. MiRNA plays an important role in diagnosis, and in the treatment of glioma, VPS25, KCNQ1OT1, KB-1460A1.5, and CKAP4 are promising prognostic indicators and a potential therapeutic targets for glioma, meanwhile, Rheb is also a potent activator of Signaling cross-talk etc. It is believed that these studies will help us to have a deeper understanding of glioma, so that we will find new and better treatment schemes to gradually conquer the problem of glioma.
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Affiliation(s)
- Hao Wu
- Graduate School of Dalian Medical University, Dalian, China
- Department of Neurosurgery, The Yangzhou School of Clinical Medicine of Dalian Medical University, Dalian, China
| | - Min Wei
- Graduate School of Dalian Medical University, Dalian, China
- Department of Neurosurgery, The Yangzhou School of Clinical Medicine of Dalian Medical University, Dalian, China
| | - Yuping Li
- Department of Neurosurgery, The Yangzhou School of Clinical Medicine of Dalian Medical University, Dalian, China
| | - Qiang Ma
- Department of Neurosurgery, The Yangzhou School of Clinical Medicine of Dalian Medical University, Dalian, China
| | - Hengzhu Zhang
- Graduate School of Dalian Medical University, Dalian, China
- Department of Neurosurgery, The Yangzhou School of Clinical Medicine of Dalian Medical University, Dalian, China
- *Correspondence: Hengzhu Zhang,
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141
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Liu X, Mei W, Padmanaban V, Alwaseem H, Molina H, Passarelli MC, Tavora B, Tavazoie SF. A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of its bound metabolic mRNAs. Mol Cell 2022; 82:2604-2617.e8. [PMID: 35654044 PMCID: PMC9444141 DOI: 10.1016/j.molcel.2022.05.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 04/04/2022] [Accepted: 05/05/2022] [Indexed: 01/09/2023]
Abstract
Stress-induced cleavage of transfer RNAs (tRNAs) into tRNA-derived fragments (tRFs) occurs across organisms from yeast to humans; yet, its mechanistic underpinnings and pathological consequences remain poorly defined. Small RNA profiling revealed increased abundance of a cysteine tRNA fragment (5'-tRFCys) during breast cancer metastatic progression. 5'-tRFCys was required for efficient breast cancer metastatic lung colonization and cancer cell survival. We identified Nucleolin as the direct binding partner of 5'-tRFCys. 5'-tRFCys promoted the oligomerization of Nucleolin and its bound metabolic transcripts Mthfd1l and Pafah1b1 into a higher-order transcript stabilizing ribonucleoprotein complex, which protected these transcripts from exonucleolytic degradation. Consistent with this, Mthfd1l and Pafah1b1 mediated pro-metastatic and metabolic effects downstream of 5'-tRFCys-impacting folate, one-carbon, and phosphatidylcholine metabolism. Our findings reveal that a tRF can promote oligomerization of an RNA-binding protein into a transcript stabilizing ribonucleoprotein complex, thereby driving specific metabolic pathways underlying cancer progression.
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Affiliation(s)
- Xuhang Liu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenbin Mei
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Veena Padmanaban
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Maria C Passarelli
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Bernardo Tavora
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA.
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142
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Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
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Bayazit MB, Jacovetti C, Cosentino C, Sobel J, Wu K, Brozzi F, Rodriguez-Trejo A, Stoll L, Guay C, Regazzi R. Small RNAs derived from tRNA fragmentation regulate the functional maturation of neonatal β cells. Cell Rep 2022; 40:111069. [PMID: 35830789 DOI: 10.1016/j.celrep.2022.111069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/03/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging class of small non-coding RNAs with distinct cellular functions. Here, we studied the contribution of tRFs to the regulation of postnatal β cell maturation, a critical process that may lead to diabetes susceptibility in adulthood. We identified three tRFs abundant in neonatal rat islets originating from 5' halves (tiRNA-5s) of histidine and glutamate tRNAs. Their inhibition in these islets reduced β cell proliferation and insulin secretion. Mitochondrial respiration was also perturbed, fitting with the mitochondrial enrichment of nuclear-encoded tiRNA-5HisGTG and tiRNA-5GluCTC. Notably, tiRNA-5 inhibition reduced Mpc1, a mitochondrial pyruvate carrier whose knock down largely phenocopied tiRNA-5 inhibition. tiRNA-5HisGTG interactome revealed binding to Musashi-1, which was essential for the mitochondrial enrichment of tiRNA-5HisGTG. Finally, tiRNA-5s were dysregulated in the islets of diabetic and diabetes-prone animals. Altogether, tiRNA-5s represent a class of regulators of β cell maturation, and their deregulation in neonatal islets may lead to diabetes susceptibility in adulthood.
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Affiliation(s)
- Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Cristina Cosentino
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Jonathan Sobel
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Kejing Wu
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Flora Brozzi
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | | | - Lisa Stoll
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland.
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144
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Deng L, Wang H, Fan T, Chen L, Shi Z, Mi J, Huang W, Wang R, Hu K. Potential Functions of the tRNA-Derived Fragment tRF-Gly-GCC Associated With Oxidative Stress in Radiation-Induced Lung Injury. Dose Response 2022; 20:15593258221128744. [PMID: 36176737 PMCID: PMC9513591 DOI: 10.1177/15593258221128744] [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] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Objective Transfer RNA-derived small RNAs (tsRNAs) are a novel type of non-coding RNA with various regulatory functions. They are associated with oxidative stress in various diseases, but their potential functions in radiation-induced lung injury (RILI) remain uncertain. Methods To explore the role of tsRNAs in RILI, we used X-rays to irradiate human bronchial epithelial cells and examined the expression profile of altered tsRNAs by RNA sequencing and bioinformatics analysis. Sequencing results were verified by qRT-PCR. tsRNA functions were explored using several methods, including CCK-8, reactive oxygen species (ROS) assays, cell transfection, and western blotting. Results Eighty-six differentially expressed tRNA-derived fragments (tRFs) were identified: 64 were upregulated, and 22 were downregulated. Among them, the regulation of tRF-Gly-GCC, associated with oxidative stress, may be mediated by the inhibition of cell proliferation, promotion of ROS production, and apoptosis in the occurrence and development of RILI. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the underlying molecular mechanism may involve the PI3K/AKT and the FOXO1 signaling pathways. Conclusion Our findings provide new insights into the molecular mechanisms underpinning RILI, advancing the clinical prevention and treatment of this disease.
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Affiliation(s)
- Lin Deng
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Oncology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Housheng Wang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ting Fan
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liuyin Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhiling Shi
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - JingLin Mi
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - WeiMei Huang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rensheng Wang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Kai Hu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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145
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He T, Guo H, Xia L, Shen X, Huang Y, Wu X, Jiang X, Xu Y, Tan Y, Zhang Y, Tan D. Alterations of RNA Modification in Mouse Germ Cell-2 Spermatids Under Hypoxic Stress. Front Mol Biosci 2022; 9:871737. [PMID: 35775084 PMCID: PMC9237606 DOI: 10.3389/fmolb.2022.871737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Hypoxia is a known stress factor in mammals and has been shown to potentially impair male fertility, which manifests as spermatogenic dysfunction and decreased semen quality. Studies have shown that RNA modifications, the novel post-transcriptional regulators, are involved in spermatogenesis, and hypoxia-induced alterations in RNA modification in testes and sperm cells may be associated with impaired spermatogenesis in mice. However, the molecular mechanisms via which RNA modifications influence spermatogenesis under hypoxic stress conditions are unclear. In this study, we generated a mouse Germ Cell-2 spermatid (GC-2spd) hypoxia model by culturing cells in a 1% O2 incubator for 48 h or treating them with CoCl2 for 24 h. The hypoxia treatment significantly inhibited proliferation and induced apoptosis in GC-2spd cells. The RNA modification signatures of total RNAs (2 types) and differentially sized RNA fragments (7 types of approximately 80 nt-sized tRNAs; 9 types of 17–50 nt-sized sncRNAs) were altered, and tRNA stability was partially affected. Moreover, the expression profiles of sncRNAs, such as microRNAs, tsRNAs, rsRNAs, and ysRNAs, were significantly regulated, and this might be related to the alterations in RNA modification and subsequent transcriptomic changes. We comprehensively analyzed alterations in RNA modification signatures in total RNAs, tRNAs (approximately 80 nt), and small RNAs (17–50 nt) as well as the expression profiles of sncRNAs and transcriptomes in hypoxia-treated GC-2spd cells; our data suggested that RNA modifications may be involved in cellular responses under hypoxic stress conditions and could provide a basis for a better understanding of the molecular mechanisms underlying male infertility.
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Affiliation(s)
- Tong He
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Huanping Guo
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Lin Xia
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xipeng Shen
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Huang
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Xiao Wu
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xuelin Jiang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yinying Xu
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yi Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
| | - Yunfang Zhang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- *Correspondence: Yunfang Zhang, ; Dongmei Tan,
| | - Dongmei Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China
- *Correspondence: Yunfang Zhang, ; Dongmei Tan,
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146
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Chen X, Xie W, Zhang M, Shi Y, Xu S, Cheng H, Wu L, Pathak JL, Zheng Z. The Emerging Role of Non-Coding RNAs in Osteogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells. Front Cell Dev Biol 2022; 10:903278. [PMID: 35652090 PMCID: PMC9150698 DOI: 10.3389/fcell.2022.903278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Autologous bone marrow-derived mesenchymal stem cells (BMSCs) are more easily available and frequently used for bone regeneration in clinics. Osteogenic differentiation of BMSCs involves complex regulatory networks affecting bone formation phenomena. Non-coding RNAs (ncRNAs) refer to RNAs that do not encode proteins, mainly including microRNAs, long non-coding RNAs, circular RNAs, piwi-interacting RNAs, transfer RNA-derived small RNAs, etc. Recent in vitro and in vivo studies had revealed the regulatory role of ncRNAs in osteogenic differentiation of BMSCs. NcRNAs had both stimulatory and inhibitory effects on osteogenic differentiation of BMSCs. During the physiological condition, osteo-stimulatory ncRNAs are upregulated and osteo-inhibitory ncRNAs are downregulated. The opposite effects might occur during bone degenerative disease conditions. Intracellular ncRNAs and ncRNAs from neighboring cells delivered via exosomes participate in the regulatory process of osteogenic differentiation of BMSCs. In this review, we summarize the recent advances in the regulatory role of ncRNAs on osteogenic differentiation of BMSCs during physiological and pathological conditions. We also discuss the prospects of the application of modulation of ncRNAs function in BMSCs to promote bone tissue regeneration in clinics.
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Affiliation(s)
- Xiaoying Chen
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Wei Xie
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Ming Zhang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Yuhan Shi
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Shaofen Xu
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Haoyu Cheng
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Lihong Wu
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,Department of Basic Oral Medicine, School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Janak L Pathak
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,Department of Basic Oral Medicine, School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zheng
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China.,Department of Basic Oral Medicine, School and Hospital of Stomatology, Guangzhou Medical University, Guangzhou, China.,Laboratory for Myology, Department of Human Movement Sciences, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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147
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Gu X, Zhang Y, Qin X, Ma S, Huang Y, Ju S. Transfer RNA-derived small RNA: an emerging small non-coding RNA with key roles in cancer. Exp Hematol Oncol 2022; 11:35. [PMID: 35658952 PMCID: PMC9164556 DOI: 10.1186/s40164-022-00290-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
Transfer RNAs (tRNAs) promote protein translation by binding to the corresponding amino acids and transporting them to the ribosome, which is essential in protein translation. tRNA-derived small RNAs (tsRNAs) are derived fragments of tRNAs that are cleaved explicitly under certain conditions. An increasing amount of research has demonstrated that tsRNAs have biological functions rather than just being degradation products. tsRNAs can exert functions such as regulating gene expression to influence cancer progression. Their dysregulation is closely associated with various cancers and can serve as diagnostic and prognostic biomarkers for cancer. This review summarizes the generation, classification, and biological functions of tsRNAs, and highlights the roles of tsRNAs in different cancers and their applications as tumor markers.
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Affiliation(s)
- Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xinyue Qin
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shuo Ma
- Medical School of Nantong University, Nantong University, Nantong, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, China. .,Department of Medical Oncology, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Xisi Road, No. 20, Nantong, China.
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148
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Filetti V, La Ferlita A, Di Maria A, Cardile V, Graziano ACE, Rapisarda V, Ledda C, Pulvirenti A, Loreto C. Dysregulation of microRNAs and tRNA-derived ncRNAs in mesothelial and mesothelioma cell lines after asbestiform fiber exposure. Sci Rep 2022; 12:9181. [PMID: 35654808 PMCID: PMC9163335 DOI: 10.1038/s41598-022-13044-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Experimental evidence demonstrated that fluoro-edenite (FE) can develop chronic respiratory diseases and elicit carcinogenic effects. Environmental exposure to FE fibers is correlated with malignant pleural mesothelioma (MPM). An early diagnosis of MPM, and a comprehensive health monitoring of the patients exposed to FE fibers are two clinical issues that may be solved by the identification of specific biomarkers. We reported the microRNA (miRNA) and transfer RNA-derived non coding RNA (tRNA-derived ncRNA) transcriptome in human normal mesothelial and malignant mesothelioma cell lines exposed or not exposed to several concentration FE fibers. Furthermore, an interactive mesothelioma-based network was derived by using NetME tool. In untreated condition, the expression of miRNAs and tRNA-derived ncRNAs in tumor cells was significantly different with respect to non-tumor samples. Moreover, interesting and significant changes were found after the exposure of both cells lines to FE fibers. The network-based pathway analysis showed several signaling and metabolic pathways potentially involved in the pathogenesis of MPM. From papers analyzed by NetME, it is clear that many miRNAs can positively or negatively influence various pathways involved in MPM. For the first time, the analysis of tRNA-derived ncRNAs molecules in the context of mesothelioma has been made by using in vitro systems. Further studies will be designed to test and validate their diagnostic potential in high-risk individuals' liquid biopsies.
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Affiliation(s)
- Veronica Filetti
- Human Anatomy and Histology Unit, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Alessandro La Ferlita
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy
- Department of Cancer Biology and Genetics, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Antonio Di Maria
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy
| | - Venera Cardile
- Physiology Unit, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Adriana C E Graziano
- Physiology Unit, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Venerando Rapisarda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy
| | - Caterina Ledda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.
| | - Alfredo Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy
| | - Carla Loreto
- Human Anatomy and Histology Unit, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy
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149
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Peng G, Zhu C, Sun Q, Li J, Chen Y, Guo Y, Ji H, Yang F, Dong W. Testicular miRNAs and tsRNAs provide insight into gene regulation during overwintering and reproduction of Onychostoma macrolepis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:481-499. [PMID: 35595880 DOI: 10.1007/s10695-022-01078-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
The late overwintering period and breeding period are two important developmental stages of testis in Onychostoma macrolepis. Small non-coding RNAs (sncRNAs) are well-known regulators of biological processes associated with numerous biological processes. This study aimed to elucidate the roles of four sncRNA classes (microRNAs [miRNAs], Piwi-interacting RNAs [piRNAs], tRNA-derived small RNAs [tsRNAs], and rRNA-derived small RNAs [rsRNAs]) across testes in the late overwintering period (in March) and breeding period (in June) by high-throughput sequencing. The testis of O. macrolepis displayed the highest levels of piRNAs and lowest levels of rsRNAs. Compared with miRNAs and tsRNAs in June, tsRNAs in March had a higher abundance, while miRNAs in March had a much lower abundance. Bioinformatics analysis identified 1,362 and 1,340 differentially expressed miRNAs and tsRNAs, respectively. Further analysis showed that miR-200-1, miR-143-1, tRFi-Lys-CTT-1, and tRFi-Glu-CTC-1 could play critical roles during the overwintering and breeding periods. Our findings provided an unprecedented insight to reveal the epigenetic mechanism underlying the overwintering and reproduction process of male O. macrolepis.
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Affiliation(s)
- Guofan Peng
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Chao Zhu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Qingfang Sun
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Jincan Li
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Yining Chen
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Yingjie Guo
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
- College of Forestry, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China
| | - Fangxia Yang
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
- College of Forestry, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
- Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, No. 22 Xinong Road, Shaanxi, 712100, China.
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150
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Peng G, Sun Q, Chen Y, Wu X, Guo Y, Ji H, Yang F, Dong W. A comprehensive overview of ovarian small non-coding RNAs in the late overwintering and breeding periods of Onychostoma macrolepis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100967. [PMID: 35168176 DOI: 10.1016/j.cbd.2022.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The development of the ovary of Onychostoma macrolepis undergoes distinct annual cyclic changes in which small non-coding RNAs (sncRNAs) could play vital roles. In this study, four sncRNA classes in the ovary, including miRNA, piRNAs, tsRNA, and rsRNAs, were systematically profiled by high-throughput sequencing. In adult ovaries of O. macrolepis, 247 miRNAs and 235 tsRNAs were identified as differentially expressing in the late overwintering period (in March) and breeding period (in June). Some up-regulated sncRNAs in March, such as miR-125-1 and tRFi-Lys-CTT-1, could be involved in inhibiting biomolecule metabolism and enhancing stress tolerance during the overwintering period. Compared with the level expression of sncRNAs in March, some sncRNAs were up-regulated in June, such as miR-146-1 and tRFi-Gly-GCC-1, and could be involved in influencing molecular synthesis and metabolism, enhancing oocyte proliferation and maturation, accelerating ovarian development, and increasing fertilization of oocytes by regulating related target mRNAs. The results suggested that sncRNAs in the ovary of Onychostoma macrolepis not only reflect characteristics of the fish's physiology at different developmental periods, but also directly affect ovarian development and oocyte maturation during the breeding period. In conclusion, these results significantly advance our understanding of the roles of sncRNA during overwintering and reproduction periods, and provide a novel perspective for uncovering characteristics of the special overwintering ecology and reproductive physiology of an atypical cavefish.
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Affiliation(s)
- Guofan Peng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingfang Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yining Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaodong Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yingjie Guo
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China; Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fangxia Yang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China; Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Wuzi Dong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Biology Research Centre of Qin Mountains Wildlife, Northwest A&F University, Yangling, Shaanxi 712100, China.
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