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Wang K, Liu CY, Fang B, Li B, Li YH, Xia QQ, Zhao Y, Cheng XL, Yang SM, Zhang MH, Wang K. The function and therapeutic potential of transfer RNA-derived small RNAs in cardiovascular diseases: A review. Pharmacol Res 2024; 206:107279. [PMID: 38942340 DOI: 10.1016/j.phrs.2024.107279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are a class of small non-coding RNA (sncRNA) molecules derived from tRNA, including tRNA derived fragments (tRFs) and tRNA halfs (tiRNAs). tsRNAs can affect cell functions by participating in gene expression regulation, translation regulation, intercellular signal transduction, and immune response. They have been shown to play an important role in various human diseases, including cardiovascular diseases (CVDs). Targeted regulation of tsRNAs expression can affect the progression of CVDs. The tsRNAs induced by pathological conditions can be detected when released into the extracellular, giving them enormous potential as disease biomarkers. Here, we review the biogenesis, degradation process and related functional mechanisms of tsRNAs, and discuss the research progress and application prospects of tsRNAs in different CVDs, to provide a new perspective on the treatment of CVDs.
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Affiliation(s)
- Kai Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Ying-Hui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Qian-Qian Xia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xue-Li Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Su-Min Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| | - Mei-Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China.
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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Wang Q, Ying X, Huang Q, Wang Z, Duan S. Exploring the role of tRNA-derived small RNAs (tsRNAs) in disease: implications for HIF-1 pathway modulation. J Mol Med (Berl) 2024; 102:973-985. [PMID: 38850298 DOI: 10.1007/s00109-024-02458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/26/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
The tRNA-derived small RNAs (tsRNAs) can be categorized into two main groups: tRNA-derived fragments (tRFs) and tRNA-derived stress-induced RNAs (tiRNAs). Each group possesses specific molecular sizes, nucleotide compositions, and distinct physiological functions. Notably, hypoxia-inducible factor-1 (HIF-1), a transcriptional activator dependent on oxygen, comprises one HIF-1β subunit and one HIF-α subunit (HIF-1α/HIF-2α/HIF-3α). The activation of HIF-1 plays a crucial role in gene transcription, influencing key aspects of cancer biology such as angiogenesis, cell survival, glucose metabolism, and invasion. The involvement of HIF-1α activation has been demonstrated in numerous human diseases, particularly cancer, making HIF-1 an attractive target for potential disease treatments. Through a series of experiments, researchers have identified two tiRNAs that interact with the HIF-1 pathway, impacting disease development: 5'tiRNA-His-GTG in colorectal cancer (CRC) and tiRNA-Val in diabetic retinopathy (DR). Specifically, 5'tiRNA-His-GTG promotes CRC development by targeting LATS2, while tiRNA-Val inhibits Sirt1, leading to HIF-1α accumulation and promoting DR development. Clinical data have further indicated that certain tsRNAs' expression levels are associated with the prognosis and pathological features of CRC patients. In CRC tumor tissues, the expression level of 5'tiRNA-His-GTG is significantly higher compared to normal tissues, and it shows a positive correlation with tumor size. Additionally, KEGG analysis has revealed multiple tRFs involved in regulating the HIF-1 pathway, including tRF-Val-AAC-016 in diabetic foot ulcers (DFU) and tRF-1001 in pathological ocular angiogenesis. This comprehensive article reviews the biological functions and mechanisms of tsRNAs related to the HIF-1 pathway in diseases, providing a promising direction for subsequent translational medicine research.
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Affiliation(s)
- Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310015, China
| | - Xiaowei Ying
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310015, China
| | - Qinyuan Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310015, China
| | - Zehua Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310015, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310015, China.
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, 310015, China.
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Wang Q, Huang Q, Ying X, Zhou Y, Duan S. Exploring the regulatory role of tsRNAs in the TNF signaling pathway: Implications for cancer and non-cancer diseases. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:1-10. [PMID: 38971324 DOI: 10.1016/j.pbiomolbio.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/31/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs), a recently identified subclass of small non-coding RNAs (sncRNAs), emerge through the cleavage of mature transfer RNA (tRNA) or tRNA precursors mediated by specific enzymes. The tumor necrosis factor (TNF) protein, a signaling molecule produced by activated macrophages, plays a pivotal role in systemic inflammation. Its multifaceted functions include the capacity to eliminate or hinder tumor cells, enhance the phagocytic capabilities of neutrophils, confer resistance against infections, induce fever, and prompt the production of acute phase proteins. Notably, four TNF-related tsRNAs have been conclusively linked to distinct diseases. Examples include 5'tiRNA-Gly in skeletal muscle injury, tsRNA-21109 in systemic lupus erythematosus (SLE), tRF-Leu-AAG-001 in endometriosis (EMs), and tsRNA-04002 in intervertebral disk degeneration (IDD). These tsRNAs exhibit the ability to suppress the expression of TNF-α. Additionally, KEGG analysis has identified seven tsRNAs potentially involved in modulating the TNF pathway, exerting their influence across a spectrum of non-cancerous diseases. Noteworthy instances include aberrant tiRNA-Ser-TGA-001 and tRF-Val-AAC-034 in intrauterine growth restriction (IUGR), irregular tRF-Ala-AGC-052 and tRF-Ala-TGC-027 in obesity, and deviant tiRNA-His-GTG-001, tRF-Ser-GCT-113, and tRF-Gln-TTG-035 in irritable bowel syndrome with diarrhea (IBS-D). This comprehensive review explores the biological functions and mechanisms of tsRNAs associated with the TNF signaling pathway in both cancer and other diseases, offering novel insights for future translational medical research.
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Affiliation(s)
- Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
| | - Qinyuan Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
| | - Xiaowei Ying
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
| | - Yang Zhou
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China; Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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Tian H, Gao S, Xu M, Yang M, Shen M, Liu J, Li G, Zhuang D, Hu Z, Wang C. tiRNA-Gly-GCC-001 in major depressive disorder: Promising diagnostic and therapeutic biomarker. Br J Pharmacol 2024; 181:1952-1972. [PMID: 38439581 DOI: 10.1111/bph.16319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND AND PURPOSE In major depressive disorder (MDD), exploration of biomarkers will be helpful in diagnosing the disorder as well as in choosing a treatment and predicting the treatment response. Currently, tRNA-derived small ribonucleic acids (tsRNAs) have been established as promising non-invasive biomarker candidates that may enable a more reliable diagnosis or monitoring of various diseases. Herein, we aimed to explore tsRNA expression together with functional activities in MDD development. EXPERIMENTAL APPROACH Serum samples were obtained from patients with MDD and healthy controls, and small RNA sequencing (RNA-Seq) was used to profile tsRNA expression. Dysregulated tsRNAs in MDD were validated by quantitative real-time polymerase chain reaction (qRT-PCR). The diagnostic utility of specific tsRNAs and the expression of these tsRNAs after antidepressant treatment were analysed. KEY RESULTS In total, 38 tsRNAs were significantly differentially expressed in MDD samples relative to healthy individuals (34 up-regulated and 4 down-regulated). qRT-PCR was used to validate the expression of six tsRNAs that were up-regulated in MDD (tiRNA-1:20-chrM.Ser-GCT, tiRNA-1:33-Gly-GCC-1, tRF-1:22-chrM.Ser-GCT, tRF-1:31-Ala-AGC-4-M6, tRF-1:31-Pro-TGG-2 and tRF-1:32-chrM.Gln-TTG). Interestingly, serum tiRNA-Gly-GCC-001 levels exhibited an area under the ROC curve of 0.844. Moreover, tiRNA-Gly-GCC-001 is predicted to suppress brain-derived neurotrophic factor (BDNF) expression. Furthermore, significant tiRNA-Gly-GCC-001 down-regulation was evident following an 8-week treatment course and served as a promising baseline predictor of patient response to antidepressant therapy. CONCLUSION AND IMPLICATIONS Our current work reports for the first time that tiRNA-Gly-GCC-001 is a promising MDD biomarker candidate that can predict patient responses to antidepressant therapy.
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Affiliation(s)
- Haihua Tian
- Zhejiang Key Laboratory of Pathophysiology, Health Center, Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Shugui Gao
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Miaomiao Xu
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Mei Yang
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Mengyuan Shen
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Jimeng Liu
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Guangxue Li
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Dingding Zhuang
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Zhenyu Hu
- Department of Psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, Zhejiang, China
- Department of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Chuang Wang
- Zhejiang Key Laboratory of Pathophysiology, Health Center, Ningbo University, Ningbo, Zhejiang, China
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Zhang J, Li Y, Chen Y, Zhang J, Jia Z, He M, Liao X, He S, Bian JS, Nie XW. o 8G Site-Specifically Modified tRF-1-AspGTC: A Novel Therapeutic Target and Biomarker for Pulmonary Hypertension. Circ Res 2024; 135:76-92. [PMID: 38747146 DOI: 10.1161/circresaha.124.324421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/18/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Hypoxia and oxidative stress contribute to the development of pulmonary hypertension (PH). tRNA-derived fragments play important roles in RNA interference and cell proliferation, but their epitranscriptional roles in PH development have not been investigated. We aimed to gain insight into the mechanistic contribution of oxidative stress-induced 8-oxoguanine in pulmonary vascular remodeling. METHODS Through small RNA modification array analysis and quantitative polymerase chain reaction, a significant upregulation of the 8-oxoguanine -modified tRF-1-AspGTC was found in the lung tissues and the serum of patients with PH. RESULTS This modification occurs at the position 5 of the tRF-1-AspGTC (5o8G tRF). Inhibition of the 5o8G tRF reversed hypoxia-induced proliferation and apoptosis resistance in pulmonary artery smooth muscle cells. Further investigation unveiled that the 5o8G tRF retargeted mRNA of WNT5A (Wingless-type MMTV integration site family, member 5A) and CASP3 (Caspase3) and inhibited their expression. Ultimately, BMPR2 (Bone morphogenetic protein receptor 2) -reactive oxygen species/5o8G tRF/WNT5A signaling pathway exacerbated the progression of PH. CONCLUSIONS Our study highlights the role of site-specific 8-oxoguanine-modified tRF in promoting the development of PH. Our findings present a promising therapeutic avenue for managing PH and propose 5o8G tRF as a potential innovative marker for diagnosing this disease.
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Affiliation(s)
- Junting Zhang
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, China (Junting Zhang, Y.L., S.H.)
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China (Junting Zhang, Z.J., M.H., J.-S.B.)
| | - Yiying Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, China (Junting Zhang, Y.L., S.H.)
| | - Yuan Chen
- Lung Transplant Group, Wuxi People's Hospital Affiliated to Nanjing Medical University, China (Y.C.)
| | - Jianchao Zhang
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
| | - Zihui Jia
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China (Junting Zhang, Z.J., M.H., J.-S.B.)
| | - Muhua He
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China (Junting Zhang, Z.J., M.H., J.-S.B.)
| | - Xueyi Liao
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
| | - Siyu He
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, China (Junting Zhang, Y.L., S.H.)
| | - Jin-Song Bian
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China (Junting Zhang, Z.J., M.H., J.-S.B.)
| | - Xiao-Wei Nie
- Shenzhen Institute of Respiratory Disease, Shenzhen Key Laboratory of Respiratory Disease, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
- The First Affiliated Hospital, Southern University of Science and Technology), China (Junting Zhang, Y.L., Jianchao Zhang, Z.J., M.H., X.L., S.H., J.-S.B., X.-W.N.)
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Dubnov S, Bennett ER, Yayon N, Yakov O, Bennett DA, Seshadri S, Mufson E, Tzur Y, Greenberg D, Kuro-O M, Paldor I, Abraham CR, Soreq H. Knockout of the longevity gene Klotho perturbs aging and Alzheimer's disease-linked brain microRNAs and tRNA fragments. Commun Biol 2024; 7:720. [PMID: 38862813 PMCID: PMC11166644 DOI: 10.1038/s42003-024-06407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
Overexpression of the longevity gene Klotho prolongs lifespan, while its knockout shortens lifespan and impairs cognition via perturbation of myelination and synapse formation. However, comprehensive analysis of Klotho knockout effects on mammalian brain transcriptomics is lacking. Here, we report that Klotho knockout alters the levels of aging- and cognition related mRNAs, long non-coding RNAs, microRNAs and tRNA fragments. These include altered neuronal and glial regulators in murine models of aging and Alzheimer's disease and in human Alzheimer's disease post-mortem brains. We further demonstrate interaction of the knockout-elevated tRNA fragments with the spliceosome, possibly affecting RNA processing. Last, we present cell type-specific short RNA-seq datasets from FACS-sorted neurons and microglia of live human brain tissue demonstrating in-depth cell-type association of Klotho knockout-perturbed microRNAs. Together, our findings reveal multiple RNA transcripts in both neurons and glia from murine and human brain that are perturbed in Klotho deficiency and are aging- and neurodegeneration-related.
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Affiliation(s)
- Serafima Dubnov
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Estelle R Bennett
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Nadav Yayon
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Or Yakov
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sudha Seshadri
- UT Health Medical Arts & Research Center, San Antonio, TX, USA
| | - Elliott Mufson
- Dept. Translational Neuroscience, Barrow Neurological Institute, St. Joseph's Medical Center, Phoenix, AZ, USA
| | - Yonat Tzur
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - David Greenberg
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Makoto Kuro-O
- Division of Anti-aging Medicine, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Iddo Paldor
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
- Dept of Neurosurgery, the Shaare Zedek Medical Center, Jerusalem, Israel
| | - Carmela R Abraham
- Departments of Biochemistry and Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Klogenix LLC., Boston, MA, USA
| | - Hermona Soreq
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.
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7
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Gotte G. Effects of Pathogenic Mutants of the Neuroprotective RNase 5-Angiogenin in Amyotrophic Lateral Sclerosis (ALS). Genes (Basel) 2024; 15:738. [PMID: 38927674 PMCID: PMC11202570 DOI: 10.3390/genes15060738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the motoneurons. More than 40 genes are related with ALS, and amyloidogenic proteins like SOD1 and/or TDP-43 mutants are directly involved in the onset of ALS through the formation of polymorphic fibrillogenic aggregates. However, efficacious therapeutic approaches are still lacking. Notably, heterozygous missense mutations affecting the gene coding for RNase 5, an enzyme also called angiogenin (ANG), were found to favor ALS onset. This is also true for the less-studied but angiogenic RNase 4. This review reports the substrate targets and illustrates the neuroprotective role of native ANG in the neo-vascularization of motoneurons. Then, it discusses the molecular determinants of many pathogenic ANG mutants, which almost always cause loss of function related to ALS, resulting in failures in angiogenesis and motoneuron protection. In addition, ANG mutations are sometimes combined with variants of other factors, thereby potentiating ALS effects. However, the activity of the native ANG enzyme should be finely balanced, and not excessive, to avoid possible harmful effects. Considering the interplay of these angiogenic RNases in many cellular processes, this review aims to stimulate further investigations to better elucidate the consequences of mutations in ANG and/or RNase 4 genes, in order to achieve early diagnosis and, possibly, successful therapies against ALS.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
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8
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Loveland AB, Koh CS, Ganesan R, Jacobson A, Korostelev AA. Structural mechanism of angiogenin activation by the ribosome. Nature 2024; 630:769-776. [PMID: 38718836 DOI: 10.1038/s41586-024-07508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/02/2024] [Indexed: 05/15/2024]
Abstract
Angiogenin, an RNase-A-family protein, promotes angiogenesis and has been implicated in cancer, neurodegenerative diseases and epigenetic inheritance1-10. After activation during cellular stress, angiogenin cleaves tRNAs at the anticodon loop, resulting in translation repression11-15. However, the catalytic activity of isolated angiogenin is very low, and the mechanisms of the enzyme activation and tRNA specificity have remained a puzzle3,16-23. Here we identify these mechanisms using biochemical assays and cryogenic electron microscopy (cryo-EM). Our study reveals that the cytosolic ribosome is the activator of angiogenin. A cryo-EM structure features angiogenin bound in the A site of the 80S ribosome. The C-terminal tail of angiogenin is rearranged by interactions with the ribosome to activate the RNase catalytic centre, making the enzyme several orders of magnitude more efficient in tRNA cleavage. Additional 80S-angiogenin structures capture how tRNA substrate is directed by the ribosome into angiogenin's active site, demonstrating that the ribosome acts as the specificity factor. Our findings therefore suggest that angiogenin is activated by ribosomes with a vacant A site, the abundance of which increases during cellular stress24-27. These results may facilitate the development of therapeutics to treat cancer and neurodegenerative diseases.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.
| | - Cha San Koh
- RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA
| | - Robin Ganesan
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, MA, USA
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Cai J, Li C, Liu S, Tan M, Sun Y, Sun X, Yang M, He B. Angiogenin-mediated tsRNAs control inflammation and metabolic disorder by regulating NLRP3 inflammasome. Cell Death Differ 2024:10.1038/s41418-024-01311-8. [PMID: 38740959 DOI: 10.1038/s41418-024-01311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
The cellular stress response system in immune cells plays a crucial role in regulating the development of inflammatory diseases. In response to cellular damage or microbial infection, the assembly of the NLRP3 inflammasome induces pyroptosis and the release of inflammatory cytokines. Meanwhile, Angiogenin (Ang)-mediated transfer RNA-derived small RNAs (tsRNAs) promote cell survival under stressful conditions. While both tsRNAs and inflammasomes are induced under stress conditions, the interplay between these two systems and their implications in regulating inflammatory diseases remains poorly understood. In this study, it was demonstrated that Ang deficiency exacerbated sodium arsenite-induced activation of NLRP3 inflammasome and pyroptosis. Moreover, Ang-induced 5'-tsRNAs inhibited NLRP3 inflammasome activation and pyroptosis. Mechanistically, 5'-tsRNAs recruit DDX3X protein into stress granules (SGs), consequently inhibiting the interaction between DDX3X and NLRP3, thus leading to the suppression of NLRP3 inflammasome activation. Furthermore, in vivo results showed that Ang deficiency led to the downregulation of tsRNAs, ultimately leading to an exacerbation of NLRP3 inflammasome-dependent inflammation, including lipopolysaccharide-induced systemic inflammation and type-2 diabetes-related inflammation. Altogether, our study sheds a new light on the role of Ang-induced 5'-tsRNAs in regulating NLRP3 inflammasome activation via SGs, and highlights tsRNAs as a promising target for the treatment of NLRP3 inflammasome-related diseases.
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Affiliation(s)
- Jiangxue Cai
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chenxuan Li
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Suyuan Liu
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Meiling Tan
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yiran Sun
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiaoxiao Sun
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Miaoxin Yang
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Bin He
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China.
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Wan X, Shi W, Ma L, Wang L, Zheng R, He J, Wang Y, Li X, Zha X, Wang J, Xu L. A 3'-pre-tRNA-derived small RNA tRF-1-Ser regulated by 25(OH)D promotes proliferation and stemness by inhibiting the function of MBNL1 in breast cancer. Clin Transl Med 2024; 14:e1681. [PMID: 38725048 PMCID: PMC11082093 DOI: 10.1002/ctm2.1681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND We explored the potential novel anticancer mechanisms of 25-hydroxyvitamin D (25(OH)D), a vitamin D metabolite with antitumour effects in breast cancer. It is stable in serum and is used to assess vitamin D levels in clinical practice. Transfer RNA-derived small RNAs are small noncoding RNAs that generate various distinct biological functions, but more research is needed on their role in breast cancer. METHODS Small RNA microarrays were used to explore the novel regulatory mechanism of 25(OH)D. High-throughput RNA-sequencing technology was used to detect transcriptome changes after 25(OH)D treatment and tRF-1-Ser knockdown. RNA pull-down and high-performance liquid chromatography-mass spectrometry/mass spectrometry were used to explore the proteins bound to tRF-1-Ser. In vitro and in vivo functional experiments were conducted to assess the influence of 25(OH)D and tRF-1-Ser on breast cancer. Semi-quantitative PCR was performed to detect alternative splicing events. Western blot assay and qPCR were used to assess protein and mRNA expression. RESULTS The expression of tRF-1-Ser is negatively regulated by 25(OH)D. In our breast cancer (BRCA) clinical samples, we found that the expression of tRF-1-Ser was higher in cancer tissues than in paired normal tissues, and was significantly associated with tumour invasion. Moreover, tRF-1-Ser inhibits the function of MBNL1 by hindering its nuclear translocation. Functional experiments and transcriptome data revealed that the downregulation of tRF-1-Ser plays a vital role in the anticancer effect of 25(OH)D. CONCLUSIONS In brief, our research revealed a novel anticancer mechanism of 25(OH)D, unveiled the vital function of tRF-1-Ser in BRCA progression, and suggested that tRF-1-Ser could emerge as a new therapeutic target for BRCA.
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Affiliation(s)
- Xinyu Wan
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Wenjie Shi
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lingjun Ma
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lexin Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ran Zheng
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinzhi He
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ye Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xuan Li
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaoming Zha
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jue Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lu Xu
- Department of NutritionThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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11
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Muthukumar S, Li CT, Liu RJ, Bellodi C. Roles and regulation of tRNA-derived small RNAs in animals. Nat Rev Mol Cell Biol 2024; 25:359-378. [PMID: 38182846 DOI: 10.1038/s41580-023-00690-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.
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Affiliation(s)
- Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
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12
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Chen Q, Li D, Jiang L, Wu Y, Yuan H, Shi G, Liu F, Wu P, Jiang K. Biological functions and clinical significance of tRNA-derived small fragment (tsRNA) in tumors: Current state and future perspectives. Cancer Lett 2024; 587:216701. [PMID: 38369004 DOI: 10.1016/j.canlet.2024.216701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
A new class of noncoding RNAs, tsRNAs are not only abundant in humans but also have high tissue specificity. Recently, an increasing number of studies have explored the correlations between tsRNAs and tumors, showing that tsRNAs can affect biological behaviors of tumor cells, such as proliferation, apoptosis and metastasis, by modulating protein translation, RNA transcription or posttranscriptional regulation. In addition, tsRNAs are widely distributed and stably expressed, which endows them with broad application prospects in diagnosing and predicting the prognosis of tumors, and they are expected to become new biomarkers. However, notably, the current research on tsRNAs still faces problems that need to be solved. In this review, we describe the characteristics of tsRNAs as well as their unique features and functions in tumors. Moreover, we also discuss the potential opportunities and challenges in clinical applications and research of tsRNAs.
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Affiliation(s)
- Qun Chen
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Danrui Li
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Luyang Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Yuan
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guodong Shi
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Fengyuan Liu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengfei Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Kuirong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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13
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Wang Q, Huang Q, Ying X, Shen J, Duan S. Unveiling the role of tRNA-derived small RNAs in MAPK signaling pathway: implications for cancer and beyond. Front Genet 2024; 15:1346852. [PMID: 38596214 PMCID: PMC11002130 DOI: 10.3389/fgene.2024.1346852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are novel small non-coding RNAs originating from mature or precursor tRNAs (pre-tRNA), typically spanning 14 to 30 nt. The Mitogen-activated protein kinases (MAPK) pathway orchestrates cellular responses, influencing proliferation, differentiation, apoptosis, and transformation. tsRNAs influence the expression of the MAPK signaling pathway by targeting specific proteins within the pathway. Presently, four MAPK-linked tsRNAs have implications in gastric cancer (GC) and high-grade serous ovarian cancer (HGSOC). Notably, tRF-Glu-TTC-027 and tRF-Val-CAC-016 modulate MAPK-related protein expression, encompassing p38, Myc, ERK, CyclinD1, CyclinB, and c-Myc, hindering GC progression via MAPK pathway inhibition. Moreover, tRF-24-V29K9UV3IU and tRF-03357 remain unexplored in specific mechanisms. KEGG analysis posits varied tsRNAs in MAPK pathway modulation for diverse non-cancer maladies. Notably, high tRF-36-F900BY4D84KRIME and tRF-23-87R8WP9IY expression relates to varicose vein (VV) risk. Elevated tiRNA-Gly-GCC-001, tRF-Gly-GCC-012, tRF-Gly-GCC-013, and tRF-Gly-GCC-016 target spinal cord injury (SCI)-related brain-derived neurotrophic factor (BDNF), influencing MAPK expression. tRF-Gly-CCC-039 associates with diabetes foot sustained healing, while tRF-5014a inhibits autophagy-linked ATG5 in diabetic cardiomyopathy (DCM). Additionally, tsRNA-14783 influences keloid formation by regulating M2 macrophage polarization. Upregulation of tRF-Arg-ACG-007 and downregulation of tRF-Ser-GCT-008 are associated with diabetes. tsRNA-04002 alleviates Intervertebral disk degeneration (IDD) by targeting PRKCA. tsRNA-21109 alleviates Systemic lupus erythematosus (SLE) by inhibiting macrophage M1 polarization. The upregulated tiNA-Gly-GCC-002 and the downregulated tRF-Ala-AGC-010, tRF-Gln-CTG-005 and tRF-Leu-AAG-001 may be involved in the pathogenesis of Lupus nephritis (LN) by affecting the expression of MAPK pathway. Downregulation of tsRNA-1018, tsRNA-3045b, tsRNA-5021a and tsRNA-1020 affected the expression of MAPK pathway, thereby improving Acute lung injury (ALI). This review comprehensively dissects tsRNA roles in MAPK signaling across cancers and other diseases, illuminating a novel avenue for translational medical exploration.
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Affiliation(s)
- Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qinyuan Huang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xiaowei Ying
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
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14
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Zhao Y, Wang K, Zhao C, Liu N, Wang Z, Yang W, Cheng Z, Zhou L, Wang K. The function of tRNA-derived small RNAs in cardiovascular diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102114. [PMID: 38314096 PMCID: PMC10835008 DOI: 10.1016/j.omtn.2024.102114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
tRNA-derived small RNAs (tsRNAs) constitute a subgroup of small noncoding RNAs (ncRNAs) originating from tRNA molecules. Their rich content, evolutionary conservatism, high stability, and widespread existence makes them significant in disease research. These characteristics have positioned tsRNAs as key players in various physiological and pathological processes. tsRNA actively participates in regulating many cellular processes, such as cell death, proliferation, and metabolism. tsRNAs could be promising diagnostic markers for cardiovascular diseases (CVDs). tsRNAs have been identified in serums, suggesting their utility as early indicators for the diagnosis of CVDs. Moreover, the regulatory roles of tsRNAs in CVDs make them promising targets for therapeutic intervention. This review provides a succinct overview of the characteristics, classification, and regulatory functions of tsRNAs in the context of CVDs. By shedding light on the intricate roles of tsRNAs, this knowledge could pave the way for the development of innovative diagnostic tools and therapeutic strategies for CVDs.
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Affiliation(s)
- Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Chun Zhao
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Ning Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zhihong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Wenting Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zewei Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Luyu Zhou
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
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15
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Huang T, Zhao Y, Jiang G, Yang Z. tsRNA: A Promising Biomarker in Breast Cancer. J Cancer 2024; 15:2613-2626. [PMID: 38577588 PMCID: PMC10988313 DOI: 10.7150/jca.93531] [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: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are a novel class of non-coding small RNAs, generated from specific cleavage sites of tRNA or pre-tRNA. tsRNAs can directly participate in RNA silencing, transcription, translation, and other processes. Their dysregulation is closely related to the occurrence and development of various cancers. Breast cancer is one of the most common and fastest-growing malignant tumors in humans. tsRNAs have been found to be dysregulated in breast cancer, serving as a new target for exploring the pathogenesis of breast cancer. They are also considered new tumor markers, providing a basis for diagnosis and treatment. This article reviews the generation, classification, mechanism of action, function of tsRNAs, and their biological effects and related mechanisms in breast cancer, in the hope of providing a new direction for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Ting Huang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yuexin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Guoqin Jiang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zhixue Yang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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16
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Jawad SF, Altalbawy FMA, Hussein RM, Fadhil AA, Jawad MA, Zabibah RS, Taraki TY, Mohan CD, Rangappa KS. The strict regulation of HIF-1α by non-coding RNAs: new insight towards proliferation, metastasis, and therapeutic resistance strategies. Cancer Metastasis Rev 2024; 43:5-27. [PMID: 37552389 DOI: 10.1007/s10555-023-10129-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/21/2023] [Indexed: 08/09/2023]
Abstract
The hypoxic environment is prominently witnessed in most solid tumors and is associated with the promotion of cell proliferation, epithelial-mesenchymal transition (EMT), angiogenesis, metabolic reprogramming, therapeutic resistance, and metastasis of tumor cells. All the effects are mediated by the expression of a transcription factor hypoxia-inducible factor-1α (HIF-1α). HIF-1α transcriptionally modulates the expression of genes responsible for all the aforementioned functions. The stability of HIF-1α is regulated by many proteins and non-coding RNAs (ncRNAs). In this article, we have critically discussed the crucial role of ncRNAs [such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), Piwi-interacting RNAs (piRNAs), and transfer RNA (tRNA)-derived small RNAs (tsRNAs)] in the regulation of stability and expression of HIF-1α. We have comprehensively discussed the molecular mechanisms and relationship of HIF-1α with each type of ncRNA in either promotion or repression of human cancers and therapeutic resistance. We have also elaborated on ncRNAs that are in clinical examination for the treatment of cancers. Overall, the majority of aspects concerning the relationship between HIF-1α and ncRNAs have been discussed in this article.
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Affiliation(s)
- Sabrean Farhan Jawad
- Department of Pharmacy, Al-Mustaqbal University College, Hilla, Babylon, 51001, Iraq
| | - Farag M A Altalbawy
- National Institute of Laser Enhanced Sciences, University of Cairo, Giza, 12613, Egypt
- Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Ali Abdulhussain Fadhil
- College of Medical Technology, Medical Lab Techniques, Al-Farahidi University, Baghdad, Iraq
| | - Mohammed Abed Jawad
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq
| | - Rahman S Zabibah
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | | | - Chakrabhavi Dhananjaya Mohan
- Department of Studies in Molecular Biology, University of Mysore, Manasagangotri, Mysore, 570006, India.
- FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226 001, India.
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Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [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: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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La Ferlita A, Alaimo S, Nigita G, Distefano R, Beane JD, Tsichlis PN, Ferro A, Croce CM, Pulvirenti A. tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer. iScience 2024; 27:108810. [PMID: 38303722 PMCID: PMC10831894 DOI: 10.1016/j.isci.2024.108810] [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: 04/28/2023] [Revised: 08/02/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
tRNA-derived ncRNAs are a heterogeneous class of non-coding RNAs recently proposed to be active regulators of gene expression and be involved in many diseases, including cancer. Consequently, several online resources on tRNA-derived ncRNAs have been released. Although interesting, such resources present only basic features and do not adequately exploit the wealth of knowledge available about tRNA-derived ncRNAs. Therefore, we introduce tRFUniverse, a novel online resource for the analysis of tRNA-derived ncRNAs in human cancer. tRFUniverse presents an extensive collection of classes of tRNA-derived ncRNAs analyzed across all the TCGA and TARGET tumor cohorts, NCI-60 cell lines, and biological fluids. Moreover, public AGO CLASH/CLIP-Seq data were analyzed to identify the molecular interactions between tRNA-derived ncRNAs and other transcripts. Importantly, tRFUniverse combines in a single resource a comprehensive set of features that we believe may be helpful to investigate the involvement of tRNA-derived ncRNAs in cancer biology.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Joal D. Beane
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
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19
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Bhatter N, Dmitriev SE, Ivanov P. Cell death or survival: Insights into the role of mRNA translational control. Semin Cell Dev Biol 2024; 154:138-154. [PMID: 37357122 PMCID: PMC10695129 DOI: 10.1016/j.semcdb.2023.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Cellular stress is an intrinsic part of cell physiology that underlines cell survival or death. The ability of mammalian cells to regulate global protein synthesis (aka translational control) represents a critical, yet underappreciated, layer of regulation during the stress response. Various cellular stress response pathways monitor conditions of cell growth and subsequently reshape the cellular translatome to optimize translational outputs. On the molecular level, such translational reprogramming involves an intricate network of interactions between translation machinery, RNA-binding proteins, mRNAs, and non-protein coding RNAs. In this review, we will discuss molecular mechanisms, signaling pathways, and targets of translational control that contribute to cellular adaptation to stress and to cell survival or death.
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Affiliation(s)
- Nupur Bhatter
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Harvard Initiative for RNA Medicine, Boston, Massachusetts, USA.
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20
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Li D, Xie X, Yin N, Wu X, Yi B, Zhang H, Zhang W. tRNA-Derived Small RNAs: A Novel Regulatory Small Noncoding RNA in Renal Diseases. KIDNEY DISEASES (BASEL, SWITZERLAND) 2024; 10:1-11. [PMID: 38322624 PMCID: PMC10843216 DOI: 10.1159/000533811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/23/2023] [Indexed: 02/08/2024]
Abstract
Background tRNA-derived small RNAs (tsRNAs) are an emerging class of small noncoding RNAs derived from tRNA cleavage. Summary With the development of high-throughput sequencing, various biological roles of tsRNAs have been gradually revealed, including regulation of mRNA stability, transcription, translation, direct interaction with proteins and as epigenetic factors, etc. Recent studies have shown that tsRNAs are also closely related to renal disease. In clinical acute kidney injury (AKI) patients and preclinical AKI models, the production and differential expression of tsRNAs in renal tissue and plasma were observed. Decreased expression of tsRNAs was also found in urine exosomes from chronic kidney disease patients. Dysregulation of tsRNAs also appears in models of nephrotic syndrome and patients with lupus nephritis. And specific tsRNAs were found in high glucose model in vitro and in serum of diabetic nephropathy patients. In addition, tsRNAs were also differentially expressed in patients with kidney cancer and transplantation. Key Messages In the present review, we have summarized up-to-date works and reviewed the relationship and possible mechanisms between tsRNAs and kidney diseases.
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Affiliation(s)
- Dan Li
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Xian Xie
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Ni Yin
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Xueqin Wu
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Bin Yi
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
| | - Wei Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
- The Critical Kidney Disease Research Center of Central South University, Changsha, China
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21
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Liang Y, Kong L, Zhang Y, Zhang Y, Shi M, Huang J, Kong H, Qi S, Yang Y, Hong J, Zhu M, Zhu X, Sun X, Zhang S, Wu L, Zhao C. Transfer RNA derived fragment, tRF-Glu-CTC, aggravates the development of neovascular age-related macular degeneration. Theranostics 2024; 14:1500-1516. [PMID: 38389841 PMCID: PMC10879880 DOI: 10.7150/thno.92943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Rationale: Angiogenesis expedites tissue impairment in many diseases, including age-related macular degeneration (AMD), a leading cause of irreversible blindness in elderly. A substantial proportion of neovascular AMD patients, characterized by aberrant choroidal neovascularization (CNV), exhibit poor responses or adverse reactions to anti-VEGF therapy. Herein, we aimed to unveil the function of newly identified transfer RNA-derived small RNA, tRF-Glu-CTC, in the pathology of CNV and determine its potential in inhibiting angiogenesis. Methods: Small non-coding RNA sequencing and quantitative polymerase chain reaction were conducted to detect expression pattern of tRF-Glu-CTC in CNV development. Immunofluorescence staining, fundus fluorescein angiography and ex vivo choroidal sprouting assays were employed for the evaluation of tRF-Glu-CTC's function in CNV development. The role of tRF-Glu-CTC in endothelial cells were determined by in vitro endothelial cell proliferation, migration and tube formation assays. Transcriptome sequencing, dual-luciferase reporter assay and in vitro experiments were conducted to investigate downstream mechanism of tRF-Glu-CTC mediated pathology. Results: tRF-Glu-CTC exhibited substantial up-regulation in AMD patients, laser-induced CNV model, and endothelial cells under hypoxia condition, which is a hallmark of CNV. Inhibiting tRF-Glu-CTC reduced angiogenesis and hypoxia stress in the neovascular region without neuroretina toxicity in laser-induced CNV model, showing an anti-angiogenic effect comparable to bevacizumab, while overexpression of tRF-Glu-CTC significantly augmented CNV. Mechanically, under hypoxia condition, angiogenin was involved in the production of tRF-Glu-CTC, which in turn triggered endothelial cell tubulogenesis, migration and promoted the secretion of inflammatory factors via the suppression of vasohibin 1 (VASH1). When downregulating VASH1 expression, the inhibition of tRF-Glu-CTC showed minimal suppression on angiogenesis. Conclusions: This study demonstrated the important role of tRF-Glu-CTC in the progression of angiogenesis. Targeting of tRF-Glu-CTC may be an alternative to current anti-VEGF therapy for CNV in AMD and other conditions with angiogenesis.
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Affiliation(s)
- Yu Liang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Lingjie Kong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yuelu Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yihan Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Mingsu Shi
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Jiaqiu Huang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Hongyu Kong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Siyi Qi
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yunlong Yang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiaxu Hong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Meidong Zhu
- Save Sight Institute, Discipline of Clinical Ophthalmology and Eye Health, University of Sydney, Camperdown, NSW 2000, Australia
- New South Weals Tissue Bank, New South Weals Organ and Tissue Donation Service, Sydney Eye Hospital, 8 Macquarie Street, Sydney 2000, Australia
| | - Xiangjia Zhu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Xinghuai Sun
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Shujie Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Lianqun Wu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Chen Zhao
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
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22
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Karousi P, Samiotaki M, Makridakis M, Zoidakis J, Sideris DC, Scorilas A, Carell T, Kontos CK. 3'-tRF-Cys GCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways. Funct Integr Genomics 2023; 23:341. [PMID: 37987851 PMCID: PMC10663186 DOI: 10.1007/s10142-023-01272-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
tRNA fragments (tRFs) are small non-coding RNAs generated through specific cleavage of tRNAs and involved in various biological processes. Among the different types of tRFs, the 3'-tRFs have attracted scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3'-tRF-CysGCA, a tRF deriving from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3'-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3'-tRF-CysGCA levels in human cells have not been investigated so far. To fill this gap, we stably overexpressed 3'-tRF-CysGCA in HEK-293 cells and performed transcriptomic and proteomic analyses. Moreover, we validated the interaction of this tRF with putative targets, the levels of which were found to be affected by 3'-tRF-CysGCA overexpression. Lastly, we investigated the implication of 3'-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3'-tRF-CysGCA overexpression led to changes in the global gene expression profile of HEK-293 cells and that multiple cellular pathways were affected by the deregulation of the levels of this tRF. Additionally, we demonstrated that 3'-tRF-CysGCA directly interacts with thymopoietin (TMPO) transcript variant 1 (also known as LAP2α), leading to modulation of its levels. In conclusion, our findings suggest that 3'-tRF-CysGCA plays a significant role in gene expression regulation and highlight the importance of this tRF in cellular processes.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center, "Alexander Fleming", Vari, Greece
| | - Manousos Makridakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jerome Zoidakis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Thomas Carell
- Department for Chemistry, Institute for Chemical Epigenetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
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23
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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24
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Zhang L, Liu J, Hou Y. Classification, function, and advances in tsRNA in non-neoplastic diseases. Cell Death Dis 2023; 14:748. [PMID: 37973899 PMCID: PMC10654580 DOI: 10.1038/s41419-023-06250-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
tRNA-derived small RNAs (tsRNAs) are non-coding small RNAs produced by specific endonucleases following the processing and splicing of precursor or mature tRNAs upon starvation, oxidative stress, hypoxia, and other adverse conditions. tRNAs are classified into two major categories, tRNA fragments (tRFs) and tRNA-derived stress-induced small RNAs (tiRNAs), based on differences in splice sites. With the development of high-throughput sequencing technologies in recent years, tsRNAs have been found to have important biological functions, including inhibition of apoptosis, epigenetic regulation, cell-cell communication, translation, and regulation of gene expression. Additionally, these molecules have been found to be aberrantly expressed in various diseases and to be involved in several pathological processes. In this article, the classification and nomenclature, biological functions, and potential use of tsRNAs as diagnostic biomarkers and therapeutic targets in non-neoplastic diseases are reviewed. Although tsRNA research is at its infancy, their potential in the treatment of non-tumor diseases warrants further investigation.
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Affiliation(s)
- Liou Zhang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jie Liu
- Translational Research Experiment Department, Science Experiment Center, China Medical University, Shenyang, China.
| | - Yang Hou
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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25
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Akiyama Y, Ivanov P. tRNA-derived RNAs: Biogenesis and roles in translational control. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1805. [PMID: 37406666 PMCID: PMC10766869 DOI: 10.1002/wrna.1805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023]
Abstract
Transfer RNA (tRNA)-derived RNAs (tDRs) are a class of small non-coding RNAs that play important roles in different aspects of gene expression. These ubiquitous and heterogenous RNAs, which vary across different species and cell types, are proposed to regulate various biological processes. In this review, we will discuss aspects of their biogenesis, and specifically, their contribution into translational control. We will summarize diverse roles of tDRs and the molecular mechanisms underlying their functions in the regulation of protein synthesis and their impact on related events such as stress-induced translational reprogramming. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Yasutoshi Akiyama
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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26
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Wei D, Niu B, Zhai B, Liu XB, Yao YL, Liang CC, Wang P. Expression profiles and function prediction of tRNA-derived fragments in glioma. BMC Cancer 2023; 23:1015. [PMID: 37864150 PMCID: PMC10588164 DOI: 10.1186/s12885-023-11532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most aggressive malignant primary brain tumor. The transfer RNA-derived fragments (tRFs) are a new group of small noncoding RNAs, which are dysregulated in many cancers. Until now, the expression and function of tRFs in glioma remain unknown. METHODS The expression profiles of tRF subtypes were analyzed using the Cancer Genome Atlas (TCGA)-low-grade gliomas (LGG)/GBM dataset. The target genes of tRFs were subjected to Gene Ontology, Kyoto Encyclopedia and Gene set enrichment analysis of Genes and Genomes pathway enrichment analysis. The protein-protein interaction enrichment analysis was performed by STRING. QRT-PCR was performed to detect the expressions of tRFs in human glioma cell lines U87, U373, U251, and human astrocyte cell line SVG p12. Western blot assay was used to detect to the expression of S100A11. The interaction between tRF-19-R118LOJX and S100A11 mRNA 3'UTR was detected by dual-luciferase reporter assay. The effects of tRF-19-R118LOJX, tRF-19-6SM83OJX and S100A11 on the glioma cell proliferation, migration and in vitro vasculogenic mimicry formation ability were examined by CCK-8 proliferation assay, EdU assay, HoloMonitor cell migration assay and tube formation assay, respectively. RESULTS tRF-19-R118LOJX and tRF-19-6SM83OJX are the most differentially expressed tRFs between LGG and GBM groups. The functional enrichment analysis showed that the target genes of tRF-19-R118LOJX and tRF-19-6SM83OJX are enriched in regulating blood vessel development. The upregulated target genes are linked to adverse survival outcomes in glioma patients. tRF-19-R118LOJX and tRF-19-6SM83OJX were identified to suppress glioma cell proliferation, migration, and in vitro vasculogenic mimicry formation. The mechanism of tRF-19-R118LOJX might be related to its function as an RNA silencer by targeting the S100A11 mRNA 3'UTR. CONCLUSION tRFs would become novel diagnostic biomarkers and therapeutic targets of glioma, and the mechanism might be related to its post-transcriptionally regulation of gene expression by targeting mRNA 3'UTR.
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Affiliation(s)
- Deng Wei
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Ben Niu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Bei Zhai
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiao-Bai Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yi-Long Yao
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Chan-Chan Liang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.
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27
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Cao J, Wang X, Advani V, Lu YW, Malizia AP, Singh GB, Huang ZP, Liu J, Wang C, Oliveira EM, Mably JD, Chen K, Wang DZ. mt-Ty 5'tiRNA regulates skeletal muscle cell proliferation and differentiation. Cell Prolif 2023; 56:e13416. [PMID: 36756712 PMCID: PMC10392060 DOI: 10.1111/cpr.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/29/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
In this study, we sought to determine the role of tRNA-derived fragments in the regulation of gene expression during skeletal muscle cell proliferation and differentiation. We employed cell culture to examine the function of mt-Ty 5' tiRNAs. Northern blotting, RT-PCR as well as RNA-Seq, were performed to determine the effects of mt-Ty 5' tiRNA loss and gain on gene expression. Standard and transmission electron microscopy (TEM) were used to characterize cell and sub-cellular structures. mt-Ty 5'tiRNAs were found to be enriched in mouse skeletal muscle, showing increased levels in later developmental stages. Gapmer-mediated inhibition of tiRNAs in skeletal muscle C2C12 myoblasts resulted in decreased cell proliferation and myogenic differentiation; consistent with this observation, RNA-Seq, transcriptome analyses, and RT-PCR revealed that skeletal muscle cell differentiation and cell proliferation pathways were also downregulated. Conversely, overexpression of mt-Ty 5'tiRNAs in C2C12 cells led to a reversal of these transcriptional trends. These data reveal that mt-Ty 5'tiRNAs are enriched in skeletal muscle and play an important role in myoblast proliferation and differentiation. Our study also highlights the potential for the development of tiRNAs as novel therapeutic targets for muscle-related diseases.
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Affiliation(s)
- Jun Cao
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Faculty of Environment and Life, Beijing University of Technology, Beijing, P. R. China
| | - Xin Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vivek Advani
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Departments of Internal Medicine, Molecular Pharmacology & Physiology, Center for Regenerative Medicine, USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Yao Wei Lu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea P Malizia
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gurinder Bir Singh
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Departments of Internal Medicine, Molecular Pharmacology & Physiology, Center for Regenerative Medicine, USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Zhan-Peng Huang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jianming Liu
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Chunbo Wang
- UNC McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Edilamar M Oliveira
- Departments of Internal Medicine, Molecular Pharmacology & Physiology, Center for Regenerative Medicine, USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- School of Physical Education and Sport, University of Sao Paulo, Sao Paulo, Brazil
| | - John D Mably
- Departments of Internal Medicine, Molecular Pharmacology & Physiology, Center for Regenerative Medicine, USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Departments of Internal Medicine, Molecular Pharmacology & Physiology, Center for Regenerative Medicine, USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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28
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Mao M, Chen W, Huang X, Ye D. Role of tRNA-derived small RNAs(tsRNAs) in the diagnosis and treatment of malignant tumours. Cell Commun Signal 2023; 21:178. [PMID: 37480078 PMCID: PMC10362710 DOI: 10.1186/s12964-023-01199-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023] Open
Abstract
Malignant tumours area leading cause of death globally, accounting for approximately 13% of all deaths. A detailed understanding of the mechanism(s) of the occurrence and development of malignant tumours and identification of relevant therapeutic targets are therefore key to tumour treatment. tsRNAs(tRNA-derived small RNAs)-also known as TRFs (tRNA-derived fragments), tiRNAs (tRNA-derived stress-induced RNAs), tRNA halves, etc.-are a recently identified class of small noncoding RNAs that are generated from mature tRNA or tRNA precursors through cleavage by enzymes such as angiogenin, Dicer, RNase Z, and RNase P. Several studies have confirmed that dysregulation of tsRNAs is closely related to the tumorigenesis of breast cancer, nasopharyngeal cancer, lung cancer, and so on. Furthermore, research indicates that tsRNAs can be used as clinical diagnostic markers and therapeutic targets for cancer. In our review, we summarized the recent research progress on the role and clinical application of tsRNAs in tumorigenesis and progression. Video Abstract.
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Affiliation(s)
- Mingwen Mao
- Department of Otorhinolaryngology-Head and Neck Surgery, Ningbo No.6 Hospital Affiliated Medical School of Ningbo University, Ningbo, 315040, Zhejiang, China
- Department of Otorhinolaryngology-Head and Neck Surgery, Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Weina Chen
- Department of Clinical Pharmacology, Yinzhou Integrated TCM & Western Medicine Hospital, Ningbo, 315040, Zhejiang, China
| | - Xingbiao Huang
- Department of General Surgery, Ningbo No.6, Hospital Affiliated Medical School of Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Dong Ye
- Department of Otorhinolaryngology-Head and Neck Surgery, Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
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29
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Lee S, Kim J, Valdmanis PN, Kim HK. Emerging roles of tRNA-derived small RNAs in cancer biology. Exp Mol Med 2023:10.1038/s12276-023-01038-5. [PMID: 37430089 PMCID: PMC10393972 DOI: 10.1038/s12276-023-01038-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023] Open
Abstract
Transfer RNAs (tRNAs) play an essential role in mRNA translation by delivering amino acids to growing polypeptide chains. Recent data demonstrate that tRNAs can be cleaved by ribonucleases, and the resultant cleavage products, tRNA-derived small RNAs (tsRNAs), have crucial roles in physiological and pathological conditions. They are classified into more than six types according to their size and cleavage positions. Since the initial discovery of the physiological functions of tsRNAs more than a decade ago, accumulating data have demonstrated that tsRNAs play critical roles in gene regulation and tumorigenesis. These tRNA-derived molecules have various regulatory functions at the transcriptional, post-transcriptional, and translational levels. More than a hundred types of modifications are found on tRNAs, affecting the biogenesis, stability, function, and biochemical properties of tsRNA. Both oncogenic and tumor suppressor functions have been reported for tsRNAs, which play important roles in the development and progression of various cancers. Abnormal expression patterns and modification of tsRNAs are associated with various diseases, including cancer and neurological disorders. In this review, we will describe the biogenesis, versatile gene regulation mechanisms, and modification-mediated regulation mechanisms of tsRNA as well as the expression patterns and potential therapeutic roles of tsRNAs in various cancers.
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Affiliation(s)
- Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jungeun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98115, USA
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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30
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Dixson AC, Dawson TR, Di Vizio D, Weaver AM. Context-specific regulation of extracellular vesicle biogenesis and cargo selection. Nat Rev Mol Cell Biol 2023; 24:454-476. [PMID: 36765164 PMCID: PMC10330318 DOI: 10.1038/s41580-023-00576-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 134.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 02/12/2023]
Abstract
To coordinate, adapt and respond to biological signals, cells convey specific messages to other cells. An important aspect of cell-cell communication involves secretion of molecules into the extracellular space. How these molecules are selected for secretion has been a fundamental question in the membrane trafficking field for decades. Recently, extracellular vesicles (EVs) have been recognized as key players in intercellular communication, carrying not only membrane proteins and lipids but also RNAs, cytosolic proteins and other signalling molecules to recipient cells. To communicate the right message, it is essential to sort cargoes into EVs in a regulated and context-specific manner. In recent years, a wealth of lipidomic, proteomic and RNA sequencing studies have revealed that EV cargo composition differs depending upon the donor cell type, metabolic cues and disease states. Analyses of distinct cargo 'fingerprints' have uncovered mechanistic linkages between the activation of specific molecular pathways and cargo sorting. In addition, cell biology studies are beginning to reveal novel biogenesis mechanisms regulated by cellular context. Here, we review context-specific mechanisms of EV biogenesis and cargo sorting, focusing on how cell signalling and cell state influence which cellular components are ultimately targeted to EVs.
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Affiliation(s)
- Andrew C Dixson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - T Renee Dawson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Extracellular Vesicle Research, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Extracellular Vesicle Research, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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31
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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32
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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33
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Wu C, Liu D, Zhang L, Wang J, Ding Y, Sun Z, Wang W. 5'-tiRNA-Gln inhibits hepatocellular carcinoma progression by repressing translation through the interaction with eukaryotic initiation factor 4A-I. Front Med 2023; 17:476-492. [PMID: 36973570 DOI: 10.1007/s11684-022-0966-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/01/2022] [Indexed: 03/29/2023]
Abstract
tRNA-derived small RNAs (tsRNAs) are novel non-coding RNAs that are involved in the occurrence and progression of diverse diseases. However, their exact presence and function in hepatocellular carcinoma (HCC) remain unclear. Here, differentially expressed tsRNAs in HCC were profiled. A novel tsRNA, tRNAGln-TTG derived 5'-tiRNA-Gln, is significantly downregulated, and its expression level is correlated with progression in patients. In HCC cells, 5'-tiRNA-Gln overexpression impaired the proliferation, migration, and invasion in vitro and in vivo, while 5'-tiRNA-Gln knockdown yielded opposite results. 5'-tiRNA-Gln exerted its function by binding eukaryotic initiation factor 4A-I (EIF4A1), which unwinds complex RNA secondary structures during translation initiation, causing the partial inhibition of translation. The suppressed downregulated proteins include ARAF, MEK1/2 and STAT3, causing the impaired signaling pathway related to HCC progression. Furthermore, based on the construction of a mutant 5'-tiRNA-Gln, the sequence of forming intramolecular G-quadruplex structure is crucial for 5'-tiRNA-Gln to strongly bind EIF4A1 and repress translation. Clinically, 5'-tiRNA-Gln expression level is negatively correlated with ARAF, MEK1/2, and STAT3 in HCC tissues. Collectively, these findings reveal that 5'-tiRJNA-Gln interacts with EIF4A1 to reduce related mRNA binding through the intramolecular G-quadruplex structure, and this process partially inhibits translation and HCC progression.
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Affiliation(s)
- Chengdong Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310009, China
| | - Dekai Liu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310009, China
| | - Lufei Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310009, China
| | - Jingjie Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310009, China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310009, China
| | - Zhongquan Sun
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310009, China
| | - Weilin Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou, 310009, China.
- Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou, 310009, China.
- Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou, 310009, China.
- Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou, 310009, China.
- Cancer Center, Zhejiang University, Hangzhou, 310009, China.
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34
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La Ferlita A, Sp N, Goryunova M, Nigita G, Pollock RE, Croce CM, Beane JD. Small Non-Coding RNAs in Soft-Tissue Sarcomas: State of the Art and Future Directions. Mol Cancer Res 2023; 21:511-524. [PMID: 37052491 PMCID: PMC10238653 DOI: 10.1158/1541-7786.mcr-22-1008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 04/14/2023]
Abstract
Soft-tissue sarcomas (STS) are a rare and heterogeneous group of tumors that arise from connective tissue and can occur anywhere in the body. Among the plethora of over 50 different STS types, liposarcoma (LPS) is one of the most common. The subtypes of STS are characterized by distinct differences in tumor biology that drive responses to pharmacologic therapy and disparate oncologic outcomes. Small non-coding RNAs (sncRNA) are a heterogeneous class of regulatory RNAs involved in the regulation of gene expression by targeting mRNAs. Among the several types of sncRNAs, miRNAs and tRNA-derived ncRNAs are the most studied in the context of tumor biology, and we are learning more about the role of these molecules as important regulators of STS tumorigenesis and differentiation. However, challenges remain in translating these findings and no biomarkers or therapeutic approaches targeting sncRNAs have been developed for clinical use. In this review, we summarize the current landscape of sncRNAs in the context of STS with an emphasis on LPS, including the role of sncRNAs in the tumorigenesis and differentiation of these rare malignancies and their potential as novel biomarkers and therapeutic targets. Finally, we provide an appraisal of published studies and outline future directions to study sncRNAs in STS, including tRNA-derived ncRNAs.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Nipin Sp
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Marina Goryunova
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Raphael E. Pollock
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Joal D. Beane
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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35
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Fatica T, Naas T, Liwak U, Slaa H, Souaid M, Frangione B, Kattini R, Gaudreau-Lapierre A, Trinkle-Mulcahy L, Chakraborty P, Holcik M. TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins. Genes (Basel) 2023; 14:genes14051043. [PMID: 37239403 DOI: 10.3390/genes14051043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondrial diseases are a group of heterogeneous disorders caused by dysfunctional mitochondria. Interestingly, a large proportion of mitochondrial diseases are caused by defects in genes associated with tRNA metabolism. We recently discovered that partial loss-of-function mutations in tRNA Nucleotidyl Transferase 1 (TRNT1), the nuclear gene encoding the CCA-adding enzyme essential for modifying both nuclear and mitochondrial tRNAs, causes a multisystemic and clinically heterogenous disease termed SIFD (sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay; SIFD). However, it is not clear how mutations in a general and essential protein like TRNT1 cause disease with such clinically broad but unique symptomatology and tissue involvement. Using biochemical, cell, and mass spectrometry approaches, we demonstrate that TRNT1 deficiency is associated with sensitivity to oxidative stress, which is due to exacerbated, angiogenin-dependent cleavage of tRNAs. Furthermore, reduced levels of TRNT1 lead to phosphorylation of Eukaryotic Translation Initiation Factor 2 Subunit Alpha (eIF2α), increased reactive oxygen species (ROS) production, and changes in the abundance of distinct proteins. Our data suggest that the observed variable SIFD phenotypes are likely due to dysregulation of tRNA maturation and abundance, which in turn negatively affects the translation of distinct proteins.
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Affiliation(s)
- Thet Fatica
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Turaya Naas
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Urszula Liwak
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Hannah Slaa
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Maryam Souaid
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Brianna Frangione
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Ribal Kattini
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
| | | | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada
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36
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Di Fazio A, Gullerova M. An old friend with a new face: tRNA-derived small RNAs with big regulatory potential in cancer biology. Br J Cancer 2023; 128:1625-1635. [PMID: 36759729 PMCID: PMC10133234 DOI: 10.1038/s41416-023-02191-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Transfer RNAs (tRNAs) are small non-coding RNAs (sncRNAs) essential for protein translation. Emerging evidence suggests that tRNAs can also be processed into smaller fragments, tRNA-derived small RNAs (tsRNAs), a novel class of sncRNAs with powerful applications and high biological relevance to cancer. tsRNAs biogenesis is heterogeneous and involves different ribonucleases, such as Angiogenin and Dicer. For many years, tsRNAs were thought to be just degradation products. However, accumulating evidence shows their roles in gene expression: either directly via destabilising the mRNA or the ribosomal machinery, or indirectly via regulating the expression of ribosomal components. Furthermore, tsRNAs participate in various biological processes linked to cancer, including apoptosis, cell cycle, immune response, and retroviral insertion into the human genome. It is emerging that tsRNAs have significant therapeutic potential. Endogenous tsRNAs can be used as cancer biomarkers, while synthetic tsRNAs and antisense oligonucleotides can be employed to regulate gene expression. In this review, we are recapitulating the regulatory roles of tsRNAs, with a focus on cancer biology.
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Affiliation(s)
- Arianna Di Fazio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
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37
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Ao X, Ding W, Li X, Xu Q, Chen X, Zhou X, Wang J, Liu Y. Non-coding RNAs regulating mitochondrial function in cardiovascular diseases. J Mol Med (Berl) 2023; 101:501-526. [PMID: 37014377 DOI: 10.1007/s00109-023-02305-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 04/05/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of disease-related death worldwide and a significant obstacle to improving patients' health and lives. Mitochondria are core organelles for the maintenance of myocardial tissue homeostasis, and their impairment and dysfunction are considered major contributors to the pathogenesis of various CVDs, such as hypertension, myocardial infarction, and heart failure. However, the exact roles of mitochondrial dysfunction involved in CVD pathogenesis remain not fully understood. Non-coding RNAs (ncRNAs), particularly microRNAs, long non-coding RNAs, and circular RNAs, have been shown to be crucial regulators in the initiation and development of CVDs. They can participate in CVD progression by impacting mitochondria and regulating mitochondrial function-related genes and signaling pathways. Some ncRNAs also exhibit great potential as diagnostic and/or prognostic biomarkers as well as therapeutic targets for CVD patients. In this review, we mainly focus on the underlying mechanisms of ncRNAs involved in the regulation of mitochondrial functions and their role in CVD progression. We also highlight their clinical implications as biomarkers for diagnosis and prognosis in CVD treatment. The information reviewed herein could be extremely beneficial to the development of ncRNA-based therapeutic strategies for CVD patients.
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Affiliation(s)
- Xiang Ao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266021, China
| | - Xiaoge Li
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Qingling Xu
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Xinhui Chen
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Xuehao Zhou
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao Medical College, Qingdao University, Qingdao, 266071, China
| | - Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China.
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38
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Ying S, Li P, Wang J, Chen K, Zou Y, Dai M, Xu K, Feng G, Zhang C, Jiang H, Li W, Zhang Y, Zhou Q. tRF-Gln-CTG-026 ameliorates liver injury by alleviating global protein synthesis. Signal Transduct Target Ther 2023; 8:144. [PMID: 37015921 PMCID: PMC10073094 DOI: 10.1038/s41392-023-01351-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 04/06/2023] Open
Abstract
tsRNAs (tRNA-derived small RNAs), as products of the stress response, exert considerable influence on stress response and injury regulation. However, it remains largely unclear whether tsRNAs can ameliorate liver injury. Here, we demonstrate the roles of tsRNAs in alleviating liver injury by utilizing the loss of NSun2 (NOP2/Sun domain family, member 2) as a tsRNAs-generating model. Mechanistically, the loss of NSun2 reduces methyluridine-U5 (m5U) and cytosine-C5 (m5C) of tRNAs, followed by the production of various tsRNAs, especially Class I tsRNAs (tRF-1s). Through further screening, we show that tRF-Gln-CTG-026 (tG026), the optimal tRF-1, ameliorates liver injury by repressing global protein synthesis through the weakened association between TSR1 (pre-rRNA-processing protein TSR1 homolog) and pre-40S ribosome. This study indicates the potential of tsRNA-reduced global protein synthesis in liver injury and repair, suggesting a potential therapeutic strategy for liver injury.
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Affiliation(s)
- Sunyang Ying
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengcheng Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, Northeast Agricultural University of China, Harbin, 150030, China
| | - Jiaqiang Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaiqiong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Moyu Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Changjian Zhang
- Central Laboratory of the Sixth Medical Center of PLA General Hospital, Beijing, 100048, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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39
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Liu S, Sharma U. Sperm RNA Payload: Implications for Intergenerational Epigenetic Inheritance. Int J Mol Sci 2023; 24:5889. [PMID: 36982962 PMCID: PMC10052761 DOI: 10.3390/ijms24065889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/03/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
There is mounting evidence that ancestral life experiences and environment can influence phenotypes in descendants. The parental environment regulates offspring phenotypes potentially via modulating epigenetic marks in the gametes. Here, we review examples of across-generational inheritance of paternal environmental effects and the current understanding of the role of small RNAs in such inheritance. We discuss recent advances in revealing the small RNA payload of sperm and how environmental conditions modulate sperm small RNAs. Further, we discuss the potential mechanism of inheritance of paternal environmental effects by focusing on sperm small RNA-mediated regulation of early embryonic gene expression and its role in influencing offspring phenotypes.
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Affiliation(s)
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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40
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Mohideen AMSH, Johansen SD, Babiak I. mtR_find: A Parallel Processing Tool to Identify and Annotate RNAs Derived from the Mitochondrial Genome. Int J Mol Sci 2023; 24:ijms24054373. [PMID: 36901804 PMCID: PMC10001721 DOI: 10.3390/ijms24054373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
RNAs originating from mitochondrial genomes are abundant in transcriptomic datasets produced by high-throughput sequencing technologies, primarily in short-read outputs. Specific features of mitochondrial small RNAs (mt-sRNAs), such as non-templated additions, presence of length variants, sequence variants, and other modifications, necessitate the need for the development of an appropriate tool for their effective identification and annotation. We have developed mtR_find, a tool to detect and annotate mitochondrial RNAs, including mt-sRNAs and mitochondria-derived long non-coding RNAs (mt-lncRNA). mtR_find uses a novel method to compute the count of RNA sequences from adapter-trimmed reads. When analyzing the published datasets with mtR_find, we identified mt-sRNAs significantly associated with the health conditions, such as hepatocellular carcinoma and obesity, and we discovered novel mt-sRNAs. Furthermore, we identified mt-lncRNAs in early development in mice. These examples show the immediate impact of miR_find in extracting a novel biological information from the existing sequencing datasets. For benchmarking, the tool has been tested on a simulated dataset and the results were concordant. For accurate annotation of mitochondria-derived RNA, particularly mt-sRNA, we developed an appropriate nomenclature. mtR_find encompasses the mt-ncRNA transcriptomes in unpreceded resolution and simplicity, allowing re-analysis of the existing transcriptomic databases and the use of mt-ncRNAs as diagnostic or prognostic markers in the field of medicine.
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41
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Drino A, König L, Capitanchik C, Sanadgol N, Janisiw E, Rappol T, Vilardo E, Schaefer MR. Identification of RNA helicases with unwinding activity on angiogenin-processed tRNAs. Nucleic Acids Res 2023; 51:1326-1352. [PMID: 36718960 PMCID: PMC9943664 DOI: 10.1093/nar/gkad033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 02/01/2023] Open
Abstract
Stress-induced tRNA fragmentation upon environmental insult is a conserved cellular process catalysed by endonucleolytic activities targeting mature tRNAs. The resulting tRNA-derived small RNAs (tsRNAs) have been implicated in various biological processes that impact cell-to-cell signalling, cell survival as well as gene expression regulation during embryonic development. However, how endonuclease-targeted tRNAs give rise to individual and potentially biologically active tsRNAs remains poorly understood. Here, we report on the in vivo identification of proteins associated with stress-induced tsRNAs-containing protein complexes, which, together with a 'tracer tRNA' assay, were used to uncover enzymatic activities that can bind and process specific endonuclease-targeted tRNAs in vitro. Among those, we identified conserved ATP-dependent RNA helicases which can robustly separate tRNAs with endonuclease-mediated 'nicks' in their anticodon loops. These findings shed light on the existence of cellular pathways dedicated to producing individual tsRNAs after stress-induced tRNA hydrolysis, which adds to our understanding as to how tRNA fragmentation and the resulting tsRNAs might exert physiological impact.
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Affiliation(s)
- Aleksej Drino
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Lisa König
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | | | - Nasim Sanadgol
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Eva Janisiw
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Tom Rappol
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Elisa Vilardo
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17-I, A-1090 Vienna, Austria
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42
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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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43
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Yang M, Mo Y, Ren D, Liu S, Zeng Z, Xiong W. Transfer RNA-derived small RNAs in tumor microenvironment. Mol Cancer 2023; 22:32. [PMID: 36797764 PMCID: PMC9933334 DOI: 10.1186/s12943-023-01742-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Transfer RNAs (tRNAs) are a class of non-coding RNAs responsible for amino acid translocation during protein synthesis and are ubiquitously found in organisms. With certain modifications and under specific conditions, tRNAs can be sheared and fragmented into small non-coding RNAs, also known as tRNA-derived small RNAs (tDRs). With the development of high-throughput sequencing technologies and bioinformatic strategies, more and more tDRs have been identified and their functions in organisms have been characterized. tRNA and it derived tDRs, have been shown to be essential not only for transcription and translation, but also for regulating cell proliferation, apoptosis, metastasis, and immunity. Aberrant expression of tDRs is associated with a wide range of human diseases, especially with tumorigenesis and tumor progression. The tumor microenvironment (TME) is a complex ecosystem consisting of various cellular and cell-free components that are mutually compatible with the tumor. It has been shown that tDRs regulate the TME by regulating cancer stem cells, immunity, energy metabolism, epithelial mesenchymal transition, and extracellular matrix remodeling, playing a pro-tumor or tumor suppressor role. In this review, the biogenesis, classification, and function of tDRs, as well as their effects on the TME and the clinical application prospects will be summarized and discussed based on up to date available knowledge.
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Affiliation(s)
- Mei Yang
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yongzhen Mo
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Daixi Ren
- grid.216417.70000 0001 0379 7164NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China ,grid.216417.70000 0001 0379 7164Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Shun Liu
- grid.452708.c0000 0004 1803 0208Department of Cardiovascular Medicine, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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44
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Fu M, Gu J, Wang M, Zhang J, Chen Y, Jiang P, Zhu T, Zhang X. Emerging roles of tRNA-derived fragments in cancer. Mol Cancer 2023; 22:30. [PMID: 36782290 PMCID: PMC9926655 DOI: 10.1186/s12943-023-01739-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging category of small non-coding RNAs that are generated from cleavage of mature tRNAs or tRNA precursors. The advance in high-throughput sequencing has contributed to the identification of increasing number of tRFs with critical functions in distinct physiological and pathophysiological processes. tRFs can regulate cell viability, differentiation, and homeostasis through multiple mechanisms and are thus considered as critical regulators of human diseases including cancer. In addition, increasing evidence suggest the extracellular tRFs may be utilized as promising diagnostic and prognostic biomarkers for cancer liquid biopsy. In this review, we focus on the biogenesis, classification and modification of tRFs, and summarize the multifaceted functions of tRFs with an emphasis on the current research status and perspectives of tRFs in cancer.
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Affiliation(s)
- Min Fu
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China ,grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jianmei Gu
- grid.260483.b0000 0000 9530 8833Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, 226361 Jiangsu China
| | - Maoye Wang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Jiahui Zhang
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Yanke Chen
- grid.440785.a0000 0001 0743 511XJiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013 Jiangsu China
| | - Pengcheng Jiang
- grid.452247.2Institute of Digestive Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, 212002 Jiangsu China
| | - Taofeng Zhu
- Department of Pulmonary and Critical Care Medicine, Yixing Hospital Affiliated to Jiangsu University, Yixing, 214200, Jiangsu, China.
| | - Xu Zhang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, China. .,Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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45
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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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46
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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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47
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Zhang S, Yu X, Xie Y, Ye G, Guo J. tRNA derived fragments:A novel player in gene regulation and applications in cancer. Front Oncol 2023; 13:1063930. [PMID: 36761955 PMCID: PMC9904238 DOI: 10.3389/fonc.2023.1063930] [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: 10/07/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
The heterogeneous species of tRNA-derived fragments (tRFs) with specific biological functions was recently identified. Distinct roles of tRFs in tumor development and viral infection, mediated through transcriptional and post-transcriptional regulation, has been demonstrated. In this review, we briefly summarize the current literatures on the classification of tRFs and the effects of tRNA modification on tRF biogenesis. Moreover, we highlight the tRF repertoire of biological roles such as gene silencing, and regulation of translation, cell apoptosis, and epigenetics. We also summarize the biological roles of various tRFs in cancer development and viral infection, their potential value as diagnostic and prognostic biomarkers for different types of cancers, and their potential use in cancer therapy.
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Affiliation(s)
- Shuangshuang Zhang
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, School of Medicine, Ningbo University, Ningbo, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, School of Medicine, Ningbo University, Ningbo, China
| | - Yaoyao Xie
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, School of Medicine, Ningbo University, Ningbo, China
| | - Guoliang Ye
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China,Institute of Digestive Diseases, Ningbo University, Ningbo, China
| | - Junming Guo
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, School of Medicine, Ningbo University, Ningbo, China,Institute of Digestive Diseases, Ningbo University, Ningbo, China,*Correspondence: Junming Guo,
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48
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Akiyama Y, Takenaka Y, Kasahara T, Abe T, Tomioka Y, Ivanov P. RTCB Complex Regulates Stress-Induced tRNA Cleavage. Int J Mol Sci 2022; 23:ijms232113100. [PMID: 36361884 PMCID: PMC9655011 DOI: 10.3390/ijms232113100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
Abstract
Under stress conditions, transfer RNAs (tRNAs) are cleaved by stress-responsive RNases such as angiogenin, generating tRNA-derived RNAs called tiRNAs. As tiRNAs contribute to cytoprotection through inhibition of translation and prevention of apoptosis, the regulation of tiRNA production is critical for cellular stress response. Here, we show that RTCB ligase complex (RTCB-LC), an RNA ligase complex involved in endoplasmic reticulum (ER) stress response and precursor tRNA splicing, negatively regulates stress-induced tiRNA production. Knockdown of RTCB significantly increased stress-induced tiRNA production, suggesting that RTCB-LC negatively regulates tiRNA production. Gel-purified tiRNAs were repaired to full-length tRNAs by RtcB in vitro, suggesting that RTCB-LC can generate full length tRNAs from tiRNAs. As RTCB-LC is inhibited under oxidative stress, we further investigated whether tiRNA production is promoted through the inhibition of RTCB-LC under oxidative stress. Although hydrogen peroxide (H2O2) itself did not induce tiRNA production, it rapidly boosted tiRNA production under the condition where stress-responsive RNases are activated. We propose a model of stress-induced tiRNA production consisting of two factors, a trigger and booster. This RTCB-LC-mediated boosting mechanism may contribute to the effective stress response in the cell.
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Affiliation(s)
- Yasutoshi Akiyama
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
- Correspondence: (Y.A.); (P.I.)
| | - Yoshika Takenaka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
| | - Tomoko Kasahara
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Takaaki Abe
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai 980-8574, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai 980-8578, Japan
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: (Y.A.); (P.I.)
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49
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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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Wang S, Luo Z, Yuan L, Lin X, Tang Y, Yin L, Liang P, Jiang B. tRNA-Derived Small RNAs: Novel Insights into the Pathogenesis and Treatment of Cardiovascular Diseases. J Cardiovasc Transl Res 2022; 16:300-309. [PMID: 36190649 DOI: 10.1007/s12265-022-10322-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/12/2022] [Indexed: 12/05/2022]
Abstract
tRNA-derived small RNAs (tsRNAs) are non-coding RNAs with diverse functions in various diseases. Although research on tsRNAs has focused on their roles in cancer, such as gene expression regulation to influence cancer progression and realize clinical effects, a growing number of studies are investigating the association of tsRNAs with cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction, and pulmonary hypertension. tsRNA expression varies across these diseases and could be regulated by epigenetics, tsRNA structure, and tRNA-binding proteins. tsRNAs play key roles in CVD progression, including the regulation of protein synthesis, and the different mechanisms underlying these functional roles of tsRNAs have been elucidated. Furthermore, tsRNAs are potential diagnostic biomarkers and therapeutic targets in CVDs. In this review, we summarize the biogenesis, classification, and regulation of tsRNAs and their potential application for CVD diagnosis and therapy. We also highlight the current challenges and provide perspectives for further investigation.
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Affiliation(s)
- Shuxin Wang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Zhengyang Luo
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Ludong Yuan
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Xiaofang Lin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Yuting Tang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Leijing Yin
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China
| | - Pengfei Liang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Bimei Jiang
- Department of Pathophysiology, Sepsis Translational Medicine Key Laboratory of Hunan Province, Xiangya School of Medicine, Central South University, Changsha, 410008, Hunan, China.
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