1
|
Sahu AK, Shah RA, Nashier D, Sharma P, Varada R, Lahry K, Singh S, Shetty S, Hussain T, Varshney U. Physiological significance of the two isoforms of initiator tRNAs in Escherichia coli. J Bacteriol 2024:e0025124. [PMID: 39171914 DOI: 10.1128/jb.00251-24] [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: 06/20/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
Escherichia coli possesses four initiator tRNA (i-tRNA) genes, three of which are present together as metZWV and the fourth one as metY. In E. coli B, all four genes (metZWV and metY) encode i-tRNAfMet1, in which the G at position 46 is modified to m7G46 by TrmB (m7G methyltransferase). However, in E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNAfMet2, having an A in place of m7G46. We generated E. coli strains to explore the importance of this polymorphism in i-tRNAs. The strains were sustained either on metYA46 (metY of E. coli K origin encoding i-tRNAfMet2) or its derivative metYG46 (encoding i-tRNAfMet1) in single (chromosomal) or plasmid-borne copies. We show that the strains sustained on i-tRNAfMet1 have a growth fitness advantage over those sustained on i-tRNAfMet2. The growth fitness advantages are more pronounced for the strains sustained on i-tRNAfMet1 in nutrient-rich media than in nutrient-poor media. The growth fitness of the strains correlates well with the relative stabilities of the i-tRNAs in vivo. Furthermore, the atomistic molecular dynamics simulations support the higher stability of i-tRNAfMet1 than that of i-tRNAfMet2. The stability of i-tRNAfMet1 remains unaffected upon the deletion of TrmB. These studies highlight how metYG46 and metYA46 alleles might influence the growth fitness of E. coli under certain nutrient-limiting conditions. IMPORTANCE Escherichia coli harbors four initiator tRNA (i-tRNA) genes: three of these at metZWV and the fourth one at metY loci. In E. coli B, all four genes encode i-tRNAfMet1. In E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNAfMet2, having an A in place of G at position 46 of i-tRNA sequence in metY. We show that G46 confers stability to i-tRNAfMet1. The strains sustained on i-tRNAfMet1 have a growth fitness advantage over those sustained on i-tRNAfMet2. Strains harboring metYG46 (B mimic) or metYA46 (K mimic) show that while in the nutrient-rich media, the K mimic is outcompeted rapidly; in the nutrient-poor medium, the K mimic is outcompeted less rapidly.
Collapse
Affiliation(s)
- Amit Kumar Sahu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Divya Nashier
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Prafful Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Rajagopal Varada
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sunil Shetty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| |
Collapse
|
2
|
Wu P, Zhang Q, Zhong P, Chai L, Luo Q, Jia C. Development of a prognostic risk model of uveal melanoma based on N7-methylguanosine-related regulators. Hereditas 2024; 161:22. [PMID: 38987843 PMCID: PMC11234703 DOI: 10.1186/s41065-024-00324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/12/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Uveal melanoma (UVM) stands as the predominant type of primary intraocular malignancy among adults. The clinical significance of N7-methylguanosine (m7G), a prevalent RNA modifications, in UVM remains unclear. METHODS Primary information from 80 UVM patients were analyzed as the training set, incorporating clinical information, mutation annotations and mRNA expression obtained from The Cancer Genome Atlas (TCGA) website. The validation set was carried out using Gene Expression Omnibus (GEO) database GSE22138 and GSE84976. Kaplan-Meier and Cox regression of univariate analyses were subjected to identify m7G-related regulators as prognostic genes. RESULT A prognostic risk model comprising EIF4E2, NUDT16, SNUPN and WDR4 was established through Cox regression of LASSO. Evaluation of the model's predictability for UVM patients' prognosis by Receiver Operating Characteristic (ROC) curves in the training set, demonstrated excellent performance Area Under the Curve (AUC) > 0.75. The high-risk prognosis within the TCGA cohort exhibit a notable worse outcome. Additionally, an independent correlation between the risk score and overall survival (OS) among UVM patients were identified. External validation of this model was carried out using the validation sets (GSE22138 and GSE84976). Immune-related analysis revealed that patients with high score of m7G-related risk model exhibited elevated level of immune infiltration and immune checkpoint gene expression. CONCLUSION We have developed a risk prediction model based on four m7G-related regulators, facilitating effective estimate UVM patients' survival by clinicians. Our findings shed novel light on essential role of m7G-related regulators in UVM and suggest potential novel targets for the diagnosis, prognosis and therapy of UVM.
Collapse
Affiliation(s)
- Pingfan Wu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Qian Zhang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Peng Zhong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Qiong Luo
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China
| | - Chengyou Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
- Institute of Nuclear Medicine, Tongji University School of Medicine, Shanghai, 200072, China.
| |
Collapse
|
3
|
Lv X, Zhang R, Li S, Jin X. tRNA Modifications and Dysregulation: Implications for Brain Diseases. Brain Sci 2024; 14:633. [PMID: 39061374 PMCID: PMC11274612 DOI: 10.3390/brainsci14070633] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 07/28/2024] Open
Abstract
Transfer RNAs (tRNAs) are well-known for their essential function in protein synthesis. Recent research has revealed a diverse range of chemical modifications that tRNAs undergo, which are crucial for various cellular processes. These modifications are necessary for the precise and efficient translation of proteins and also play important roles in gene expression regulation and cellular stress response. This review examines the role of tRNA modifications and dysregulation in the pathophysiology of various brain diseases, including epilepsy, stroke, neurodevelopmental disorders, brain tumors, Alzheimer's disease, and Parkinson's disease. Through a comprehensive analysis of existing research, our study aims to elucidate the intricate relationship between tRNA dysregulation and brain diseases. This underscores the critical need for ongoing exploration in this field and provides valuable insights that could facilitate the development of innovative diagnostic tools and therapeutic approaches, ultimately improving outcomes for individuals grappling with complex neurological conditions.
Collapse
Affiliation(s)
- Xinxin Lv
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| | - Ruorui Zhang
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Shanshan Li
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| | - Xin Jin
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| |
Collapse
|
4
|
Du D, Zhou M, Ju C, Yin J, Wang C, Xu X, Yang Y, Li Y, Cui L, Wang Z, Lei Y, Li H, He F, He J. METTL1-mediated tRNA m 7G methylation and translational dysfunction restricts breast cancer tumorigenesis by fueling cell cycle blockade. J Exp Clin Cancer Res 2024; 43:154. [PMID: 38822363 PMCID: PMC11140866 DOI: 10.1186/s13046-024-03076-x] [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: 03/18/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND RNA modifications of transfer RNAs (tRNAs) are critical for tRNA function. Growing evidence has revealed that tRNA modifications are related to various disease processes, including malignant tumors. However, the biological functions of methyltransferase-like 1 (METTL1)-regulated m7G tRNA modifications in breast cancer (BC) remain largely obscure. METHODS The biological role of METTL1 in BC progression were examined by cellular loss- and gain-of-function tests and xenograft models both in vitro and in vivo. To investigate the change of m7G tRNA modification and mRNA translation efficiency in BC, m7G-methylated tRNA immunoprecipitation sequencing (m7G tRNA MeRIP-seq), Ribosome profiling sequencing (Ribo-seq), and polysome-associated mRNA sequencing were performed. Rescue assays were conducted to decipher the underlying molecular mechanisms. RESULTS The tRNA m7G methyltransferase complex components METTL1 and WD repeat domain 4 (WDR4) were down-regulated in BC tissues at both the mRNA and protein levels. Functionally, METTL1 inhibited BC cell proliferation, and cell cycle progression, relying on its enzymatic activity. Mechanistically, METTL1 increased m7G levels of 19 tRNAs to modulate the translation of growth arrest and DNA damage 45 alpha (GADD45A) and retinoblastoma protein 1 (RB1) in a codon-dependent manner associated with m7G. Furthermore, in vivo experiments showed that overexpression of METTL1 enhanced the anti-tumor effectiveness of abemaciclib, a cyclin-dependent kinases 4 and 6 (CDK4/6) inhibitor. CONCLUSION Our study uncovered the crucial tumor-suppressive role of METTL1-mediated tRNA m7G modification in BC by promoting the translation of GADD45A and RB1 mRNAs, selectively blocking the G2/M phase of the cell cycle. These findings also provided a promising strategy for improving the therapeutic benefits of CDK4/6 inhibitors in the treatment of BC patients.
Collapse
Affiliation(s)
- Dan Du
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Mingxia Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chenxi Ju
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jie Yin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chang Wang
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xinyu Xu
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yunqing Yang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yun Li
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Le Cui
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhengyang Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yuqing Lei
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Hongle Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China.
| | - Fucheng He
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Jing He
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
5
|
Lee BST, Sinha A, Dedon P, Preiser P. Charting new territory: The Plasmodium falciparum tRNA modification landscape. Biomed J 2024:100745. [PMID: 38734409 DOI: 10.1016/j.bj.2024.100745] [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: 03/26/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024] Open
Abstract
Ribonucleoside modifications comprising the epitranscriptome are present in all organisms and all forms of RNA, including mRNA, rRNA and tRNA, the three major RNA components of the translational machinery. Of these, tRNA is the most heavily modified and the tRNA epitranscriptome has the greatest diversity of modifications. In addition to their roles in tRNA biogenesis, quality control, structure, cleavage, and codon recognition, tRNA modifications have been shown to regulate gene expression post-transcriptionally in prokaryotes and eukaryotes, including humans. However, studies investigating the impact of tRNA modifications on gene expression in the malaria parasite Plasmodium falciparum are currently scarce. Current evidence shows that the parasite has a limited capacity for transcriptional control, which points to a heavier reliance on strategies for posttranscriptional regulation such as tRNA epitranscriptome reprogramming. This review addresses the known functions of tRNA modifications in the biology of P. falciparum while highlighting the potential therapeutic opportunities and the value of using P. falciparum as a model organism for addressing several open questions related to the tRNA epitranscriptome.
Collapse
Affiliation(s)
- Benjamin Sian Teck Lee
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore
| | - Ameya Sinha
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore;; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Peter Dedon
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore;; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA.
| | - Peter Preiser
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore;; School of Biological Sciences, Nanyang Technological University, Singapore;.
| |
Collapse
|
6
|
Lin S, Kuang M. RNA modification-mediated mRNA translation regulation in liver cancer: mechanisms and clinical perspectives. Nat Rev Gastroenterol Hepatol 2024; 21:267-281. [PMID: 38243019 DOI: 10.1038/s41575-023-00884-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 01/21/2024]
Abstract
Malignant liver cancer is characterized by rapid tumour progression and a high mortality rate, whereas the molecular mechanisms underlying liver cancer initiation and progression are still poorly understood. The dynamic and reversible RNA modifications have crucial functions in gene expression regulation by modulating RNA processing and mRNA translation. Emerging evidence has revealed that alterations in RNA modifications facilitate the selective translation of oncogenic transcripts and promote the diverse tumorigenic processes of liver cancer. In this Review, we first highlight the current progress on the functions and mechanisms underlying RNA modifications in the regulation of mRNA translation and then summarize the exciting discoveries on aberrant RNA modification-mediated mRNA translation in the regulation of tumour initiation, metastasis, metabolism, tumour microenvironment, and drug and radiotherapy resistance in liver cancer. Finally, we discuss the diagnostic and therapeutic potentials of targeting RNA modifications and mRNA translation for the clinical management of liver cancer.
Collapse
Affiliation(s)
- Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ming Kuang
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China.
| |
Collapse
|
7
|
Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024; 9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.
Collapse
Affiliation(s)
- Wei-Wei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Clinical Medicine, Shandong University, Jinan, China
| | - Si-Qing Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Tian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Yun-Fei Fei
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Chen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Shuang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
| |
Collapse
|
8
|
Añazco-Guenkova AM, Miguel-López B, Monteagudo-García Ó, García-Vílchez R, Blanco S. The impact of tRNA modifications on translation in cancer: identifying novel therapeutic avenues. NAR Cancer 2024; 6:zcae012. [PMID: 38476632 PMCID: PMC10928989 DOI: 10.1093/narcan/zcae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Recent advancements have illuminated the critical role of RNA modifications in post-transcriptional regulation, shaping the landscape of gene expression. This review explores how tRNA modifications emerge as critical players, fine-tuning functionalities that not only maintain the fidelity of protein synthesis but also dictate gene expression and translation profiles. Highlighting their dysregulation as a common denominator in various cancers, we systematically investigate the intersection of both cytosolic and mitochondrial tRNA modifications with cancer biology. These modifications impact key processes such as cell proliferation, tumorigenesis, migration, metastasis, bioenergetics and the modulation of the tumor immune microenvironment. The recurrence of altered tRNA modification patterns across different cancer types underscores their significance in cancer development, proposing them as potential biomarkers and as actionable targets to disrupt tumorigenic processes, offering new avenues for precision medicine in the battle against cancer.
Collapse
Affiliation(s)
- Ana M Añazco-Guenkova
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Borja Miguel-López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Óscar Monteagudo-García
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Raquel García-Vílchez
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| |
Collapse
|
9
|
Han M, Huang Q, Li X, Chen X, Zhu H, Pan Y, Zhang B. M7G-related tumor immunity: novel insights of RNA modification and potential therapeutic targets. Int J Biol Sci 2024; 20:1238-1255. [PMID: 38385078 PMCID: PMC10878144 DOI: 10.7150/ijbs.90382] [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: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024] Open
Abstract
RNA modifications play a pivotal role in regulating cellular biology by exerting influence over distribution features and molecular functions at the post-transcriptional level. Among these modifications, N7-methylguanosine (m7G) stands out as one of the most prevalent. Over recent years, significant attention has been directed towards understanding the implications of m7G modification. This modification is present in diverse RNA molecules, including transfer RNAs, messenger RNAs, ribosomal RNAs, and other noncoding RNAs. Its regulation occurs through a series of specific methyltransferases and m7G-binding proteins. Notably, m7G modification has been implicated in various diseases, prominently across multiple cancer types. Earlier studies have elucidated the significance of m7G modification in the context of immune biology regulation within the tumor microenvironment. This comprehensive review culminates in a synthesis of findings related to the modulation of immune cells infiltration, encompassing T cells, B cells, and various innate immune cells, all orchestrated by m7G modification. Furthermore, the interplay between m7G modification and its regulatory proteins can profoundly affect the efficacy of diverse adjuvant therapeutics, thereby potentially serving as a pivotal biomarker and therapeutic target for combinatory interventions in diverse cancer types.
Collapse
Affiliation(s)
- Mengzhen Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Qibo Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Xinxin Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - He Zhu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei 430030, China
| |
Collapse
|
10
|
McGuffey JC, Jackson-Litteken CD, Di Venanzio G, Zimmer AA, Lewis JM, Distel JS, Kim KQ, Zaher HS, Alfonzo J, Scott NE, Feldman MF. The tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection. mBio 2023; 14:e0141623. [PMID: 37589464 PMCID: PMC10653896 DOI: 10.1128/mbio.01416-23] [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: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
IMPORTANCE As deficiencies in tRNA modifications have been linked to human diseases such as cancer and diabetes, much research has focused on the modifications' impacts on translational regulation in eukaryotes. However, the significance of tRNA modifications in bacterial physiology remains largely unexplored. In this paper, we demonstrate that the m7G tRNA methyltransferase TrmB is crucial for a top-priority pathogen, Acinetobacter baumannii, to respond to stressors encountered during infection, including oxidative stress, low pH, and iron deprivation. We show that loss of TrmB dramatically attenuates a murine pulmonary infection. Given the current efforts to use another tRNA methyltransferase, TrmD, as an antimicrobial therapeutic target, we propose that TrmB, and other tRNA methyltransferases, may also be viable options for drug development to combat multidrug-resistant A. baumannii.
Collapse
Affiliation(s)
- Jenna C. McGuffey
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Clay D. Jackson-Litteken
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gisela Di Venanzio
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Aubree A. Zimmer
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jessica M. Lewis
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jesus S. Distel
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Juan Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
11
|
Wang Z, Xu X, Li X, Fang J, Huang Z, Zhang M, Liu J, Qiu X. Investigations of Single-Subunit tRNA Methyltransferases from Yeast. J Fungi (Basel) 2023; 9:1030. [PMID: 37888286 PMCID: PMC10608323 DOI: 10.3390/jof9101030] [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: 08/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
tRNA methylations, including base modification and 2'-O-methylation of ribose moiety, play critical roles in the structural stabilization of tRNAs and the fidelity and efficiency of protein translation. These modifications are catalyzed by tRNA methyltransferases (TRMs). Some of the TRMs from yeast can fully function only by a single subunit. In this study, after performing the primary bioinformatic analyses, the progress of the studies of yeast single-subunit TRMs, as well as the studies of their homologues from yeast and other types of eukaryotes and the corresponding TRMs from other types of organisms was systematically reviewed, which will facilitate the understanding of the evolutionary origin of functional diversity of eukaryotic single-subunit TRM.
Collapse
Affiliation(s)
- Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiangbin Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xinhai Li
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| |
Collapse
|
12
|
Singh S, Yeat NY, Wang YT, Lin SY, Kuo IY, Wu KP, Wang WJ, Wang WC, Su WC, Wang YC, Chen RH. PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer therapeutic target. Cell Death Dis 2023; 14:671. [PMID: 37821451 PMCID: PMC10567730 DOI: 10.1038/s41419-023-06201-4] [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: 04/05/2023] [Revised: 09/19/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Aberrant overexpression or activation of EGFR drives the development of non-small cell lung cancer (NSCLC) and acquired resistance to EGFR tyrosine kinase inhibitors (TKIs) by secondary EGFR mutations or c-MET amplification/activation remains as a major hurdle for NSCLC treatment. We previously identified WDR4 as a substrate adaptor of Cullin 4 ubiquitin ligase and an association of WDR4 high expression with poor prognosis of lung cancer. Here, using an unbiased ubiquitylome analysis, we uncover PTPN23, a component of the ESCRT complex, as a substrate of WDR4-based ubiquitin ligase. WDR4-mediated PTPN23 ubiquitination leads to its proteasomal degradation, thereby suppressing lysosome trafficking and degradation of wild type EGFR, EGFR mutant, and c-MET. Through this mechanism, WDR4 sustains EGFR and c-MET signaling to promote NSCLC proliferation, migration, invasion, stemness, and metastasis. Clinically, PTPN23 is downregulated in lung cancer and its low expression correlates with WDR4 high expression and poor prognosis. Targeting WDR4-mediated PTPN23 ubiquitination by a peptide that competes with PTPN23 for binding WDR4 promotes EGFR and c-MET degradation to block the growth and progression of EGFR TKI-resistant NSCLC. These findings identify a central role of WDR4/PTPN23 axis in EGFR and c-MET trafficking and a potential therapeutic target for treating EGFR TKI-resistant NSCLC.
Collapse
Affiliation(s)
- Shaifali Singh
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Molecular & Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Nai Yang Yeat
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ya-Ting Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - I-Ying Kuo
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
| | - Won-Jing Wang
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Wen-Ching Wang
- Institute of Molecular & Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wu-Chou Su
- Division of Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Jin X, Guan Z, Hu N, He C, Yin P, Gong Z, Zhang D. Structural insight into how WDR4 promotes the tRNA N7-methylguanosine methyltransferase activity of METTL1. Cell Discov 2023; 9:65. [PMID: 37369656 PMCID: PMC10300002 DOI: 10.1038/s41421-023-00562-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/10/2023] [Indexed: 06/29/2023] Open
Affiliation(s)
- Xiaohuan Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Na Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunjie He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
| |
Collapse
|
15
|
Zhu S, Wu Y, Zhang X, Peng S, Xiao H, Chen S, Xu L, Su T, Kuang M. Targeting N 7-methylguanosine tRNA modification blocks hepatocellular carcinoma metastasis after insufficient radiofrequency ablation. Mol Ther 2023; 31:1596-1614. [PMID: 35965412 PMCID: PMC10278047 DOI: 10.1016/j.ymthe.2022.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Radiofrequency heat ablation is an ideal radical treatment for hepatocellular carcinoma (HCC). However, insufficient radiofrequency ablation (IRFA) could lead to high recurrence of HCC. N7-methylguanosine (m7G) on tRNAs, an evolutionally conservative modification in mammals and yeast, modulates heat stress responses and tumor progression, while its function in HCC recurrence after IRFA remains unknown. Here, we found that IRFA significantly upregulates the level of m7G tRNA modification and its methyltransferase complex components METTL1/WDR4 in multiple systems including HCC patient-derived xenograft (PDX) mouse, patients' HCC tissues, sublethal-heat-treated models of HCC cell lines, and organoids. Functionally, gain-/loss-of-function assays showed that METTL1-mediated m7G tRNA modification promotes HCC metastasis under sublethal heat exposure both in vitro and in vivo. Mechanistically, we found that METTL1 and m7G tRNA modification enhance the translation of SLUG/SNAIL in a codon frequency-dependent manner under sublethal heat stress. Overexpression of SLUG/SNAIL rescued the malignant potency of METTL1 knockdown HCC cells after sublethal heat exposure. Our study uncovers the key functions of m7G tRNA modification in heat stress responses and HCC recurrence after IRFA, providing molecular basis for targeting METTL1-m7G-SLUG/SNAIL axis to prevent HCC metastasis after radiofrequency heat ablation treatment.
Collapse
Affiliation(s)
- Shenghua Zhu
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yifan Wu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xinyue Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Sui Peng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Han Xiao
- Division of Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shuling Chen
- Division of Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Lixia Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Tianhong Su
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Ming Kuang
- Department of Liver Surgery, Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Cancer Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| |
Collapse
|
16
|
Deng L, Hua RX, Deng C, Zhu J, Zhang Z, Cheng J, Zhang J, Zhou H, Li S, Ruan J, Liu G, He J, Fu W. WDR4 gene polymorphisms and Wilms tumor susceptibility in Chinese children: A five-center case-control study. J Cancer 2023; 14:1293-1300. [PMID: 37283791 PMCID: PMC10240673 DOI: 10.7150/jca.83747] [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: 02/22/2023] [Accepted: 04/27/2023] [Indexed: 06/08/2023] Open
Abstract
Wilms tumor is the most common embryonal renal malignancy in children. WDR4 is an indispensable noncatalytic subunit of the RNA N7-methylguanosine (m7G) methyltransferase complex and plays an essential role in tumorigenesis. However, the relationship between polymorphisms in the WDR4 gene and susceptibility to Wilms tumor remains to be fully investigated. We performed a large case-control study involving 414 patients and 1199 cancer-free controls to investigate whether single nucleotide polymorphisms (SNPs) in the WDR4 gene are associated with Wilms tumor susceptibility. WDR4 gene polymorphisms (rs2156315 C > T, rs2156316 C > G, rs6586250 C > T, rs15736 G > A, and rs2248490 C > G) were genotyped using the TaqMan assay. In addition, unconditioned logistic regression analysis was performed, odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the association between WDR4 gene SNPs and Wilms tumor susceptibility as well as the strength of the associations. We found that only the rs6586250 C>T polymorphism was significantly associated with an increased risk of Wilms tumor (adjusted OR=2.99, 95% CI = 1.28-6.97, P = 0.011 for the rs6586250 TT genotype; adjusted OR=3.08, 95% CI = 1.33-7.17, P = 0.009 for the rs6586250 CC/CT genotype). Furthermore, the stratification analysis revealed that patients with the rs6586250 TT genotype and carriers with 1-5 risk genotypes exhibited statistically significant associations with increased Wilms tumor risk in specific subgroups. However, the rs2156315 CT/TT genotype was identified as having a protective effect against Wilms tumor in the age >18 months subgroup compared with the rs2156315 CC genotype. In brief, our study demonstrated that the rs6586250 C > T polymorphism of the WDR4 gene was significantly associated with Wilms tumor. This finding may contribute to the understanding of the genetic mechanism of Wilms tumor.
Collapse
Affiliation(s)
- Linqing Deng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| | - Rui-Xi Hua
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| | - Changmi Deng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| | - Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Zhengtao Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| | - Jiwen Cheng
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Jiao Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Haixia Zhou
- Department of Hematology, The Key Laboratory of Pediatric Hematology and Oncology Diseases of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Suhong Li
- Department of Pathology, Children Hospital and Women Health Center of Shanxi, Taiyuan 030013, Shannxi, China
| | - Jichen Ruan
- Department of Hematology, The Key Laboratory of Pediatric Hematology and Oncology Diseases of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Guochang Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| | - Wen Fu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, Guangdong, China
| |
Collapse
|
17
|
Wang Z, Yu P, Zou Y, Ma J, Han H, Wei W, Yang C, Zheng S, Guo S, Wang J, Liu L, Lin S. METTL1/WDR4-mediated tRNA m 7G modification and mRNA translation control promote oncogenesis and doxorubicin resistance. Oncogene 2023:10.1038/s41388-023-02695-6. [PMID: 37185458 DOI: 10.1038/s41388-023-02695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Osteosarcoma is the most common bone tumor that leads to high mortality in adolescents and children. The tRNA N7-methylguanosine methyltransferase METTL1 is located in chromosome 12q14.1, a region that is frequently amplified in osteosarcoma patients, while its functions and underlying mechanisms in regulation of osteosarcoma remain unknown. Herein we show that METTL1 and WDR4 are overexpressed in osteosarcoma and associated with poor patient prognosis. Knockdown of METTL1 or WDR4 causes decreased tRNA m7G modification level and impairs osteosarcoma progression in vitro and in vivo. Conversely, METTL1/WDR4 overexpression promotes osteosarcoma proliferation, migration and invasion capacities. tRNA methylation and mRNA translation profiling indicate that METTL1/WDR4 modified tRNAs enhance translation of mRNAs with more m7G tRNA-decoded codons, including extracellular matrix (ECM) remodeling effectors, which facilitates osteosarcoma progression and chemoresistance to doxorubicin. Our study demonstrates METTL1/WDR4 mediated tRNA m7G modification plays crucial oncogenic functions to enhance osteosarcoma progression and chemoresistance to doxorubicin via alteration of oncogenic mRNA translation, suggesting METTL1 inhibition combined with chemotherapy is a promising strategy for treatment of osteosarcoma patients.
Collapse
Affiliation(s)
- Zhaoyu Wang
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Peng Yu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, China
| | - Yutong Zou
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Jieyi Ma
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Laboratory of General Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Hui Han
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Wei Wei
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Chunlong Yang
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Siyi Zheng
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Siyao Guo
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Juan Wang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Lianlian Liu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| |
Collapse
|
18
|
Zeng X, Liao G, Li S, Liu H, Zhao X, Li S, Lei K, Zhu S, Chen Z, Zhao Y, Ren X, Su T, Cheng ASL, Peng S, Lin S, Wang J, Chen S, Kuang M. Eliminating METTL1-mediated accumulation of PMN-MDSCs prevents hepatocellular carcinoma recurrence after radiofrequency ablation. Hepatology 2023; 77:1122-1138. [PMID: 35598182 DOI: 10.1002/hep.32585] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Radiofrequency ablation (RFA) is an important curative therapy in hepatocellular carcinoma (HCC), but recurrence rate remains as high as all the other HCC therapeutic modalities. Methyltransferase 1 (METTL1), an enzyme for m 7 G tRNA modification, was reported to promote HCC development. Here, we assessed the role of METTL1 in shaping the immunosuppressive tumor microenvironment after insufficient RFA (iRFA). APPROACH AND RESULTS By immunohistochemistry and multiplex immunofluorescence (mIF) staining, we showed that METTL1 expression was enhanced in post-RFA recurrent HCC, accompanied by increased CD11b + CD15 + polymorphonuclear-myeloid-derived suppressor cells (PMN-MDSCs) and decreased CD8 + T cells. Mechanistically, heat-mediated METTL1 upregulation enhanced TGF-β2 translation to form the immunosuppressive environment by induction of myeloid-derived suppressor cell. Liver-specific overexpression or knockdown of Mettl1 significantly affected the accumulation of PMN-MDSCs and subsequently affected CD8 + T cell infiltration. Complete RFA successfully eliminated the tumor, whereas iRFA-treated mice exhibited enhanced tumor growth and metastasis with increased PMN-MDSC accumulation and decreased CD8 + T cells compared to sham surgery. Interrupting METTL1-TGF-β2-PMN-MDSC axis by anti-Ly6G antibody, or knockdown of hepatoma-intrinsic Mettl1 or Tgfb2 , or TGF-β signaling blockade significantly mitigated tumor progression induced by iRFA and restored CD8 + T cell population. CONCLUSIONS Our study sheds light on the pivotal role of METTL1 in modulating an immunosuppressive microenvironment and demonstrated that interrupting METTL1-TGF-β2-PMN-MDSC axis could be a therapeutic strategy to restore antitumor immunity and prevent HCC recurrence after RFA treatment, meriting further clinical studies.
Collapse
Affiliation(s)
- Xuezhen Zeng
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Guanrui Liao
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Shumin Li
- Department of Gastroenterology and Hepatology , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Haining Liu
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Xiao Zhao
- Department of Oncology , The First Affiliated Hospital of Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Shuang Li
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Kai Lei
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Shenghua Zhu
- Department of Gastroenterology and Hepatology , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Zhihang Chen
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Yi Zhao
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Xuxin Ren
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Tianhong Su
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Department of Oncology , The First Affiliated Hospital of Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Alfred Sze-Lok Cheng
- School of Biomedical Sciences , The Chinese University of Hong Kong , Hong Kong , China
| | - Sui Peng
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Department of Gastroenterology and Hepatology , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Clinical Trials Unit , The First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Shuibin Lin
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Center for Translational Medicine , The First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Ji Wang
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Shuling Chen
- Division of Interventional Ultrasound , The First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| | - Ming Kuang
- Department of Liver Surgery , Center of Hepato-Pancreato-Biliary Surgery , The First Affiliated Hospital, Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Institute of Precision Medicine , the First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Department of Oncology , The First Affiliated Hospital of Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Division of Interventional Ultrasound , The First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
- Cancer Center , The First Affiliated Hospital , Sun Yat-sen University , Guangzhou , Guangdong Province , China
| |
Collapse
|
19
|
Du D, He J, Ju C, Wang C, Li H, He F, Zhou M. When N7-methyladenosine modification meets cancer: Emerging frontiers and promising therapeutic opportunities. Cancer Lett 2023; 562:216165. [PMID: 37028699 DOI: 10.1016/j.canlet.2023.216165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023]
Abstract
N7-methylguanosine (m7G) methylation, one of the most common RNA modifications in eukaryotes, has recently gained considerable attention. The biological functions of m7G modification in RNAs, including tRNA, rRNA, mRNA, and miRNA, remain largely unknown in human diseases. Owing to rapid advances in high-throughput technologies, increasing evidence suggests that m7G modification plays a critical role in cancer initiation and progression. As m7G modification and hallmarks of cancer are inextricably linked together, targeting m7G regulators may provide new possibilities for future cancer diagnoses and potential intervention targets. This review summarizes various detection methods for m7G modification, recent advances in m7G modification and tumor biology regarding their interplay and regulatory mechanisms. We conclude with an outlook on the future of diagnosing and treating m7G-related diseases.
Collapse
|
20
|
Schultz SK, Meadows K, Kothe U. Molecular mechanism of tRNA binding by the Escherichia coli N7 guanosine methyltransferase TrmB. J Biol Chem 2023; 299:104612. [PMID: 36933808 PMCID: PMC10130221 DOI: 10.1016/j.jbc.2023.104612] [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: 11/01/2022] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Among the large and diverse collection of tRNA modifications, 7-methylguanosine (m7G) is frequently found in the tRNA variable loop at position 46. This modification is introduced by the TrmB enzyme, which is conserved in bacteria and eukaryotes. However, the molecular determinants and the mechanism for tRNA recognition by TrmB are not well understood. Complementing the report of various phenotypes for different organisms lacking TrmB homologs, we report here hydrogen peroxide sensitivity for the Escherichia coli ΔtrmB knockout strain. To gain insight into the molecular mechanism of tRNA binding by E. coli TrmB in real-time, we developed a new assay based on introducing a 4-thiouridine modification at position 8 of in vitro transcribed tRNAPhe enabling us to fluorescently label this unmodified tRNA. Using rapid kinetic stopped-flow measurements with this fluorescent tRNA, we examined the interaction of wildtype and single substitution variants of TrmB with tRNA. Our results reveal the role of SAM for rapid and stable tRNA binding, the rate-limiting nature of m7G46 catalysis for tRNA release, and the importance of residues R26, T127 and R155 across the entire surface of TrmB for tRNA binding.
Collapse
Affiliation(s)
- Sarah K Schultz
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kieran Meadows
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada; Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
21
|
Zhu Y, Zhao Z, Thandar M, Cheng J, Chi P, Huang S. Expression patterns and prognostic value of key regulators associated with m7G RNA modification based on all gene expression in colon adenocarcinoma. BMC Gastroenterol 2023; 23:22. [PMID: 36681801 PMCID: PMC9867544 DOI: 10.1186/s12876-023-02657-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND N7-methylguanosine (m7G) is present in a wide variety of organisms and has important roles. m7G has been reported to be involved in multiple biological processes, and recent studies have reported that changes in RNA modifications result in tumor cellular transformation and cancer, such as colon adenocarcinoma, lung cancer, and intrahepatic cholangiocarcinoma. However, little is known about the function of the m7G in colon adenocarcinoma. METHODS We established two clusters based on the expression of all genes associated with m7G to explore the expression pattern of 31 key regulatory factors of m7G RNA and assess the prognostic value of regulatory factors. Wilcoxon test and differential box line plots were applied for bioinformatics analysis. Receiver Operating and Kaplan‒Meier curves were utilized to evaluate the prognostic value. Finally, four genes' expression in the colon cancer cell line was confirmed by qRT-PCR. RESULTS From The Cancer Genome Atlas database, we found that the expression levels of 25 out of the 31 key N7-methylguanosine RNA modification regulators were significantly different in colon adenocarcinoma. According to 25 methylation regulators' expression, we identified two subgroups by consensus clustering, in which the prognosis was worse in Group 2 than in Group 1 and was significantly correlated with age. Cluster 2 was significantly enriched in tumor-associated pathways, and immune cells were highly infiltrated in Cluster 1 but weakly infiltrated in Cluster 2. Further results indicated that this risk profile may serve as a standalone predictive factor for colon adenocarcinoma, and the four genetic risk profiles' prognostic relatedness was successfully verified through Gene Expression Omnibus dataset. At last, A nomogram for prognosis was created according to age, sex, histological grading, clinicopathological staging, and hazard score to accurately predict patient prognosis in colon adenocarcinoma. We successfully validated the differential expression of four genes using qRT-PCR. CONCLUSIONS In the present study, we revealed the important contribution of key regulators associated with m7G RNA modifications based on all gene expression in colon adenocarcinoma and developed a signature of risk that serves as a promising prognostic marker for patients with colon adenocarcinoma.
Collapse
Affiliation(s)
- Yuanchang Zhu
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Zeyi Zhao
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Mya Thandar
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Junhao Cheng
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China
| | - Pan Chi
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China ,grid.411176.40000 0004 1758 0478Training Center of Minimally Invasive Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian China
| | - Shenghui Huang
- grid.411176.40000 0004 1758 0478Department of Colorectal Surgery, Fujian Medical University Union Hospital, No. 29, Xinquan Road, Gulou District, Fuzhou City, Fujian Province China ,grid.411176.40000 0004 1758 0478Training Center of Minimally Invasive Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian China
| |
Collapse
|
22
|
Xia X, Wang Y, Zheng JC. Internal m7G methylation: A novel epitranscriptomic contributor in brain development and diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:295-308. [PMID: 36726408 PMCID: PMC9883147 DOI: 10.1016/j.omtn.2023.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In recent years, N7-methylguanosine (m7G) methylation, originally considered as messenger RNA (mRNA) 5' caps modifications, has been identified at defined internal positions within multiple types of RNAs, including transfer RNAs, ribosomal RNAs, miRNA, and mRNAs. Scientists have put substantial efforts to discover m7G methyltransferases and methylated sites in RNAs to unveil the essential roles of m7G modifications in the regulation of gene expression and determine the association of m7G dysregulation in various diseases, including neurological disorders. Here, we review recent findings regarding the distribution, abundance, biogenesis, modifiers, and functions of m7G modifications. We also provide an up-to-date summary of m7G detection and profile mapping techniques, databases for validated and predicted m7G RNA sites, and web servers for m7G methylation prediction. Furthermore, we discuss the pathological roles of METTL1/WDR-driven m7G methylation in neurological disorders. Last, we outline a roadmap for future directions and trends of m7G modification research, particularly in the central nervous system.
Collapse
Affiliation(s)
- Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Corresponding author: Xiaohuan Xia, Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200065, China.
| | - Yi Wang
- Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Translational Research Center, Shanghai Yangzhi Rehabilitation Hospital affiliated to Tongji University School of Medicine, Shanghai 201613, China
| | - Jialin C. Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai 200331, China,Corresponding author: Jialin C. Zheng, Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai 200065, China.
| |
Collapse
|
23
|
Huang M, Long J, Yao Z, Zhao Y, Zhao Y, Liao J, Lei K, Xiao H, Dai Z, Peng S, Lin S, Xu L, Kuang M. METTL1-Mediated m7G tRNA Modification Promotes Lenvatinib Resistance in Hepatocellular Carcinoma. Cancer Res 2023; 83:89-102. [PMID: 36102722 DOI: 10.1158/0008-5472.can-22-0963] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/18/2022] [Accepted: 09/07/2022] [Indexed: 02/03/2023]
Abstract
The tyrosine kinase inhibitor lenvatinib is a first-line drug for treating patients with advanced hepatocellular carcinoma (HCC). However, its efficacy is severely hampered by drug resistance. Insights into the molecular mechanisms underlying lenvatinib resistance could provide new strategies to improve and prolong responses. Here, we performed unbiased proteomic screening of parental and lenvatinib-resistant HCC cells and discovered that methyltransferase-like protein-1 (METTL1) and WD repeat domain 4 protein (WDR4), the two key components of the tRNA N7-methylguanosine (m7G) methyltransferase complex, were dramatically upregulated in lenvatinib-resistant cells. METTL1 knockdown overrode resistance by impairing the proliferation capacity of HCC cells and promoting apoptosis under lenvatinib treatment. In addition, overexpression of wild-type METTL1 but not its catalytic dead mutant induced lenvatinib resistance. Animal experiments including hydrodynamic injection, subcutaneous implantation, and orthotopic xenograft mouse models further demonstrated the critical function of METTL1/WDR4-mediated m7G tRNA modification in promoting lenvatinib resistance in vivo. Mechanistically, METTL1 promoted translation of EGFR pathway genes to trigger drug resistance. This work reveals the important role of METTL1-mediated m7G tRNA modification in promoting lenvatinib resistance and provides a promising prediction marker and intervention target for resistance. SIGNIFICANCE Upregulation of tRNA m7G methyltransferase complex components METTL1 and WDR4 promotes lenvatinib resistance in HCC and confers a sensitivity to METTL1 targeting, providing a promising strategy to override resistance.
Collapse
Affiliation(s)
- Manling Huang
- Department of Oncology, Cancer Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jianting Long
- Department of Oncology, Cancer Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zhijia Yao
- Department of Oncology, Cancer Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yi Zhao
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yutong Zhao
- Department of Oncology, Cancer Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Junbin Liao
- Center of Hepato-Pancreate-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
| | - Kai Lei
- Center of Hepato-Pancreate-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
| | - Han Xiao
- Department of Medical Ultrasonics, The First Affililated Hospital of Sun Yat-sen University, Guangzhou, P.R. China
| | - Zihao Dai
- Center of Hepato-Pancreate-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
| | - Sui Peng
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Department of Gastroenterology and Hepatology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Clinical Trial Unit, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Shuibin Lin
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
| | - Lixia Xu
- Department of Oncology, Cancer Center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Ming Kuang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China.,Center of Hepato-Pancreate-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China.,Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
| |
Collapse
|
24
|
Ruiz-Arroyo VM, Raj R, Babu K, Onolbaatar O, Roberts PH, Nam Y. Structures and mechanisms of tRNA methylation by METTL1-WDR4. Nature 2023; 613:383-390. [PMID: 36599982 PMCID: PMC9930641 DOI: 10.1038/s41586-022-05565-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/16/2022] [Indexed: 01/06/2023]
Abstract
Specific, regulated modification of RNAs is important for proper gene expression1,2. tRNAs are rich with various chemical modifications that affect their stability and function3,4. 7-Methylguanosine (m7G) at tRNA position 46 is a conserved modification that modulates steady-state tRNA levels to affect cell growth5,6. The METTL1-WDR4 complex generates m7G46 in humans, and dysregulation of METTL1-WDR4 has been linked to brain malformation and multiple cancers7-22. Here we show how METTL1 and WDR4 cooperate to recognize RNA substrates and catalyse methylation. A crystal structure of METTL1-WDR4 and cryo-electron microscopy structures of METTL1-WDR4-tRNA show that the composite protein surface recognizes the tRNA elbow through shape complementarity. The cryo-electron microscopy structures of METTL1-WDR4-tRNA with S-adenosylmethionine or S-adenosylhomocysteine along with METTL1 crystal structures provide additional insights into the catalytic mechanism by revealing the active site in multiple states. The METTL1 N terminus couples cofactor binding with conformational changes in the tRNA, the catalytic loop and the WDR4 C terminus, acting as the switch to activate m7G methylation. Thus, our structural models explain how post-translational modifications of the METTL1 N terminus can regulate methylation. Together, our work elucidates the core and regulatory mechanisms underlying m7G modification by METTL1, providing the framework to understand its contribution to biology and disease.
Collapse
Affiliation(s)
- Victor M Ruiz-Arroyo
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rishi Raj
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kesavan Babu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Otgonbileg Onolbaatar
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paul H Roberts
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yunsun Nam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
25
|
Abstract
The methyltransferase-like (METTL) family is a diverse group of methyltransferases that can methylate nucleotides, proteins, and small molecules. Despite this diverse array of substrates, they all share a characteristic seven-beta-strand catalytic domain, and recent evidence suggests many also share an important role in stem cell biology. The most well characterized family members METTL3 and METTL14 dimerize to form an N6-methyladenosine (m6A) RNA methyltransferase with established roles in cancer progression. However, new mouse models indicate that METTL3/METTL14 are also important for embryonic stem cell (ESC) development and postnatal hematopoietic and neural stem cell self-renewal and differentiation. METTL1, METTL5, METTL6, METTL8, and METTL17 also have recently identified roles in ESC pluripotency and differentiation, while METTL11A/11B, METTL4, METTL7A, and METTL22 have been shown to play roles in neural, mesenchymal, bone, and hematopoietic stem cell development, respectively. Additionally, a variety of other METTL family members are translational regulators, a role that could place them as important players in the transition from stem cell quiescence to differentiation. Here we will summarize what is known about the role of METTL proteins in stem cell differentiation and highlight the connection between their growing importance in development and their established roles in oncogenesis.
Collapse
Affiliation(s)
- John G Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - James P Catlin
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA.
| |
Collapse
|
26
|
Zhang LS, Ju CW, Liu C, Wei J, Dai Q, Chen L, Ye C, He C. m 7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine. ACS Chem Biol 2022; 17:3306-3312. [PMID: 36398936 PMCID: PMC9764283 DOI: 10.1021/acschembio.2c00792] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Methods for the precise detection and quantification of RNA modifications are critical to uncover functional roles of diverse RNA modifications. The internal m7G modification in mammalian cytoplasmic tRNAs is known to affect tRNA function and impact embryonic stem cell self-renewal, tumorigenesis, cancer progression, and other cellular processes. Here, we introduce m7G-quant-seq, a quantitative method that accurately detects internal m7G sites in human cytoplasmic tRNAs at single-base resolution. The efficient chemical reduction and mild depurination can almost completely convert internal m7G sites into RNA abasic sites (AP sites). We demonstrate that RNA abasic sites induce a mixed variation pattern during reverse transcription, including G → A or C or T mutations as well as deletions. We calculated the total variation ratio to quantify the m7G modification fraction at each methylated site. The calibration curves of all relevant motif contexts allow us to more quantitatively determine the m7G methylation level. We detected internal m7G sites in 22 human cytoplasmic tRNAs from HeLa and HEK293T cells and successfully estimated the corresponding m7G methylation stoichiometry. m7G-quant-seq could be applied to monitor the tRNA m7G methylation level change in diverse biological processes.
Collapse
Affiliation(s)
- Li-Sheng Zhang
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States,Division
of Life Science, Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China,
| | - Cheng-Wei Ju
- Pritzker
School of Molecular Engineering, The University
of Chicago, Chicago, Illinois 60637, United
States
| | - Chang Liu
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jiangbo Wei
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Qing Dai
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Li Chen
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chang Ye
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States,Howard
Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815, United States,
| |
Collapse
|
27
|
Guo P, Wang P, Liu L, Wang P, Qu Z, Yu Z, Liu N. A novel
N7
‐methylguanosine‐related long noncoding
RNAs
signature for predicting prognosis and immune microenvironment in gastric cancer patients. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Peisen Guo
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Panpan Wang
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
| | - Limin Liu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Peixi Wang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Zhi Qu
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
| | - Zengli Yu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
| | - Nan Liu
- College of Public Health Zhengzhou University Zhengzhou People's Republic of China
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Jinming Avenue North Section Henan University Kaifeng People's Republic of China
- Institute of Environment and Health, South China Hospital, Health Science Center Shenzhen University Shenzhen People's Republic of China
| |
Collapse
|
28
|
Abstract
tRNAs are key adaptor molecules that decipher the genetic code during translation of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously expressed housekeeping molecules, awareness is now growing that tRNA-encoding genes display tissue-specific and cell type-specific patterns of expression, and that tRNA gene expression and function are both dynamically regulated by post-transcriptional RNA modifications. Moreover, dysregulation of tRNAs, mediated by alterations in either their abundance or function, can have deleterious consequences that contribute to several distinct human diseases, including neurological disorders and cancer. Accumulating evidence shows that reprogramming of mRNA translation through altered tRNA activity can drive pathological processes in a codon-dependent manner. This Review considers the emerging evidence in support of the precise control of functional tRNA levels as an important regulatory mechanism that coordinates mRNA translation and protein expression in physiological cell homeostasis, and highlights key examples of human diseases that are linked directly to tRNA dysregulation.
Collapse
Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Siegal
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Harvard University, Boston, MA, USA.
| |
Collapse
|
29
|
Zha L, Wang J, Cheng X. The effects of
RNA
methylation on immune cells development and function. FASEB J 2022; 36:e22552. [DOI: 10.1096/fj.202200716r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ling‐Feng Zha
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Jing‐Lin Wang
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Xiang Cheng
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| |
Collapse
|
30
|
Abstract
As one of the prevalent posttranscriptional modifications of RNA, N7-methylguanosine (m7G) plays essential roles in RNA processing, metabolism, and function, mainly regulated by the methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4) complex. Emerging evidence suggests that the METTL1/WDR4 complex promoted or inhibited the processes of many tumors, including head and neck, lung, liver, colon, bladder cancer, and teratoma, dependent on close m7G methylation modification of tRNA or microRNA (miRNA). Therefore, METTL1 and m7G modification can be used as biomarkers or potential intervention targets, providing new possibilities for early diagnosis and treatment of tumors. This review will mainly focus on the mechanisms of METTL1/WDR4 via m7G in tumorigenesis and the corresponding detection methods.
Collapse
Affiliation(s)
- Wenli Cheng
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Aili Gao
- Guangzhou Institution of Dermatology, Guangzhou, Guangdong 510095, P.R. China
| | - Hui Lin
- Department of Radiation Oncology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P. R. China
| | - Wenjuan Zhang
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| |
Collapse
|
31
|
Huang Y, Ma J, Yang C, Wei P, Yang M, Han H, Chen HD, Yue T, Xiao S, Chen X, Li Z, Tang Y, Luo J, Lin S, Huang L. METTL1 promotes neuroblastoma development through m 7G tRNA modification and selective oncogenic gene translation. Biomark Res 2022; 10:68. [PMID: 36071474 PMCID: PMC9454133 DOI: 10.1186/s40364-022-00414-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/20/2022] [Indexed: 11/21/2022] Open
Abstract
Background Neuroblastoma (NBL) is the most common extra-cranial solid tumour in childhood, with prognosis ranging from spontaneous remission to high risk for rapid and fatal progression. Despite existing therapy approaches, the 5-year event-free survival (EFS) for patients with advanced NBL remains below 30%, emphasizing urgent necessary for novel therapeutic strategies. Studies have shown that epigenetic disorders play an essential role in the pathogenesis of NBL. However, the function and mechanism of N7-methylguanosine (m7G) methyltransferase in NBL remains unknown. Methods The expression levels of m7G tRNA methyltransferase Methyltransferase-like 1 (METTL1) were analyzed by querying the Gene Expression Omnibus (GEO) database and further confirmed by immunohistochemistry (IHC) assay. Kaplan-Meier, univariate and multivariate cox hazard analysis were performed to reveal the prognostic role of METTL1. Cell function assays were performed to evaluate how METTL1 works in proliferation, apoptosis and migration in cell lines and xenograft mouse models. The role of METTL1 on mRNA translation activity of NBL cells was measured using puromycin intake assay and polysome profiling assay. The m7G modified tRNAs were identified by tRNA reduction and cleavage sequencing (TRAC-seq). Ribosome nascent-chain complex-bound mRNA sequencing (RNC-seq) was utilized to identify the variation of gene translation efficiency (TE). Analyzed the codon frequency decoded by m7G tRNA to clarify the translation regulation and mechanism of m7G modification in NBL. Results This study found that METTL1 were significantly up-regulated in advanced NBL, which acted as an independent risk factor and predicted poor prognosis. Further in NBL cell lines and BALB/c-nu female mice, we found METTL1 played a crucial role in promoting NBL progression. Furthermore, m7G profiling and translation analysis revealed downregulation of METTL1 would inhibit puromycin intake efficiency of NBL cells, indicating that METTL1 did count crucially in regulation of NBL cell translation. With all tRNAs with m7G modification identified in NBL cells, knockdown of METTL1 would significantly reduce the levels of both m7G modification and m7G tRNAs expressions. Result of RNC-seq shew there were 339 overlapped genes with impaired translation in NBL cells upon METTL1 knockdown. Further analysis revealed these genes contained higher frequency of codons decoded by m7G-modified tRNAs and were enriched in oncogenic pathways. Conclusion This study revealed the critical role and mechanism of METTL1-mediated tRNA m7G modification in regulating NBL progression, providing new insights for developing therapeutic approaches for NBL patients. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-022-00414-z.
Collapse
Affiliation(s)
- Ying Huang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.,Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jieyi Ma
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Cuiyun Yang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Paijia Wei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China
| | - Minghui Yang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hui Han
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hua Dong Chen
- Department of Pediatric Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Tianfang Yue
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shu Xiao
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xuanyu Chen
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zuoqing Li
- Department of Pediatric Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yanlai Tang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiesi Luo
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Libin Huang
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
| |
Collapse
|
32
|
RNA Modifications in Gastrointestinal Cancer: Current Status and Future Perspectives. Biomedicines 2022; 10:biomedicines10081918. [PMID: 36009465 PMCID: PMC9405978 DOI: 10.3390/biomedicines10081918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 01/05/2023] Open
Abstract
Gastrointestinal (GI) cancer, referring to cancers of the digestive system such as colorectal cancer (CRC), gastric cancer (GC), and liver cancer, is a major cause of cancer-related deaths in the world. A series of genetic, epigenetic, and epitranscriptomic changes occur during the development of GI cancer. The identification of these molecular events provides potential diagnostic, prognostic, and therapeutic targets for cancer patients. RNA modification is required in the posttranscriptional regulation of RNA metabolism, including splicing, intracellular transport, degradation, and translation. RNA modifications such as N6-methyladenosine (m6A) and N1-methyladenosine (m1A) are dynamically regulated by three different types of regulators named methyltransferases (writers), RNA binding proteins (readers), and demethylases (erasers). Recent studies have pointed out that abnormal RNA modification contributes to GI tumorigenesis and progression. In this review, we summarize the latest findings on the functional significance of RNA modification in GI cancer and discuss the therapeutic potential of epitranscriptomic inhibitors for cancer treatment.
Collapse
|
33
|
Zhang C, Zhou D, Wang Z, Ju Z, He J, Zhao G, Wang R. Risk Model and Immune Signature of m7G-Related lncRNA Based on Lung Adenocarcinoma. Front Genet 2022; 13:907754. [PMID: 35754819 PMCID: PMC9214213 DOI: 10.3389/fgene.2022.907754] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Lung cancer is a major cause of cancer-related deaths globally, with a dismal prognosis. N7-methylguanosine (m7G) is essential for the transcriptional phenotypic modification of messenger RNA (mRNA) and long noncoding RNA (lncRNA). However, research on m7G-related lncRNAs involved in lung adenocarcinoma (LUAD) regulation is still limited. Herein, we aim to establish a prognostic model of m7G-related lncRNAs and investigate their immune properties. Eight prognostic m7G-related lncRNAs were identified using univariate Cox analysis. Six m7G-related lncRNAs were identified using LASSO-Cox regression analysis to construct risk models, and all LUAD patients in The Cancer Genome Atlas (TCGA) cohort was divided into low-risk and high-risk subgroups. The accuracy of the model was verified by Kaplan-Meier analysis, time-dependent receiver operating characteristic, principal component analysis, independent prognostic analysis, nomogram, and calibration curve. Further studies were conducted on the gene set enrichment and disease ontology enrichment analyses. The gene set enrichment analysis (GSEA) revealed that the high-risk group enriched for cancer proliferation pathways, and the enrichment analysis of disease ontology (DO) revealed that lung disease was enriched, rationally explaining the superiority of the risk model. Finally, we found that the low-risk group had higher immune infiltration and checkpoint expression. It can be speculated that the low-risk group has a better effect on immunotherapy. Susceptibility to antitumor drugs in different risk subgroups was assessed, and it found that the high-risk group showed high sensitivity to first-line treatment drugs for non-small cell lung cancer. In conclusion, a risk model based on 6 m7G-related lncRNAs can not only predict the overall survival (OS) rate of LUAD patients but also guide individualized treatment for these patients.
Collapse
Affiliation(s)
- Chuanhao Zhang
- Graduate School of Dalian Medical University, Dalian, China.,Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Dong Zhou
- Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Zhe Wang
- Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Zaishuang Ju
- Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Jiabei He
- Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Genghao Zhao
- Graduate School of Dalian Medical University, Dalian, China.,Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Ruoyu Wang
- Departement of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| |
Collapse
|
34
|
N 7-methylguanosine tRNA modification promotes esophageal squamous cell carcinoma tumorigenesis via the RPTOR/ULK1/autophagy axis. Nat Commun 2022; 13:1478. [PMID: 35304469 PMCID: PMC8933395 DOI: 10.1038/s41467-022-29125-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/25/2022] [Indexed: 12/24/2022] Open
Abstract
Mis-regulated RNA modifications promote the processing and translation of oncogenic mRNAs to facilitate cancer progression, while the molecular mechanisms remain unclear. Here we reveal that tRNA m7G methyltransferase complex proteins METTL1 and WDR4 are significantly up-regulated in esophageal squamous cell carcinoma (ESCC) tissues and associated with poor ESCC prognosis. In addition, METTL1 and WDR4 promote ESCC progression via the tRNA m7G methyltransferase activity in vitro and in vivo. Mechanistically, METTL1 or WDR4 knockdown leads to decreased expression of m7G-modified tRNAs and reduces the translation of a subset of oncogenic transcripts enriched in RPTOR/ULK1/autophagy pathway. Furthermore, ESCC models using Mettl1 conditional knockout and knockin mice uncover the essential function of METTL1 in promoting ESCC tumorigenesis in vivo. Our study demonstrates the important oncogenic function of mis-regulated tRNA m7G modification in ESCC, and suggest that targeting METTL1 and its downstream signaling axis could be a promising therapeutic target for ESCC treatment. Deregulation of METTL1-mediated N7- methylguanosine tRNA modification can promote oncogenesis. Here, the authors report that this modification regulates the translation of proteins in both the mTOR and negative regulators of autophagy pathways, resulting in the progression of esophageal squamous cell carcinoma.
Collapse
|
35
|
Shoombuatong W, Basith S, Pitti T, Lee G, Manavalan B. THRONE: a new approach for accurate prediction of human RNA N7-methylguanosine sites. J Mol Biol 2022; 434:167549. [DOI: 10.1016/j.jmb.2022.167549] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/30/2022]
|
36
|
Chen J, Li K, Chen J, Wang X, Ling R, Cheng M, Chen Z, Chen F, He Q, Li S, Zhang C, Jiang Y, Chen Q, Wang A, Chen D. Aberrant translation regulated by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives head and neck squamous cell carcinoma progression. Cancer Commun (Lond) 2022; 42:223-244. [PMID: 35179319 PMCID: PMC8923133 DOI: 10.1002/cac2.12273] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/25/2021] [Accepted: 02/06/2022] [Indexed: 12/16/2022] Open
Abstract
Background Cancer cells selectively promote the translation of oncogenic transcripts to stimulate cancer progression. Although growing evidence has revealed that tRNA modifications and related genes participate in this process, their roles in head and neck squamous cell carcinoma (HNSCC) remain largely uncharacterized. Here, we sought to investigate the function and mechanisms of the transfer RNA (tRNA) N7‐methylguanosine (m7G) modification in regulating the occurrence and development of HNSCC. Methods Cell lost‐of‐function and gain‐of‐function assays, xenograft models, conditional knockout and knockin mouse models were used to study the physiological functions of tRNA m7G modification in HNSCC tumorigenesis. tRNA modification and expression profiling, mRNA translation profiling and rescue assays were performed to uncover the underlying molecular mechanisms. Single‐cell RNA sequencing (scRNA‐seq) was conducted to explore the tumor microenvironment changes. Results The tRNA m7G methyltransferase complex components Methyltransferase‐like 1 (METTL1)/WD repeat domain 4 (WDR4) were upregulated in HNSCC and associated with a poor prognosis. Functionally, METTL1/WDR4 promoted HNSCC progression and metastasis in cell‐based and transgenic mouse models. Mechanistically, ablation of METTL1 reduced the m7G levels of 16 tRNAs, inhibiting the translation of a subset of oncogenic transcripts, including genes related to the phosphatidylinositol‐3‐kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway. In addition, chemical modulators of the PI3K/Akt/mTOR signaling pathway reversed the effects of Mettl1 in mouse HNSCC. Furthermore, scRNA‐seq results revealed that Mettl1 knockout in mouse tumor cells altered the immune landscape and cell‐cell interaction between the tumor and stromal compartment. Conclusions The tRNA m7G methyltransferase METTL1 was found to promote the development and malignancy of HNSCC through regulating global mRNA translation, including the PI3K/AKT/mTOR signaling pathway, and found to alter immune landscape. METTL1 could be a promising treatment target for HNSCC patients.
Collapse
Affiliation(s)
- Jie Chen
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Kang Li
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Jianwen Chen
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Xiaochen Wang
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518000, P. R. China
| | - Maosheng Cheng
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Zhi Chen
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Fangfang Chen
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Qianting He
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Shuai Li
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Caihua Zhang
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Yizhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, 518000, P. R. China
| | - Qianming Chen
- School of Stomatology, Cancer Center, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Clinical Research Center of Oral Diseases of Zhejiang Province, Stomatology Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, P. R. China
| | - Anxun Wang
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Demeng Chen
- Department of Oral and Maxillofacial Surgery, Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| |
Collapse
|
37
|
Chen Z, Zhu W, Zhu S, Sun K, Liao J, Liu H, Dai Z, Han H, Ren X, Yang Q, Zheng S, Peng B, Peng S, Kuang M, Lin S. METTL1 promotes hepatocarcinogenesis via m 7 G tRNA modification-dependent translation control. Clin Transl Med 2021; 11:e661. [PMID: 34898034 PMCID: PMC8666584 DOI: 10.1002/ctm2.661] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND N7 -methylguanosine (m7 G) modification is one of the most common transfer RNA (tRNA) modifications in humans. The precise function and molecular mechanism of m7 G tRNA modification in hepatocellular carcinoma (HCC) remain poorly understood. METHODS The prognostic value and expression level of m7 G tRNA methyltransferase complex components methyltransferase-like protein-1 (METTL1) and WD repeat domain 4 (WDR4) in HCC were evaluated using clinical samples and TCGA data. The biological functions and mechanisms of m7 G tRNA modification in HCC progression were studied in vitro and in vivo using cell culture, xenograft model, knockin and knockout mouse models. The m7 G reduction and cleavage sequencing (TRAC-seq), polysome profiling and polyribosome-associated mRNA sequencing methods were used to study the levels of m7 G tRNA modification, tRNA expression and mRNA translation efficiency. RESULTS The levels of METTL1 and WDR4 are elevated in HCC and associated with advanced tumour stages and poor patient survival. Functionally, silencing METTL1 or WDR4 inhibits HCC cell proliferation, migration and invasion, while forced expression of wild-type METTL1 but not its catalytic dead mutant promotes HCC progression. Knockdown of METTL1 reduces m7 G tRNA modification and decreases m7 G-modified tRNA expression in HCC cells. Mechanistically, METTL1-mediated tRNA m7 G modification promotes the translation of target mRNAs with higher frequencies of m7 G-related codons. Furthermore, in vivo studies with Mettl1 knockin and conditional knockout mice reveal the essential physiological function of Mettl1 in hepatocarcinogenesis using hydrodynamics transfection HCC model. CONCLUSIONS Our work reveals new insights into the role of the misregulated tRNA modifications in liver cancer and provides molecular basis for HCC diagnosis and treatment.
Collapse
Affiliation(s)
- Zhihang Chen
- Department of Liver SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Wanjie Zhu
- Department of Gastroenterology and HepatologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Shenghua Zhu
- Department of Gastroenterology and HepatologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Kaiyu Sun
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Junbin Liao
- Department of Liver SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Haining Liu
- Department of Liver SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Zihao Dai
- Department of Liver SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Hui Han
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Xuxin Ren
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Qingxia Yang
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Siyi Zheng
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Baogang Peng
- Department of Liver SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Sui Peng
- Department of Gastroenterology and HepatologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Ming Kuang
- Department of Liver SurgeryThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Cancer Center, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Shuibin Lin
- Center for Translational MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- State Key Laboratory of Oncology in South ChinaSun Yat‐sen University Cancer CenterGuangzhouChina
| |
Collapse
|
38
|
Manduzio S, Kang H. RNA methylation in chloroplasts or mitochondria in plants. RNA Biol 2021; 18:2127-2135. [PMID: 33779501 PMCID: PMC8632092 DOI: 10.1080/15476286.2021.1909321] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in our understanding of epitranscriptomic RNA methylation have expanded the complexity of gene expression regulation beyond epigenetic regulation involving DNA methylation and histone modifications. The instalment, removal, and interpretation of methylation marks on RNAs are carried out by writers (methyltransferases), erasers (demethylases), and readers (RNA-binding proteins), respectively. Contrary to an emerging body of evidence demonstrating the importance of RNA methylation in the diverse fates of RNA molecules, including splicing, export, translation, and decay in the nucleus and cytoplasm, their roles in plant organelles remain largely unclear and are only now being discovered. In particular, extremely high levels of methylation marks in chloroplast and mitochondrial RNAs suggest that RNA methylation plays essential roles in organellar biogenesis and functions in plants that are crucial for plant development and responses to environmental stimuli. Thus, unveiling the cellular components involved in RNA methylation in cell organelles is essential to better understand plant biology.
Collapse
Affiliation(s)
- Stefano Manduzio
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| |
Collapse
|
39
|
Katsara O, Schneider RJ. m 7G tRNA modification reveals new secrets in the translational regulation of cancer development. Mol Cell 2021; 81:3243-3245. [PMID: 34416137 PMCID: PMC10883294 DOI: 10.1016/j.molcel.2021.07.030] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Orellana et al. (2021) and Dai et al. (2021) demonstrate that increased m7G modification of a subset of tRNAs by the METTL1/WDR4 complex stabilizes these mRNAs against decay, increases translation efficiency, reduces ribosome pausing, is associated with poor survival in human cancers, and is directly transforming.
Collapse
Affiliation(s)
- Olga Katsara
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J Schneider
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
40
|
Orellana EA, Liu Q, Yankova E, Pirouz M, De Braekeleer E, Zhang W, Lim J, Aspris D, Sendinc E, Garyfallos DA, Gu M, Ali R, Gutierrez A, Mikutis S, Bernardes GJL, Fischer ES, Bradley A, Vassiliou GS, Slack FJ, Tzelepis K, Gregory RI. METTL1-mediated m 7G modification of Arg-TCT tRNA drives oncogenic transformation. Mol Cell 2021; 81:3323-3338.e14. [PMID: 34352207 PMCID: PMC8380730 DOI: 10.1016/j.molcel.2021.06.031] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 02/02/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023]
Abstract
The emerging "epitranscriptomics" field is providing insights into the biological and pathological roles of different RNA modifications. The RNA methyltransferase METTL1 catalyzes N7-methylguanosine (m7G) modification of tRNAs. Here we find METTL1 is frequently amplified and overexpressed in cancers and is associated with poor patient survival. METTL1 depletion causes decreased abundance of m7G-modified tRNAs and altered cell cycle and inhibits oncogenicity. Conversely, METTL1 overexpression induces oncogenic cell transformation and cancer. Mechanistically, we find increased abundance of m7G-modified tRNAs, in particular Arg-TCT-4-1, and increased translation of mRNAs, including cell cycle regulators that are enriched in the corresponding AGA codon. Accordingly, Arg-TCT expression is elevated in many tumor types and is associated with patient survival, and strikingly, overexpression of this individual tRNA induces oncogenic transformation. Thus, METTL1-mediated tRNA modification drives oncogenic transformation through a remodeling of the mRNA "translatome" to increase expression of growth-promoting proteins and represents a promising anti-cancer target.
Collapse
Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Liu
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eliza Yankova
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Storm Therapeutics Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Wencai Zhang
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Jihoon Lim
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - Erdem Sendinc
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Dimitrios A Garyfallos
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Muxin Gu
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Raja Ali
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alejandro Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sigitas Mikutis
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Allan Bradley
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Frank J Slack
- Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Konstantinos Tzelepis
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
| |
Collapse
|
41
|
Khonsari B, Klassen R, Schaffrath R. Role of SSD1 in Phenotypic Variation of Saccharomyces cerevisiae Strains Lacking DEG1-Dependent Pseudouridylation. Int J Mol Sci 2021; 22:ijms22168753. [PMID: 34445460 PMCID: PMC8396022 DOI: 10.3390/ijms22168753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/16/2022] Open
Abstract
Yeast phenotypes associated with the lack of wobble uridine (U34) modifications in tRNA were shown to be modulated by an allelic variation of SSD1, a gene encoding an mRNA-binding protein. We demonstrate that phenotypes caused by the loss of Deg1-dependent tRNA pseudouridylation are similarly affected by SSD1 allelic status. Temperature sensitivity and protein aggregation are elevated in deg1 mutants and further increased in the presence of the ssd1-d allele, which encodes a truncated form of Ssd1. In addition, chronological lifespan is reduced in a deg1 ssd1-d mutant, and the negative genetic interactions of the U34 modifier genes ELP3 and URM1 with DEG1 are aggravated by ssd1-d. A loss of function mutation in SSD1, ELP3, and DEG1 induces pleiotropic and overlapping phenotypes, including sensitivity against target of rapamycin (TOR) inhibitor drug and cell wall stress by calcofluor white. Additivity in ssd1 deg1 double mutant phenotypes suggests independent roles of Ssd1 and tRNA modifications in TOR signaling and cell wall integrity. However, other tRNA modification defects cause growth and drug sensitivity phenotypes, which are not further intensified in tandem with ssd1-d. Thus, we observed a modification-specific rather than general effect of SSD1 status on phenotypic variation in tRNA modification mutants. Our results highlight how the cellular consequences of tRNA modification loss can be influenced by protein targeting specific mRNAs.
Collapse
|
42
|
Ma J, Han H, Huang Y, Yang C, Zheng S, Cai T, Bi J, Huang X, Liu R, Huang L, Luo Y, Li W, Lin S. METTL1/WDR4 mediated m 7G tRNA modifications and m 7G codon usage promote mRNA translation and lung cancer progression. Mol Ther 2021; 29:3422-3435. [PMID: 34371184 DOI: 10.1016/j.ymthe.2021.08.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 06/14/2021] [Accepted: 07/20/2021] [Indexed: 11/29/2022] Open
Abstract
Mis-regulated epigenetic modifications in RNAs are associated with human cancers. The transfer RNAs (tRNAs) are the most heavily modified RNA species in cells, however, little is known about the functions of tRNA modifications in cancers. In this study, we uncovered that the expression levels of tRNA N7-methylguanosine (m7G) methyltransferase complex components METTL1 and WDR4 are significantly elevated in human lung cancer samples and negatively associated with patient prognosis. Impaired m7G tRNA modification upon METTL1/WDR4 depletion resulted in decreased cell proliferation, colony formation, cell invasion and impaired tumorigenic capacities of lung cancer cells in vitro and in vivo. Moreover, gain-of-function and mutagenesis experiments revealed that METTL1 promoted lung cancer growth and invasion through regulation of m7G tRNA modifications. Profiling of tRNA methylation and mRNA translation revealed that highly translated mRNAs have higher frequencies of m7G tRNA decoded codons and knockdown of METTL1 resulted in decreased translation of mRNAs with higher frequencies of m7G tRNA codons, suggesting that tRNA modifications and codon usage play essential function in mRNA translation regulation. Our data uncovered novel insights on mRNA translation regulation through tRNA modifications and the corresponding mRNA codon compositions in lung cancer, providing new molecular basis underlying lung cancer progression.
Collapse
Affiliation(s)
- Jieyi Ma
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080; Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Hui Han
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Ying Huang
- Department of Pediatrics, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Chunlong Yang
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Siyi Zheng
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Tiancai Cai
- Xiamen special service convalescent center, Xiamen, China 361005
| | - Jiong Bi
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Xiaohui Huang
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Ruiming Liu
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Libin Huang
- Department of Pediatrics, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080
| | - Yifeng Luo
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China 510080.
| | - Wen Li
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080.
| | - Shuibin Lin
- Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China 510080; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China 510060.
| |
Collapse
|
43
|
N 7-Methylguanosine tRNA modification enhances oncogenic mRNA translation and promotes intrahepatic cholangiocarcinoma progression. Mol Cell 2021; 81:3339-3355.e8. [PMID: 34352206 DOI: 10.1016/j.molcel.2021.07.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/08/2021] [Accepted: 07/04/2021] [Indexed: 12/12/2022]
Abstract
Cancer cells selectively promote translation of specific oncogenic transcripts to facilitate cancer survival and progression, but the underlying mechanisms are poorly understood. Here, we find that N7-methylguanosine (m7G) tRNA modification and its methyltransferase complex components, METTL1 and WDR4, are significantly upregulated in intrahepatic cholangiocarcinoma (ICC) and associated with poor prognosis. We further reveal the critical role of METTL1/WDR4 in promoting ICC cell survival and progression using loss- and gain-of-function assays in vitro and in vivo. Mechanistically, m7G tRNA modification selectively regulates the translation of oncogenic transcripts, including cell-cycle and epidermal growth factor receptor (EGFR) pathway genes, in m7G-tRNA-decoded codon-frequency-dependent mechanisms. Moreover, using overexpression and knockout mouse models, we demonstrate the crucial oncogenic function of Mettl1-mediated m7G tRNA modification in promoting ICC tumorigenesis and progression in vivo. Our study uncovers the important physiological function and mechanism of METTL1-mediated m7G tRNA modification in the regulation of oncogenic mRNA translation and cancer progression.
Collapse
|
44
|
Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
Collapse
Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
| |
Collapse
|
45
|
Blersch KF, Burchert JP, August SC, Welp L, Neumann P, Köster S, Urlaub H, Ficner R. Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA. RNA Biol 2021; 18:2466-2479. [PMID: 34006170 DOI: 10.1080/15476286.2021.1925477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TrmB belongs to the class I S-adenosylmethionine (SAM)-dependent methyltransferases (MTases) and introduces a methyl group to guanine at position 7 (m7G) in tRNA. In tRNAs m7G is most frequently found at position 46 in the variable loop and forms a tertiary base pair with C13 and U22, introducing a positive charge at G46. The TrmB/Trm8 enzyme family is structurally diverse, as TrmB proteins exist in a monomeric, homodimeric, and heterodimeric form. So far, the exact enzymatic mechanism, as well as the tRNA-TrmB crystal structure is not known. Here we present the first crystal structures of B. subtilis TrmB in complex with SAM and SAH. The crystal structures of TrmB apo and in complex with SAM and SAH have been determined by X-ray crystallography to 1.9 Å (apo), 2.5 Å (SAM), and 3.1 Å (SAH). The obtained crystal structures revealed Tyr193 to be important during SAM binding and MTase activity. Applying fluorescence polarization, the dissociation constant Kd of TrmB and tRNAPhe was determined to be 0.12 µM ± 0.002 µM. Luminescence-based methyltransferase activity assays revealed cooperative effects during TrmB catalysis with half-of-the-site reactivity at physiological SAM concentrations. Structural data retrieved from small-angle x-ray scattering (SAXS), mass-spectrometry of cross-linked complexes, and molecular docking experiments led to the determination of the TrmB-tRNAPhe complex structure.
Collapse
Affiliation(s)
- Katharina F Blersch
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Jan-Philipp Burchert
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | | | - Luisa Welp
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| |
Collapse
|
46
|
Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. Methods Protoc 2021; 4:mps4010022. [PMID: 33808611 PMCID: PMC8006020 DOI: 10.3390/mps4010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/01/2023] Open
Abstract
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
Collapse
|
47
|
De Zoysa T, Phizicky EM. Hypomodified tRNA in evolutionarily distant yeasts can trigger rapid tRNA decay to activate the general amino acid control response, but with different consequences. PLoS Genet 2020; 16:e1008893. [PMID: 32841241 PMCID: PMC7473580 DOI: 10.1371/journal.pgen.1008893] [Citation(s) in RCA: 20] [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: 05/22/2020] [Revised: 09/04/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
All tRNAs are extensively modified, and modification deficiency often results in growth defects in the budding yeast Saccharomyces cerevisiae and neurological or other disorders in humans. In S. cerevisiae, lack of any of several tRNA body modifications results in rapid tRNA decay (RTD) of certain mature tRNAs by the 5'-3' exonucleases Rat1 and Xrn1. As tRNA quality control decay mechanisms are not extensively studied in other eukaryotes, we studied trm8Δ mutants in the evolutionarily distant fission yeast Schizosaccharomyces pombe, which lack 7-methylguanosine at G46 (m7G46) of their tRNAs. We report here that S. pombe trm8Δ mutants are temperature sensitive primarily due to decay of tRNATyr(GUA) and that spontaneous mutations in the RAT1 ortholog dhp1+ restored temperature resistance and prevented tRNA decay, demonstrating conservation of the RTD pathway. We also report for the first time evidence linking the RTD and the general amino acid control (GAAC) pathways, which we show in both S. pombe and S. cerevisiae. In S. pombe trm8Δ mutants, spontaneous GAAC mutations restored temperature resistance and tRNA levels, and the trm8Δ temperature sensitivity was precisely linked to GAAC activation due to tRNATyr(GUA) decay. Similarly, in the well-studied S. cerevisiae trm8Δ trm4Δ RTD mutant, temperature sensitivity was closely linked to GAAC activation due to tRNAVal(AAC) decay; however, in S. cerevisiae, GAAC mutations increased tRNA loss and exacerbated temperature sensitivity. A similar exacerbated growth defect occurred upon GAAC mutation in S. cerevisiae trm8Δ and other single modification mutants that triggered RTD. Thus, these results demonstrate a conserved GAAC activation coincident with RTD in S. pombe and S. cerevisiae, but an opposite impact of the GAAC response in the two organisms. We speculate that the RTD pathway and its regulation of the GAAC pathway is widely conserved in eukaryotes, extending to other mutants affecting tRNA body modifications.
Collapse
Affiliation(s)
- Thareendra De Zoysa
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
- * E-mail:
| |
Collapse
|
48
|
Edwards AM, Addo MA, Dos Santos PC. Extracurricular Functions of tRNA Modifications in Microorganisms. Genes (Basel) 2020; 11:genes11080907. [PMID: 32784710 PMCID: PMC7466049 DOI: 10.3390/genes11080907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 12/29/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular viability. Hence, the placement and prevalence of tRNA modifications affects the efficiency of aminoacyl tRNA synthetase (aaRS) reactions, interactions with the ribosome, and transient pairing with messenger RNA (mRNA). The synthesis and abundance of tRNA modifications respond directly and indirectly to a range of environmental and nutritional factors involved in the maintenance of metabolic homeostasis. The dynamic landscape of the tRNA epitranscriptome suggests a role for tRNA modifications as markers of cellular status and regulators of translational capacity. This review discusses the non-canonical roles that tRNA modifications play in central metabolic processes and how their levels are modulated in response to a range of cellular demands.
Collapse
|
49
|
Chen L, Wang P, Bahal R, Manautou JE, Zhong XB. Ontogenic mRNA expression of RNA modification writers, erasers, and readers in mouse liver. PLoS One 2019; 14:e0227102. [PMID: 31891622 PMCID: PMC6938302 DOI: 10.1371/journal.pone.0227102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
RNA modifications are recently emerged epigenetic modifications. These diverse RNA modifications have been shown to regulate multiple biological processes, including development. RNA modifications are dynamically controlled by the “writers, erasers, and readers”, where RNA modifying proteins are able to add, remove, and recognize specific chemical modification groups on RNAs. However, little is known about the ontogenic expression of these RNA modifying proteins in various organs, such as liver. In the present study, the hepatic mRNA expression of selected RNA modifying proteins involve in m6A, m1A, m5C, hm5C, m7G, and Ψ modifications was analyzed using the RNA-seq technique. Liver samples were collected from male C57BL/6 mice at several ages from prenatal through neonatal, infant, child to young adult. Results showed that most of the RNA modifying proteins were highly expressed in prenatal mouse liver with a dramatic drop at birth. After birth, most of the RNA modifying proteins showed a downregulation trend during liver maturation. Moreover, the RNA modifying proteins that belong to the same enzyme family were expressed at different abundances at the same ages in mouse liver. In conclusion, this study unveils that the mRNA expression of RNA modifying proteins follows specific ontogenic expression patterns in mice liver during maturation. These data indicated that the changes in expression of RNA modifying proteins might have a potential role to regulate gene expression in liver through alteration of RNA modification status.
Collapse
Affiliation(s)
- Liming Chen
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Raman Bahal
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - José E. Manautou
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - Xiao-bo Zhong
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
50
|
Thongdee N, Jaroensuk J, Atichartpongkul S, Chittrakanwong J, Chooyoung K, Srimahaeak T, Chaiyen P, Vattanaviboon P, Mongkolsuk S, Fuangthong M. TrmB, a tRNA m7G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa. Nucleic Acids Res 2019; 47:9271-9281. [PMID: 31428787 PMCID: PMC6755087 DOI: 10.1093/nar/gkz702] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 07/13/2019] [Accepted: 08/06/2019] [Indexed: 11/14/2022] Open
Abstract
Cellular response to oxidative stress is a crucial mechanism that promotes the survival of Pseudomonas aeruginosa during infection. However, the translational regulation of oxidative stress response remains largely unknown. Here, we reveal a tRNA modification-mediated translational response to H2O2 in P. aeruginosa. We demonstrated that the P. aeruginosa trmB gene encodes a tRNA guanine (46)-N7-methyltransferase that catalyzes the formation of m7G46 in the tRNA variable loop. Twenty-three tRNA substrates of TrmB with a guanosine residue at position 46 were identified, including 11 novel tRNA substrates. We showed that loss of trmB had a strong negative effect on the translation of Phe- and Asp-enriched mRNAs. The trmB-mediated m7G modification modulated the expression of the catalase genes katA and katB, which are enriched with Phe/Asp codons at the translational level. In response to H2O2 exposure, the level of m7G modification increased, consistent with the increased translation efficiency of Phe- and Asp-enriched mRNAs. Inactivation of trmB led to decreased KatA and KatB protein abundance and decreased catalase activity, resulting in H2O2-sensitive phenotype. Taken together, our observations reveal a novel role of m7G46 tRNA modification in oxidative stress response through translational regulation of Phe- and Asp-enriched genes, such as katA and katB.
Collapse
Affiliation(s)
- Narumon Thongdee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Juthamas Jaroensuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand.,School of Biomolecular Sciences and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | | | - Jurairat Chittrakanwong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Kamonchanok Chooyoung
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Thanyaporn Srimahaeak
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Sciences and Engineering, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Paiboon Vattanaviboon
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Mayuree Fuangthong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok, Thailand.,Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| |
Collapse
|