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Yi M, Zhou F, Deng Y. STM-ac4C: a hybrid model for identification of N4-acetylcytidine (ac4C) in human mRNA based on selective kernel convolution, temporal convolutional network, and multi-head self-attention. Front Genet 2024; 15:1408688. [PMID: 38873109 PMCID: PMC11169723 DOI: 10.3389/fgene.2024.1408688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
N4-acetylcysteine (ac4C) is a chemical modification in mRNAs that alters the structure and function of mRNA by adding an acetyl group to the N4 position of cytosine. Researchers have shown that ac4C is closely associated with the occurrence and development of various cancers. Therefore, accurate prediction of ac4C modification sites on human mRNA is crucial for revealing its role in diseases and developing new diagnostic and therapeutic strategies. However, existing deep learning models still have limitations in prediction accuracy and generalization ability, which restrict their effectiveness in handling complex biological sequence data. This paper introduces a deep learning-based model, STM-ac4C, for predicting ac4C modification sites on human mRNA. The model combines the advantages of selective kernel convolution, temporal convolutional networks, and multi-head self-attention mechanisms to effectively extract and integrate multi-level features of RNA sequences, thereby achieving high-precision prediction of ac4C sites. On the independent test dataset, STM-ac4C showed improvements of 1.81%, 3.5%, and 0.37% in accuracy, Matthews correlation coefficient, and area under the curve, respectively, compared to the existing state-of-the-art technologies. Moreover, its performance on additional balanced and imbalanced datasets also confirmed the model's robustness and generalization ability. Various experimental results indicate that STM-ac4C outperforms existing methods in predictive performance. In summary, STM-ac4C excels in predicting ac4C modification sites on human mRNA, providing a powerful new tool for a deeper understanding of the biological significance of mRNA modifications and cancer treatment. Additionally, the model reveals key sequence features that influence the prediction of ac4C sites through sequence region impact analysis, offering new perspectives for future research. The source code and experimental data are available at https://github.com/ymy12341/STM-ac4C.
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Affiliation(s)
- Mengyue Yi
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, China
| | - Fenglin Zhou
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, China
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2
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Schiffers S, Oberdoerffer S. ac4C: a fragile modification with stabilizing functions in RNA metabolism. RNA (NEW YORK, N.Y.) 2024; 30:583-594. [PMID: 38531654 PMCID: PMC11019744 DOI: 10.1261/rna.079948.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
In recent years, concerted efforts to map and understand epitranscriptomic modifications in mRNA have unveiled new complexities in the regulation of gene expression. These studies cumulatively point to diverse functions in mRNA metabolism, spanning pre-mRNA processing, mRNA degradation, and translation. However, this emerging landscape is not without its intricacies and sources of discrepancies. Disparities in detection methodologies, divergent interpretations of functional outcomes, and the complex nature of biological systems across different cell types pose significant challenges. With a focus of N4-acetylcytidine (ac4C), this review endeavors to unravel conflicting narratives by examining the technological, biological, and methodological factors that have contributed to discrepancies and thwarted research progress. Our goal is to mitigate detection inconsistencies and establish a unified model to elucidate the contribution of ac4C to mRNA metabolism and cellular equilibrium.
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Affiliation(s)
- Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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Zhou C, Jin L, Yu J, Gao Z. Integrated analysis identifies cuproptosis-related gene DLAT and its competing endogenous RNAs network to predict the prognosis of pancreatic adenocarcinoma patients. Medicine (Baltimore) 2024; 103:e37322. [PMID: 38428843 PMCID: PMC10913044 DOI: 10.1097/md.0000000000037322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/30/2024] [Indexed: 03/03/2024] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is a highly malignant tumor with poor prognosis. However, the relationship between cuproptosis-related genes (CRGs) and its competing endogenous RNA (ceRNA) network with the prognosis of PAAD patients remains unclear. To investigate this relationship, we calculated the difference in CRGs between PAAD tissues and normal tissues using the 'limma' R package. Additionally, we employed least absolute shrinkage and selection operator (LASSO) Cox regression analysis to construct a prognostic signature for CRGs. Survival analysis of patients with PAAD was performed using Kaplan-Meier analysis. Furthermore, we used bioinformatics tools to screen for CRGs-related MicroRNA (miRNA) and lncRNAs. To validate these findings, we conducted real-time quantitative polymerase chain reaction (RT-qPCR), CCK-8, colony formation, and Transwell assays to assess the effect of DLAT in vitro. Our results revealed a cuproptosis-related prognostic signature consisting of 3 prognostic genes (DLAT, LIAS, and LIPT1). Notably, patients with a high-risk score for the CRGs signature exhibited poor prognosis in terms of overall survival (OS) (P < .05). The receiver operating characteristic (ROC) curve was used to evaluate the prognostic signature of CRGs. The results showed that the 1-year, 3-year, and 5-year area under the curve values for predicting OS were 0.62, 0.66, and 0.79, respectively. Additionally, the CRGs-related ceRNA network revealed the regulatory axis of LINC00857/has-miR-1179/DLAT in PAAD. In vitro experiments demonstrated that knockdown of LINC00857 and DLAT inhibited the growth and invasion of PAAD cells. This study identified a CRG-related prognostic signature consisting of 3 biomarkers (DLAT, LIAS, and LIPT1) for PAAD. Furthermore, ceRNA network analysis suggested the involvement of the LINC00857/has-miR-1179/DLAT axis in the development of PAAD. Overall, this study provides theoretical support for the investigation of diagnostic and prognostic biomarkers as well as potential therapeutic targets in PAAD.
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Affiliation(s)
- Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Long Jin
- Department of Radiation Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Jiao Yu
- Department of Radiation Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Zhengchao Gao
- Department of Orthopaedics, Shaanxi Provincial People’s Hospital, Xi’an, China
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Fu M, Gao Q, Xiao M, Sun XY, Li SL, Ge XY. NAT10/CEBPB/vimentin signalling axis promotes adenoid cystic carcinoma malignant phenotypes in vitro. Oral Dis 2024. [PMID: 38287502 DOI: 10.1111/odi.14879] [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: 10/10/2023] [Revised: 12/08/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVE To explore the biological function and mechanisms of CEBPB and NAT10-mediated N4-acetylcytidine (ac4c) modification in salivary adenoid cystic carcinoma (SACC). MATERIALS AND METHODS CEBPB and NAT10 were knocked down in SACC-LM cells by siRNA transfection and overexpressed in SACC-83 cells by plasmid transfection. Malignant phenotypes were evaluated using CCK-8, Transwell migration and colony formation assays. Real-time PCR, western blotting, ChIP and acRIP were used to investigate the molecular mechanisms involved. RESULTS We found that CEBPB was highly expressed in SACC tissues and correlated with lung metastasis and unfavourable prognosis. Gain- and loss-of-function experiments revealed that CEBPB promoted SACC malignant phenotypes. Mechanistically, CEBPB exerted its oncogenic effect by binding to the vimentin gene promoter region to enhance its expression. Moreover, NAT10-mediated ac4c modification led to stabilization and overexpression of CEBPB in SACC cells. We also found that NAT10, the only known human enzyme responsible for ac4C modification, promoted SACC cell migration, proliferation and colony formation. Moreover, CEBPB overexpression restored the inhibitory effect of NAT10 knockdown on malignant phenotypes. CONCLUSIONS Our study reveals the critical role of the newly identified NAT10/CEBPB/vimentin axis in SACC malignant progression, and the findings may be applied to improve treatment for SACC.
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Affiliation(s)
- Min Fu
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, PR China
- National Clinical Research Center for Oral Diseases, Beijing, PR China
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, PR China
- Beijing Key Laboratory of Digital Stomatology, Beijing, PR China
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Qian Gao
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Mian Xiao
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Xin-Yi Sun
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Sheng-Lin Li
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, PR China
- National Clinical Research Center for Oral Diseases, Beijing, PR China
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, PR China
- Beijing Key Laboratory of Digital Stomatology, Beijing, PR China
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Xi-Yuan Ge
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, PR China
- National Clinical Research Center for Oral Diseases, Beijing, PR China
- National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, PR China
- Beijing Key Laboratory of Digital Stomatology, Beijing, PR China
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
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Zhang S, Liu Y, Ma X, Gao X, Ru Y, Hu X, Gu X. Recent advances in the potential role of RNA N4-acetylcytidine in cancer progression. Cell Commun Signal 2024; 22:49. [PMID: 38233930 PMCID: PMC10795262 DOI: 10.1186/s12964-023-01417-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/02/2023] [Indexed: 01/19/2024] Open
Abstract
N4-acetylcytidine (ac4C) is a highly conserved chemical modification widely found in eukaryotic and prokaryotic RNA, such as tRNA, rRNA, and mRNA. This modification is significantly associated with various human diseases, especially cancer, and its formation depends on the catalytic activity of N-acetyltransferase 10 (NAT10), the only known protein that produces ac4C. This review discusses the detection techniques and regulatory mechanisms of ac4C and summarizes ac4C correlation with tumor occurrence, development, prognosis, and drug therapy. It also comments on a new biomarker for early tumor diagnosis and prognosis prediction and a new target for tumor therapy. Video Abstract.
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Affiliation(s)
- Shujun Zhang
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Yafeng Liu
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Xiao Ma
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohui Gao
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Yi Ru
- Hepatobiliary Pancreatic Surgery, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Xinjun Hu
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China.
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China.
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Xu T, Wang J, Wu Y, Wu J, Lu W, Liu M, Zhang S, Xie D, Xin W, Xie J. Ac4C Enhances the Translation Efficiency of Vegfa mRNA and Mediates Central Sensitization in Spinal Dorsal Horn in Neuropathic Pain. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303113. [PMID: 37877615 PMCID: PMC10724395 DOI: 10.1002/advs.202303113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/25/2023] [Indexed: 10/26/2023]
Abstract
N4-Acetylcytidine (ac4C), a highly conserved post-transcriptional machinery with extensive existence for RNA modification, plays versatile roles in various cellular processes and functions. However, the molecular mechanism by which ac4C modification mediates neuropathic pain remains elusive. Here, it is found that the enhanced ac4C modification promotes the recruitment of polysome in Vegfa mRNA and strengthens the translation efficiency following SNI. Nerve injury increases the expression of NAT10 and the interaction between NAT10 and Vegfa mRNA in the dorsal horn neurons, and the gain and loss of NAT10 function further confirm that NAT10 is involved in the ac4C modification in Vegfa mRNA and pain behavior. Moreover, the ac4C-mediated VEGFA upregulation contributes to the central sensitivity and neuropathic pain induced by SNI or AAV-hSyn-NAT10. Finally, SNI promotes the binding of HNRNPK in Vegfa mRNA and subsequently recruits the NAT10. The enhanced interaction between HNRNPK and NAT10 contributes to the ac4C modification of Vegfa mRNA and neuropathic pain. These findings suggest that the enhanced interaction between HNRNPK and Vegfa mRNA upregulates the ac4C level by recruiting NAT10 and contributes to the central sensitivity and neuropathic pain following SNI. Blocking this cascade may be a novel therapeutic approach in patients with neuropathic pain.
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Affiliation(s)
- Ting Xu
- Neuroscience ProgramZhongshan School of MedicineThe Fifth Affiliated HospitalGuangdong Province Key Laboratory of Brain Function and DiseaseDepartment of Physiology and Pain Research CenterSun Yat‐Sen UniversityGuangzhou510080China
| | - Jing Wang
- Neuroscience ProgramZhongshan School of MedicineThe Fifth Affiliated HospitalGuangdong Province Key Laboratory of Brain Function and DiseaseDepartment of Physiology and Pain Research CenterSun Yat‐Sen UniversityGuangzhou510080China
- Department of Pain ManagementHenan Provincial People's HospitalZhengzhou UniversityZhengzhou450000China
| | - Yan Wu
- Department of AnesthesiologyThe First Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouGuangdong510062China
| | - Jia‐Yan Wu
- Neuroscience ProgramZhongshan School of MedicineThe Fifth Affiliated HospitalGuangdong Province Key Laboratory of Brain Function and DiseaseDepartment of Physiology and Pain Research CenterSun Yat‐Sen UniversityGuangzhou510080China
| | - Wei‐Cheng Lu
- State Key Laboratory of Oncology in Southern ChinaCollaborative Innovation for Cancer MedicineSun Yat‐Sen University Cancer CenterGuangzhou510060China
| | - Meng Liu
- Department of Anesthesia and Pain MedicineGuangzhou First People's HospitalGuangzhou510180China
| | - Su‐Bo Zhang
- State Key Laboratory of Oncology in Southern ChinaCollaborative Innovation for Cancer MedicineSun Yat‐Sen University Cancer CenterGuangzhou510060China
| | - Dan Xie
- State Key Laboratory of Oncology in Southern ChinaCollaborative Innovation for Cancer MedicineSun Yat‐Sen University Cancer CenterGuangzhou510060China
| | - Wen‐Jun Xin
- Neuroscience ProgramZhongshan School of MedicineThe Fifth Affiliated HospitalGuangdong Province Key Laboratory of Brain Function and DiseaseDepartment of Physiology and Pain Research CenterSun Yat‐Sen UniversityGuangzhou510080China
| | - Jing‐Dun Xie
- State Key Laboratory of Oncology in Southern ChinaCollaborative Innovation for Cancer MedicineSun Yat‐Sen University Cancer CenterGuangzhou510060China
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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Xu D, Huang K, Chen Y, Yang F, Xia C, Yang H. Immune response and drug therapy based on ac4C-modified gene in pancreatic cancer typing. Front Immunol 2023; 14:1133166. [PMID: 36949954 PMCID: PMC10025374 DOI: 10.3389/fimmu.2023.1133166] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
N-4 cytidine acetylation (ac4C) is an epitranscriptome modification catalyzed by N-acetyltransferase 10 (NAT10) and is essential for cellular mRNA stability, rRNA biosynthesis, cell proliferation, and epithelial-mesenchymal transition (EMT). Numerous studies have confirmed the inextricable link between NAT10 and the clinical characteristics of malignancies. It is unclear, however, how NAT10 might affect pancreatic ductal adenocarcinoma. We downloaded pancreatic ductal adenocarcinoma patients from the TCGA database. We obtained the corresponding clinical data for data analysis, model construction, differential gene expression analysis, and the GEO database for external validation. We screened the published papers for NAT10-mediated ac4C modifications in 2156 genes. We confirmed that the expression levels and genomic mutation rates of NAT10 differed significantly between cancer and normal tissues. Additionally, we constructed a NAT10 prognostic model and examined immune infiltration and altered biological pathways across the models. The NAT10 isoforms identified in this study can effectively predict clinical outcomes in pancreatic ductal adenocarcinoma. Furthermore, our study showed that elevated levels of NAT10 expression correlated with gemcitabine resistance, that aberrant NAT10 expression may promote the angiogenic capacity of pancreatic ductal adenocarcinoma through activation of the TGF-β pathway, which in turn promotes distal metastasis of pancreatic ductal adenocarcinoma, and that NAT10 knockdown significantly inhibited the migration and clonogenic capacity of pancreatic ductal adenocarcinoma cells. In conclusion, we proposed a predictive model based on NAT10 expression levels, a non-invasive predictive approach for genomic profiling, which showed satisfactory and effective performance in predicting patients' survival outcomes and treatment response. Medicine and electronics will be combined in more interdisciplinary areas in the future.
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Affiliation(s)
- Dong Xu
- Department of General Surgery, Gaochun People’s Hospital, Nanjing, Jiangsu, China
| | - Kaige Huang
- Department of General Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yang Chen
- Department of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Fei Yang
- Department of General Surgery, Gaochun People’s Hospital, Nanjing, Jiangsu, China
| | - Cunbing Xia
- Department of General Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Cunbing Xia, ; Hongbao Yang,
| | - Hongbao Yang
- Center for New Drug Safety Evaluation and Research, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, China
- *Correspondence: Cunbing Xia, ; Hongbao Yang,
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Zhang L, Zhang Y, Zhang S, Qiu L, Zhang Y, Zhou Y, Han J, Xie J. Translational Regulation by eIFs and RNA Modifications in Cancer. Genes (Basel) 2022; 13:2050. [PMID: 36360287 PMCID: PMC9690228 DOI: 10.3390/genes13112050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/04/2023] Open
Abstract
Translation is a fundamental process in all living organisms that involves the decoding of genetic information in mRNA by ribosomes and translation factors. The dysregulation of mRNA translation is a common feature of tumorigenesis. Protein expression reflects the total outcome of multiple regulatory mechanisms that change the metabolism of mRNA pathways from synthesis to degradation. Accumulated evidence has clarified the role of an increasing amount of mRNA modifications at each phase of the pathway, resulting in translational output. Translation machinery is directly affected by mRNA modifications, influencing translation initiation, elongation, and termination or altering mRNA abundance and subcellular localization. In this review, we focus on the translation initiation factors associated with cancer as well as several important RNA modifications, for which we describe their association with cancer.
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Affiliation(s)
- Linzhu Zhang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- The Third People’s Hospital of Chengdu, Clinical College of Southwest Jiao Tong University, Chengdu 610014, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Su Zhang
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Zhang
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ying Zhou
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-Related Molecular Network and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiang Xie
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- The Third People’s Hospital of Chengdu, Clinical College of Southwest Jiao Tong University, Chengdu 610014, China
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Arango D, Sturgill D, Yang R, Kanai T, Bauer P, Roy J, Wang Z, Hosogane M, Schiffers S, Oberdoerffer S. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell 2022; 82:2797-2814.e11. [PMID: 35679869 PMCID: PMC9361928 DOI: 10.1016/j.molcel.2022.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
Abstract
mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.
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Affiliation(s)
- Daniel Arango
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Tapan Kanai
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Paulina Bauer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jyoti Roy
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ziqiu Wang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Masaki Hosogane
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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