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Cheng L, Yang C, Lu J, Huang M, Xie R, Lynch S, Elfman J, Huang Y, Liu S, Chen S, He B, Lin T, Li H, Chen X, Huang J. Oncogenic SLC2A11-MIF fusion protein interacts with polypyrimidine tract binding protein 1 to facilitate bladder cancer proliferation and metastasis by regulating mRNA stability. MedComm (Beijing) 2024; 5:e685. [PMID: 39156764 PMCID: PMC11324686 DOI: 10.1002/mco2.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 07/03/2024] [Accepted: 07/14/2024] [Indexed: 08/20/2024] Open
Abstract
Chimeric RNAs, distinct from DNA gene fusions, have emerged as promising therapeutic targets with diverse functions in cancer treatment. However, the functional significance and therapeutic potential of most chimeric RNAs remain unclear. Here we identify a novel fusion transcript of solute carrier family 2-member 11 (SLC2A11) and macrophage migration inhibitory factor (MIF). In this study, we investigated the upregulation of SLC2A11-MIF in The Cancer Genome Atlas cohort and a cohort of patients from Sun Yat-Sen Memorial Hospital. Subsequently, functional investigations demonstrated that SLC2A11-MIF enhanced the proliferation, antiapoptotic effects, and metastasis of bladder cancer cells in vitro and in vivo. Mechanistically, the fusion protein encoded by SLC2A11-MIF interacted with polypyrimidine tract binding protein 1 (PTBP1) and regulated the mRNA half-lives of Polo Like Kinase 1, Roundabout guidance receptor 1, and phosphoinositide-3-kinase regulatory subunit 3 in BCa cells. Moreover, PTBP1 knockdown abolished the enhanced impact of SLC2A11-MIF on biological function and mRNA stability. Furthermore, the expression of SLC2A11-MIF mRNA is regulated by CCCTC-binding factor and stabilized through RNA N4-acetylcytidine modification facilitated by N-acetyltransferase 10. Overall, our findings revealed a significant fusion protein orchestrated by the SLC2A11-MIF-PTBP1 axis that governs mRNA stability during the multistep progression of bladder cancer.
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Affiliation(s)
- Liang Cheng
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Chenwei Yang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Junlin Lu
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Ming Huang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ruihui Xie
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Sarah Lynch
- Department of PathologySchool of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Justin Elfman
- Department of PathologySchool of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Yuhang Huang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Sen Liu
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Siting Chen
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Baoqing He
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
| | - Tianxin Lin
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Hui Li
- Department of PathologySchool of MedicineUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Xu Chen
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jian Huang
- Department of UrologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene RegulationDepartment of Urology,Sun Yat‐sen Memorial Hospital,Sun Yat‐Sen UniversityGuangzhouGuangdongChina
- Guangdong Provincial Clinical Research Center for Urological DiseasesDepartment of Urology, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouGuangdongChina
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Wang K, Wang Y, Li Y, Fang B, Li B, Cheng W, Wang K, Yang S. The potential of RNA methylation in the treatment of cardiovascular diseases. iScience 2024; 27:110524. [PMID: 39165846 PMCID: PMC11334793 DOI: 10.1016/j.isci.2024.110524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
RNA methylation has emerged as a dynamic regulatory mechanism that impacts gene expression and protein synthesis. Among the known RNA methylation modifications, N6-methyladenosine (m6A), 5-methylcytosine (m5C), 3-methylcytosine (m3C), and N7-methylguanosine (m7G) have been studied extensively. In particular, m6A is the most abundant RNA modification and has attracted significant attention due to its potential effect on multiple biological processes. Recent studies have demonstrated that RNA methylation plays an important role in the development and progression of cardiovascular disease (CVD). To identify key pathogenic genes of CVD and potential therapeutic targets, we reviewed several common RNA methylation and summarized the research progress of RNA methylation in diverse CVDs, intending to inspire effective treatment strategies.
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Affiliation(s)
- Kai Wang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - YuQin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - YingHui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Wei Cheng
- Department of Cardiovascular Surgery, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing 100045, China
| | - Kun Wang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - SuMin Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
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Cai Z, Jiang Z, Li S, Mo S, Wang S, Liang M, Tan X, Zhong W, Zhang L, Deng J, Zhong C, Lu J. RNA modification Regulators' Co-Expression Score (RMRCoeS) predicts biochemical recurrence and therapy response in prostate cancer: A multi-omics and experimental validation study. Int Immunopharmacol 2024; 139:112723. [PMID: 39053228 DOI: 10.1016/j.intimp.2024.112723] [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: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Owing to the heterogeneity of prostate cancer (PCa), the clinical indicators traditionally fall short of meeting the requirements for personalized medicine. The realm of RNA modification has emerged as an increasingly relevant domain, shedding light on its pivotal role in tumor heterogeneity. However, the specific contributions of RNA modification regulators within the context of PCa remain largely unexplored. METHODS In this study, we undertook a literature review to summarize the common 8 types of RNA modifications (ac4c, AI, APA, m1A, m5c, m6A, m7G, Ψ) encompassing a total of 84 regulators. Moreover, we integrated multi-center cohorts with Ridge regression to develop the Regulators' Co-Expression Score (RMRCoeS). Then we assessed the role of RMRCoeS in several clinical aspects such as biochemical recurrence (BCR), responses to chemotherapy, androgen receptor signaling inhibitor (ARSI) therapy and immunotherapy in PCa. Finally, we validated the cancer-promoting performance of five hub genes through immunohistochemistry and in vitro assays. RESULTS Within the mutation landscape of RNA modification regulators, we observed a relatively low overall mutation rate. Remarkably, RMRCoeS, comprising 81 RNA modification regulators, exhibited a notable capability for accurately predicting the prognosis and therapeutic responses in PCa patients subjected to BCR, chemotherapy, ARSI therapy, and immunotherapy. A high RMRCoeS was indicative of a poor prognosis and unfavorable therapy responses. Functional enrichment analysis unveiled that RMRCoeS may exert its influence on PCa progression through various metabolic pathways. Furthermore, a higher RMRCoeS showed a positive correlation with elevated CNV mutations. Lastly, we validated the oncogene effects of CPSF4, WBSCR22, RPUSD3, TRMT61A, and NSUN5-five hub regulators-within the context of PCa. CONCLUSION The function of different RNA modifications is interconnected. Comprising eight distinct RNA modifications' regulators, RMRCoeS exhibits multifaceted roles in various aspects of PCa, including disease progression, prognosis, and responses to multiple therapies. Furthermore, we provide the initial validation of the oncogene effect associated with WBSCR22, RPUSD3, TRMT61A and NSUN5 in PCa. Our findings offer novel insights into the significance of RNA modifications in PCa personalized medicine.
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Affiliation(s)
- Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China
| | - Zhaojun Jiang
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China; The Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China
| | - Songbo Li
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Urology, The Second People's Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi 541002, China
| | - Shanshan Mo
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China
| | - Shuo Wang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510282, China
| | - Min Liang
- Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China; The Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510700, Guangzhou, China
| | - Xiao Tan
- Department of Urology, School of Clinical Medicine, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Weide Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa 999078, Macau
| | - Le Zhang
- Institute for Integrative Genome Biology, University of California, Riverside 92507, CA, USA
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| | - Chuanfan Zhong
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
| | - Jianming Lu
- Department of Andrology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China; Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, China.
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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Wulczyn KE, Shafi T, Anderson A, Rincon-Choles H, Clish CB, Denburg M, Feldman HI, He J, Hsu CY, Kelly T, Kimmel PL, Mehta R, Nelson RG, Ramachandran V, Ricardo A, Shah VO, Srivastava A, Xie D, Rhee EP, Kalim S. Metabolites Associated With Uremic Symptoms in Patients With CKD: Findings From the Chronic Renal Insufficiency Cohort (CRIC) Study. Am J Kidney Dis 2024; 84:49-61.e1. [PMID: 38266973 PMCID: PMC11193655 DOI: 10.1053/j.ajkd.2023.11.013] [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: 06/03/2023] [Revised: 10/30/2023] [Accepted: 11/20/2023] [Indexed: 01/26/2024]
Abstract
RATIONALE & OBJECTIVE The toxins that contribute to uremic symptoms in patients with chronic kidney disease (CKD) are unknown. We sought to apply complementary statistical modeling approaches to data from untargeted plasma metabolomic profiling to identify solutes associated with uremic symptoms in patients with CKD. STUDY DESIGN Cross-sectional. SETTING & PARTICIPANTS 1,761 Chronic Renal Insufficiency Cohort (CRIC) participants with CKD not treated with dialysis. PREDICTORS Measurement of 448 known plasma metabolites. OUTCOMES The uremic symptoms of fatigue, anorexia, pruritus, nausea, paresthesia, and pain were assessed by single items on the Kidney Disease Quality of Life-36 instrument. ANALYTICAL APPROACH Multivariable adjusted linear regression, least absolute shrinkage and selection operator linear regression, and random forest models were used to identify metabolites associated with symptom severity. After adjustment for multiple comparisons, metabolites selected in at least 2 of the 3 modeling approaches were deemed "overall significant." RESULTS Participant mean estimated glomerular filtration rate was 43mL/min/1.73m2, with 44% self-identifying as female and 41% as non-Hispanic Black. The prevalence of uremic symptoms ranged from 22% to 55%. We identified 17 metabolites for which a higher level was associated with greater severity of at least one uremic symptom and 9 metabolites inversely associated with uremic symptom severity. Many of these metabolites exhibited at least a moderate correlation with estimated glomerular filtration rate (Pearson's r≥0.5), and some were also associated with the risk of developing kidney failure or death in multivariable adjusted Cox regression models. LIMITATIONS Lack of a second independent cohort for external validation of our findings. CONCLUSIONS Metabolomic profiling was used to identify multiple solutes associated with uremic symptoms in adults with CKD, but future validation and mechanistic studies are needed. PLAIN-LANGUAGE SUMMARY Individuals living with chronic kidney disease (CKD) often experience symptoms related to CKD, traditionally called uremic symptoms. It is likely that CKD results in alterations in the levels of numerous circulating substances that, in turn, cause uremic symptoms; however, the identity of these solutes is not known. In this study, we used metabolomic profiling in patients with CKD to gain insights into the pathophysiology of uremic symptoms. We identified 26 metabolites whose levels were significantly associated with at least one of the symptoms of fatigue, anorexia, itchiness, nausea, paresthesia, and pain. The results of this study lay the groundwork for future research into the biological causes of symptoms in patients with CKD.
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Affiliation(s)
- Kendra E Wulczyn
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts.
| | - Tariq Shafi
- Division of Nephrology, Department of Medicine, Houston Methodist Hospital, Houston, Texas
| | - Amanda Anderson
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
| | - Hernan Rincon-Choles
- Department of Nephrology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, Ohio
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michelle Denburg
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Division of Pediatric Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Harold I Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA
| | - Chi-Yuan Hsu
- Division of Nephrology, University of California, San Francisco, School of Medicine, San Francisco, California; Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Tanika Kelly
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland
| | - Rupal Mehta
- Division of Nephrology, Northwestern University, Chicago, Illinois
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona
| | - Vasan Ramachandran
- Department of Epidemiology and Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Public Health, Boston, Massachusetts
| | - Ana Ricardo
- Division of Nephrology, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Vallabh O Shah
- Department of Internal Medicine and Biochemistry, School of Medicine, University of New Mexico, Albuquerque, New Mexico
| | - Anand Srivastava
- Center for Translational Metabolism and Health, Institute for Public Health and Medicine, Division of Nephrology and Hypertension, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Dawei Xie
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Eugene P Rhee
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts; Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Sahir Kalim
- Nephrology Division, Massachusetts General Hospital, Boston, Massachusetts
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Zhang QR, Zhang JB, Shen F, Xue R, Yang RX, Ren TY, Fan JG. Loss of NAT10 alleviates maternal high-fat diet-induced hepatic steatosis in male offspring of mice. Obesity (Silver Spring) 2024; 32:1349-1361. [PMID: 38816990 DOI: 10.1002/oby.24041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/02/2024] [Accepted: 03/21/2024] [Indexed: 06/01/2024]
Abstract
OBJECTIVE Metabolic dysfunction-associated steatotic liver disease (MASLD) is becoming an escalating health problem in pediatric populations. This study aimed to investigate the role of N-acetyltransferase 10 (NAT10) in maternal high-fat diet (HFD)-induced MASLD in offspring at early life. METHODS We generated male hepatocyte-specific NAT10 knockout (Nat10HKO) mice and mated them with female Nat10fl/fl mice under chow or HFD feeding. Body weight, liver histopathology, and expression of lipid metabolism-associated genes (Srebp1c, Fasn, Pparα, Cd36, Fatp2, Mttp, and Apob) were assessed in male offspring at weaning. Lipid uptake assays were performed both in vivo and in vitro. The mRNA stability assessment and RNA immunoprecipitation were performed to determine NAT10-regulated target genes. RESULTS NAT10 deletion in hepatocytes of male offspring alleviated perinatal lipid accumulation induced by maternal HFD, decreasing expression levels of Srebp1c, Fasn, Cd36, Fatp2, Mttp, and Apob while enhancing Pparα expression. Furthermore, Nat10HKO male mice exhibited reduced lipid uptake. In vitro, NAT10 promoted lipid uptake by enhancing the mRNA stability of CD36 and FATP2. RNA immunoprecipitation assays exhibited direct interactions between NAT10 and CD36/FATP2 mRNA. CONCLUSIONS NAT10 deletion in offspring hepatocytes ameliorates maternal HFD-induced hepatic steatosis through decreasing mRNA stability of CD36 and FATP2, highlighting NAT10 as a potential therapeutic target for pediatric MASLD.
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Affiliation(s)
- Qian-Ren Zhang
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian-Bin Zhang
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Shen
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Xue
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui-Xu Yang
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tian-Yi Ren
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Jian-Gao Fan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai, China
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7
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Ding M, Yu Z, Lu T, Hu S, Zhou X, Wang X. N-acetyltransferase 10 facilitates tumorigenesis of diffuse large B-cell lymphoma by regulating AMPK/mTOR signalling through N4-acetylcytidine modification of SLC30A9. Clin Transl Med 2024; 14:e1747. [PMID: 38961519 PMCID: PMC11222071 DOI: 10.1002/ctm2.1747] [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: 12/16/2023] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Accumulating studies suggested that posttranscriptional modifications exert a vital role in the tumorigenesis of diffuse large B-cell lymphoma (DLBCL). N4-acetylcytidine (ac4C) modification, catalyzed by the N-acetyltransferase 10 (NAT10), was a novel type of chemical modification that improves translation efficiency and mRNA stability. METHODS GEO databases and clinical samples were used to explore the expression and clinical value of NAT10 in DLBCL. CRISPER/Cas9-mediated knockout of NAT10 was performed to determine the biological functions of NAT10 in DLBCL. RNA sequencing, acetylated RNA immunoprecipitation sequencing (acRIP-seq), LC-MS/MS, RNA immunoprecipitation (RIP)-qPCR and RNA stability assays were performed to explore the mechanism by which NAT10 contributed to DLBCL progression. RESULTS Here, we demonstrated that NAT10-mediated ac4C modification regulated the occurrence and progression of DLBCL. Dysregulated N-acetyltransferases expression was found in DLBCL samples. High expression of NAT10 was associated with poor prognosis of DLBCL patients. Deletion of NAT10 expression inhibited cell proliferation and induced G0/G1 phase arrest. Furthermore, knockout of NAT10 increased the sensitivity of DLBCL cells to ibrutinib. AcRIP-seq identified solute carrier family 30 member 9 (SLC30A9) as a downstream target of NAT10 in DLBCL. NAT10 regulated the mRNA stability of SLC30A9 in an ac4C-dependent manner. Genetic silencing of SLC30A9 suppressed DLBCL cell growth via regulating the activation of AMP-activated protein kinase (AMPK) pathway. CONCLUSION Collectively, these findings highlighted the essential role of ac4C RNA modification mediated by NAT10 in DLBCL, and provided insights into novel epigenetic-based therapeutic strategies.
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Affiliation(s)
- Mengfei Ding
- Department of Hematology, Shandong Provincial HospitalShandong UniversityJinanShandongChina
| | - Zhuoya Yu
- Department of Hematology, Shandong Provincial HospitalShandong UniversityJinanShandongChina
| | - Tiange Lu
- Department of Hematology, Shandong Provincial HospitalShandong UniversityJinanShandongChina
| | - Shunfeng Hu
- Department of Hematology, Shandong Provincial HospitalShandong UniversityJinanShandongChina
| | - Xiangxiang Zhou
- Department of HematologyShandong Provincial Hospital, Affiliated to Shandong First Medical UniversityJinanShandongChina
- National Clinical Research Center for Hematologic Diseasesthe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xin Wang
- Department of Hematology, Shandong Provincial HospitalShandong UniversityJinanShandongChina
- Department of HematologyShandong Provincial Hospital, Affiliated to Shandong First Medical UniversityJinanShandongChina
- National Clinical Research Center for Hematologic Diseasesthe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Taishan Scholars Program of Shandong ProvinceJinanShandongChina
- Branch of National Clinical Research Center for Hematologic DiseasesJinanShandongChina
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Pham NT, Terrance AT, Jeon YJ, Rakkiyappan R, Manavalan B. ac4C-AFL: A high-precision identification of human mRNA N4-acetylcytidine sites based on adaptive feature representation learning. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102192. [PMID: 38779332 PMCID: PMC11108997 DOI: 10.1016/j.omtn.2024.102192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
RNA N4-acetylcytidine (ac4C) is a highly conserved RNA modification that plays a crucial role in controlling mRNA stability, processing, and translation. Consequently, accurate identification of ac4C sites across the genome is critical for understanding gene expression regulation mechanisms. In this study, we have developed ac4C-AFL, a bioinformatics tool that precisely identifies ac4C sites from primary RNA sequences. In ac4C-AFL, we identified the optimal sequence length for model building and implemented an adaptive feature representation strategy that is capable of extracting the most representative features from RNA. To identify the most relevant features, we proposed a novel ensemble feature importance scoring strategy to rank features effectively. We then used this information to conduct the sequential forward search, which individually determine the optimal feature set from the 16 sequence-derived feature descriptors. Utilizing these optimal feature descriptors, we constructed 176 baseline models using 11 popular classifiers. The most efficient baseline models were identified using the two-step feature selection approach, whose predicted scores were integrated and trained with the appropriate classifier to develop the final prediction model. Our rigorous cross-validations and independent tests demonstrate that ac4C-AFL surpasses contemporary tools in predicting ac4C sites. Moreover, we have developed a publicly accessible web server at https://balalab-skku.org/ac4C-AFL/.
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Affiliation(s)
- Nhat Truong Pham
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Annie Terrina Terrance
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Young-Jun Jeon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Rajan Rakkiyappan
- Department of Mathematics, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
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9
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Guo Q, Yu W, Tan J, Zhang J, Chen J, Rao S, Guo X, Cai K. Remodelin delays non-small cell lung cancer progression by inhibiting NAT10 via the EMT pathway. Cancer Med 2024; 13:e7283. [PMID: 38826095 PMCID: PMC11145023 DOI: 10.1002/cam4.7283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/22/2024] [Accepted: 04/28/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Lung cancer remains the foremost reason of cancer-related mortality, with invasion and metastasis profoundly influencing patient prognosis. N-acetyltransferase 10 (NAT10) catalyzes the exclusive N (4)-acetylcytidine (ac4C) modification in eukaryotic RNA. NAT10 dysregulation is linked to various diseases, yet its role in non-small cell lung cancer (NSCLC) invasion and metastasis remains unclear. Our study delves into the clinical significance and functional aspects of NAT10 in NSCLC. METHODS We investigated NAT10's clinical relevance using The Cancer Genome Atlas (TCGA) and a group of 98 NSCLC patients. Employing WB, qRT-PCR, and IHC analyses, we assessed NAT10 expression in NSCLC tissues, bronchial epithelial cells (BECs), NSCLC cell lines, and mouse xenografts. Further, knockdown and overexpression techniques (siRNA, shRNA, and plasmid) were employed to evaluate NAT10's effects. A series of assays were carried out, including CCK-8, colony formation, wound healing, and transwell assays, to elucidate NAT10's role in proliferation, invasion, and metastasis. Additionally, we utilized lung cancer patient-derived 3D organoids, mouse xenograft models, and Remodelin (NAT10 inhibitor) to corroborate these findings. RESULTS Our investigations revealed high NAT10 expression in NSCLC tissues, cell lines and mouse xenograft models. High NAT10 level correlated with advanced T stage, lymph node metastasis and poor overall survive. NAT10 knockdown curtailed proliferation, invasion, and migration, whereas NAT10 overexpression yielded contrary effects. Furthermore, diminished NAT10 levels correlated with increased E-cadherin level whereas decreased N-cadherin and vimentin expressions, while heightened NAT10 expression displayed contrasting results. Notably, Remodelin efficiently attenuated NSCLC proliferation, invasion, and migration by inhibiting NAT10 through the epithelial-mesenchymal transition (EMT) pathway. CONCLUSIONS Our data underscore NAT10 as a potential therapeutic target for NSCLC, presenting avenues for targeted intervention against lung cancer through NAT10 inhibition.
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Affiliation(s)
- Quanwei Guo
- The First School of Clinical MedicineSouthern Medical UniversityGuangzhouChina
- Department of Thoracic Surgery, Shenzhen HospitalSouthern Medical UniversityShenzhenChina
| | - Weijun Yu
- Bao'an District Hospital for Chronic Diseases Prevention and CureShenzhenChina
| | - Jianfeng Tan
- Department of Thoracic Surgery, Shenzhen HospitalSouthern Medical UniversityShenzhenChina
| | - Jianhua Zhang
- Department of Thoracic Surgery, Shenzhen HospitalSouthern Medical UniversityShenzhenChina
| | - Jin Chen
- Science and Education Department, Shenzhen HospitalSouthern Medical UniversityShenzhenChina
| | - Shuan Rao
- Department of Thoracic Surgery, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Xia Guo
- Center for Clinical Research and Innovation, Shenzhen HospitalSouthern Medical UniversityShenzhenChina
- Shenzhen Key Laboratory of Viral OncologyShenzhenChina
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
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10
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Chen M, Chen Y, Wang K, Deng X, Chen J. Non‐m 6A RNA modifications in haematological malignancies. Clin Transl Med 2024; 14:e1666. [PMID: 38880983 PMCID: PMC11180698 DOI: 10.1002/ctm2.1666] [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: 11/05/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/18/2024] Open
Abstract
Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N6-methyladenosine (m6A) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-m6A RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the m6A modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-m6A RNA modifications. In this review, we mainly focus on the roles and implications of non-m6A RNA modifications, including N4-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N1-methyladenosine and N7-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-m6A RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-m6A RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-m6A modifiers in blood cancer.
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Affiliation(s)
- Meiling Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Yuanzhong Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
| | - Kitty Wang
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Xiaolan Deng
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
- Gehr Family Center for Leukemia ResearchCity of Hope Medical Center and Comprehensive Cancer CenterDuarteCaliforniaUSA
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11
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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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12
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Li Q, Yuan Z, Wang Y, Zhai P, Wang J, Zhang C, Shao Z, Xing C. Unveiling YWHAH: A potential therapeutic target for overcoming CD8 + T cell exhaustion in colorectal cancer. Int Immunopharmacol 2024; 135:112317. [PMID: 38796965 DOI: 10.1016/j.intimp.2024.112317] [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: 05/12/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
Colorectal cancer (CRC) is a significant global health challenge, with increasing rates of incidence and mortality. Despite advancements in immunotherapy, resistance, particularly due to T cell exhaustion, remains a major hurdle. This study explores the role of YWHAH, mediated by N4-acetylcytidine (ac4C) modification, in CRC progression and its impact on CD8+ T cell exhaustion. Analysis of five paired CRC patient tissue samples using acetylated RNA immunoprecipitation and sequencing (acRIP-seq)identified ac4C-modified mRNAs. Functional assays, including cell culture, transfection, qRT-PCR, and immune assays, investigated the influence of YWHAH expression on CRC advancement. Bioinformatics analysis of TCGA data assessed the correlation between YWHAH and immune responses, as well as checkpoint inhibitors. Flow cytometry and Immunohistochemistry validated these findings, complemented by a co-culture experiment involving CD8+ T cells and CRC cell lines (LOVO and HCT116). acRIP-seq revealed YWHAH as a potential driver of CRC progression, exhibiting ac4C modification-mediated stability and upregulation. High YWHAH levels correlated with adverse outcomes and immune evasion in CRC patients, showing strong associations with immune checkpoint proteins and modest correlations with CD8+ T cell infiltration. Co-culture experiments demonstrated YWHAH-induced CD8+ T cell exhaustion, characterized by decreased proliferation and increased exhaustion markers. NAT10-mediated ac4C modification enhanced YWHAH stability in CRC. The involvement of YWHAH in CD8 + T cell exhaustion suggests its potential as a therapeutic target and prognostic marker in CRC immunotherapy, highlighting the intricate interplay between epitranscriptomic modifications, the tumor microenvironment, and immune responses in CRC progression.
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Affiliation(s)
- Qiang Li
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu Province, China; Department of General Surgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, Jiangsu Province, China
| | - Zhao Yuan
- Department of General Surgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, Jiangsu Province, China
| | - Yuan Wang
- Department of General Surgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, Jiangsu Province, China
| | - Peng Zhai
- Fifth People's Hospital of Huai'an City, Department of General Surgery, Huai'an 223300, Jiangsu Province, China
| | - Jian Wang
- Department of General Surgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, Jiangsu Province, China
| | - Chen Zhang
- Department of General Surgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, Jiangsu Province, China
| | - Ziqi Shao
- Department of General Surgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, Jiangsu Province, China
| | - Chungen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu Province, China.
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13
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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14
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Ma CR, Liu N, Li H, Xu H, Zhou XL. Activity reconstitution of Kre33 and Tan1 reveals a molecular ruler mechanism in eukaryotic tRNA acetylation. Nucleic Acids Res 2024; 52:5226-5240. [PMID: 38613394 PMCID: PMC11109946 DOI: 10.1093/nar/gkae262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
RNA acetylation is a universal post-transcriptional modification that occurs in various RNAs. Transfer RNA (tRNA) acetylation is found at position 34 (ac4C34) in bacterial tRNAMet and position 12 (ac4C12) in eukaryotic tRNASer and tRNALeu. The biochemical mechanism, structural basis and functional significance of ac4C34 are well understood; however, despite being discovered in the 1960s and identification of Kre33/NAT10 and Tan1/THUMPD1 as modifying apparatuses, ac4C12 modification activity has never been reconstituted for nearly six decades. Here, we successfully reconstituted the ac4C12 modification activity of yeast Kre33 and Tan1. Biogenesis of ac4C12 is primarily dependent on a minimal set of elements, including a canonical acceptor stem, the presence of the 11CCG13 motif and correct D-arm orientation, indicating a molecular ruler mechanism. A single A13G mutation conferred ac4C12 modification to multiple non-substrate tRNAs. Moreover, we were able to introduce ac4C modifications into small RNAs. ac4C12 modification contributed little to tRNA melting temperature and aminoacylation in vitro and in vivo. Collectively, our results realize in vitro activity reconstitution, delineate tRNA substrate selection mechanism for ac4C12 biogenesis and develop a valuable system for preparing acetylated tRNAs as well as non-tRNA RNA species, which will advance the functional interpretation of the acetylation in RNA structures and functions.
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Affiliation(s)
- Chun-Rui Ma
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Na Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Heng Shan Road, Shanghai 200030, China
| | - Hong Li
- Core Facility of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Hong Xu
- International Peace Maternity & Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Heng Shan Road, Shanghai 200030, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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15
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Gao LP, Li TD, Yang SZ, Ma HM, Wang X, Zhang DK. NAT10-mediated ac 4C modification promotes stemness and chemoresistance of colon cancer by stabilizing NANOGP8. Heliyon 2024; 10:e30330. [PMID: 38726177 PMCID: PMC11079091 DOI: 10.1016/j.heliyon.2024.e30330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Background Colon cancer (CC) stem cells can self-renew as well as expand, thereby promoting tumor progression and conferring resistance to chemotherapeutic agents. The acetyltransferase NAT10 mediates N4-acetylcytidine (ac4C) modification, which in turn drives tumorigenesis, metastasis, stemness properties maintenance, and cell fate decisions. Nonetheless, the specific involvement of ac4C modification mediated by NAT10 in regulating stemness and chemosensitivity in CC remains undetermined. Methods The levels of NAT10 in normal colon and chemoresistant CC tissues were determined utilizing quantitative real-time polymerase chain reaction alongside immunohistochemistry. Assessing cancer cell stemness and chemosensitivity was conducted by various methods including spheroid and colony formation, western blotting, and flow cytometry. RNA-Seq was used to identify target genes, and RNA immunoprecipitation analysis was used to explore the potential mechanisms. Results We observed NAT10 overexpression and increased ac4C modification levels in chemoresistant CC tissues. The in vivo and in vitro analysis findings suggested that NAT10 promoted CC cell stemness while suppressing their chemosensitivity. Conversely, Remodelin, a NAT10-specific inhibitor, enhanced CC cell chemosensitivity. Mechanistically, NAT10 increased the level of NANOGP8 ac4C modification and promoted NANOGP8 mRNA stability. Conclusions NAT10 promotes the maintenance of stemness and chemoresistance in CC cells by augmenting the mRNA stability of NANOGP8. The inhibition of NAT10 via Remodelin improves chemotherapeutic efficacy and impedes CC progression.
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Affiliation(s)
- Li-ping Gao
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - Ting-dong Li
- Department of Musculoskeletal Tumor, Gansu Provincial Cancer Hospital, Gansu Provincial Academic Institute for Medical Research, Lanzhou, PR China
| | - Su-zhen Yang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - Hui-min Ma
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - Xiang Wang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
| | - De-kui Zhang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, PR China
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Gao Y, Peng J, Qiao Y, Wang G. Natural Allelic Variations of Bch10G006400 Controlling Seed Size in Chieh-qua ( Benincasa hispida Cogn. var. Chieh-qua How). Int J Mol Sci 2024; 25:4236. [PMID: 38673826 PMCID: PMC11050567 DOI: 10.3390/ijms25084236] [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: 02/16/2024] [Revised: 03/17/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Seeds are the most important reproductive organs of higher plants, the beginning and end of a plant's lifecycle. They are very important to plant growth and development, and also an important factor affecting yield. In this study, genetic analysis and BSA-seq of the F2 population crossed with the large-seeded material 'J16' and small-seeded material 'FJ5' were carried out, and the seed size locus was initially located within the 1.31 Mb region on chr10. In addition, 2281 F2 plants were used to further reduce the candidate interval to 48.8 Kb. This region contains only one gene encoding the N-acetyltransferase (NAT) protein (Bch10G006400). Transcriptome and expression analysis revealed that the gene was significantly more highly expressed in 'J16' than in 'FJ5'. Variation analysis of Bch10G006400 among parents and 50 chieh-qua germplasms revealed that as well as a nonsynonymous mutation (SNP_314) between parents, two mutations (SNP_400 and InDel_551) were detected in other materials. Combining these three mutations completely distinguished the seed size of the chieh-qua. GO and KEGG enrichment analyses revealed that DGEs played the most important roles in carbohydrate metabolism and plant hormone signal transduction, respectively. The results of this study provide important information for molecular marker-assisted breeding and help to reveal the molecular mechanism of seed size.
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Affiliation(s)
- Yin Gao
- Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou 510335, China;
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China;
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jiazhu Peng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China;
| | - Yanchun Qiao
- Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou 510335, China;
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China;
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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17
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Zhao C, Sun X, Chen J, Geng BD. NAT10-mediated mRNA N4-acetylcytidine modification of MDR1 and BCRP promotes breast cancer progression. Thorac Cancer 2024; 15:820-829. [PMID: 38409918 PMCID: PMC10995701 DOI: 10.1111/1759-7714.15262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND N-acetyltransferase 10 (NAT10) serves as a critical enzyme in mediating the N4-acetylcytidine (ac4C) that ensures RNA stability and effective translation processes. The role of NAT10 in driving the advancement of breast cancer remains uninvestigated. METHODS We observed an increase in NAT10 expression, both at mRNA level through the analysis of the Cancer Genome Atlas (TCGA) database and at the protein level of tumor tissues from breast cancer patients. We determined that a heightened expression of NAT10 served as a predictor of an unfavorable clinical outcome. By screening the Cancer Cell Line Encyclopedia (CCLE) cell bank, this expression pattern of NAT10 was consistency found across almost all the classic breast cancer cell lines. RESULTS Functionally, interference of NAT10 expression exerts an inhibitory effect on proliferation and invasion of breast cancer cells. By using ac4C RNA immunoprecipitation (ac4c-RIP) and acRIP-qPCR assays, we identified a reduction of ac4C enrichment within the ATP binding cassette (ABC) transporters, multidrug resistance protein 1 (MDR1) and breast cancer resistance protein (BCRP), consequent to NAT10 suppression. Expressions of MDR1 and BCRP exhibited a positive correlation with NAT10 expression in tumor tissues, and the inhibition of NAT10 in breast cancer cells resulted in a decrease of MDR1 and BCRP expression. Therefore, the overexpressing of MDR1 and BCRP could partially rescue the adverse consequences of NAT10 depletion. In addition, we found that, remodelin, a NAT10 inhibitor, reinstated the susceptibility of capecitabine-resistant breast cancer cells to the chemotherapy, both in vitro and in vivo. CONCLUSION The results of our study demonstrated the essential role of NAT10-mediated ac4c-modification in breast cancer progression and provide a novel strategy for overcoming chemoresistance challenges.
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Affiliation(s)
- Cui‐Cui Zhao
- Department of VIP Ward, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy (Tianjin), Key Laboratory of Breast Cancer Prevention and TherapyTianjin Medical University, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & HospitalTianjinChina
| | - Xuan Sun
- The First Department of Breast Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy (Tianjin), Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & HospitalTianjinChina
| | - Jing Chen
- Department of Pancreatic Oncology, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy (Tianjin), Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute & HospitalTianjinChina
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18
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Liu D, Yang X, Wang X. Neutrophil extracellular traps promote gastric cancer cell metastasis via the NAT10-mediated N4-acetylcytidine modification of SMYD2. Cell Signal 2024; 116:111014. [PMID: 38110168 DOI: 10.1016/j.cellsig.2023.111014] [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: 09/06/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
It has been reported that the formation of neutrophil extracellular traps (NETs) is associated with cancer metastasis. The current study aimed to explore the effects of NETs on gastric cancer (GC) cell metastasis and uncover their underlying mechanism. NETs were measured in the plasma of patients with GC. Then, GC cells were treated with NETs to assess cell viability, migration, and invasion using cell counting kit 8 and Transwell assay, The liver metastasis and xenograft tumor mouse models were established to assess tumor growth and metastasis. The N4-acetylcytidine (ac4C) modification of SET and MYND domain containing 2 (SMYD2) mediated by NAT10 was evaluated using acetylated RNA immunoprecipitation. The results showed that the level of NETs was increased in the plasma of patients with GC, particularly in those with metastatic GC. In addition, GC cell co-treatment with NETs promoted cell viability, migration and invasion, while NAT10 or SMYD2 knockdown abrogated this effect. NAT10 also promoted the ac4C modification of SMYD2, thus increasing SMYD2 stability. Furthermore, NETs promoted the metastasis of GC cells in the liver in vivo. Overall, the results of the present study demonstrated that NETs promoted GC cell metastasis via the NAT10-mediated ac4C modification of SMYD2. These findings suggested that inhibiting the formation of NETs could be an effective approach for attenuating GC progression.
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Affiliation(s)
- Donghui Liu
- School of Life Science and Technology, Harbin Institute of Technology, Building 2E, phase II, Science Park, Xiangfang District, Harbin 150000, Heilongjiang, China; Department of Oncology, Heilongjiang Provincial Hospital, No. 82, Zhongshan Road, Xiangfang District, Harbin 150000, Heilongjiang, China
| | - Xiaoyao Yang
- Department of Science and Education, Heilongjiang Provincial Hospital, Harbin 150000, Heilongjiang, China
| | - Xuyao Wang
- Department of Pharmacy, Harbin Second Hospital, No. 38, Weixing Road, Daowai District, Harbin 150000, Heilongjiang, China.
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19
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Tao L, Lu Y, Chen Z, Ge L, He J, Peng J, Wang H. RNA ac 4C modification in cancer biology: from regulatory mechanisms to clinical applications. SCIENCE CHINA. LIFE SCIENCES 2024; 67:832-835. [PMID: 38324129 DOI: 10.1007/s11427-023-2496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/26/2023] [Indexed: 02/08/2024]
Affiliation(s)
- Lijun Tao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yunqing Lu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhuojia Chen
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Lichen Ge
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Junming He
- Department of Hepatobiliary Surgery, Guangdong Province Traditional Chinese Medical Hospital, Guangzhou, 510120, China
| | - Jianxin Peng
- Department of Hepatobiliary Surgery, Guangdong Province Traditional Chinese Medical Hospital, Guangzhou, 510120, China.
| | - Hongsheng Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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20
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Zhou M, Gamage ST, Tran KA, Bartee D, Wei X, Yin B, Berger S, Meier JL, Marmorstein R. Molecular Basis for RNA Cytidine Acetylation by NAT10. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587050. [PMID: 38585770 PMCID: PMC10996708 DOI: 10.1101/2024.03.27.587050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Human NAT10 acetylates the N4 position of cytidine in RNA, predominantly on rRNA and tRNA, to facilitate ribosome biogenesis and protein translation. NAT10 has been proposed as a therapeutic target in cancers as well as aging-associated pathologies such as Hutchinson-Gilford Progeria Syndrome (HGPS). The ∼120 kDa NAT10 protein uses its acetyl-CoA-dependent acetyltransferase, ATP-dependent helicase, and RNA binding domains in concert to mediate RNA-specific N4-cytidine acetylation. While the biochemical activity of NAT10 is well known, the molecular basis for catalysis of eukaryotic RNA acetylation remains relatively undefined. To provide molecular insights into the RNA-specific acetylation by NAT10, we determined the single particle cryo-EM structures of Chaetomium thermophilum NAT10 ( Ct NAT10) bound to a bisubstrate cytidine-CoA probe with and without ADP. The structures reveal that NAT10 forms a symmetrical heart-shaped dimer with conserved functional domains surrounding the acetyltransferase active sites harboring the cytidine-CoA probe. Structure-based mutagenesis with analysis of mutants in vitro supports the catalytic role of two conserved active site residues (His548 and Tyr549 in Ct NAT10), and two basic patches, both proximal and distal to the active site for RNA-specific acetylation. Yeast complementation analyses and senescence assays in human cells also implicates NAT10 catalytic activity in yeast thermoadaptation and cellular senescence. Comparison of the NAT10 structure to protein lysine and N-terminal acetyltransferase enzymes reveals an unusually open active site suggesting that these enzymes have been evolutionarily tailored for RNA recognition and cytidine-specific acetylation.
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21
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Li X, Wang Y, Zhang S, Zhang P, Huang S. Nanopore Identification of N-Acetylation by Hydroxylamine Deacetylation (NINAHD). ACS Sens 2024; 9:1359-1371. [PMID: 38449100 DOI: 10.1021/acssensors.3c02350] [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] [Indexed: 03/08/2024]
Abstract
N-Acetyl modification, a chemical modification commonly found on biomacromolecules, plays a crucial role in the regulation of cell activities and is related to a variety of diseases. However, due to the instability of N-acetyl modification, accurate and rapid identification of N-acetyl modification with a low measurement cost is still technically challenging. Here, based on hydroxylamine deacetylation and nanopore single molecule chemistry, a universal sensing strategy for N-acetyl modification has been developed. Acetohydroxamic acid (AHA), which is produced by the hydroxylamine deacetylation reaction and serves as a reporter for N-acetylation identification, is specifically sensed by a phenylboronic acid (PBA)-modified Mycobacterium smegmatis porin A (MspA). With this strategy, N-acetyl modifications on RNA, DNA, proteins, and glycans were identified, demonstrating its generality. Specifically, histones can be treated with hydroxylamine deacetylation, from which the generated AHA can represent the amount of N-acetyl modification detected by a nanopore sensor. The unique event features of AHA also demonstrate the robustness of sensing against other interfering analytes in the environment.
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Affiliation(s)
- Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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22
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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.
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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
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23
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Gao J, Xu P, Wang F, Zhang W, Min M, Urba R, Fan L. Revealing the pharmacological effects of Remodelin against osteosarcoma based on network pharmacology, acRIP-seq and experimental validation. Sci Rep 2024; 14:3577. [PMID: 38347067 PMCID: PMC10861577 DOI: 10.1038/s41598-024-54197-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/09/2024] [Indexed: 02/15/2024] Open
Abstract
Osteosarcoma (OS) is the most common primary malignant tumor of bone. Remodelin, an inhibitor of the N (4)-Acetylcytidine (ac4C) acetylation modifying enzyme N-acetyltransferase 10 (NAT10), has been shown to have therapeutic effects on cancer in several studies, and our previous studies have confirmed the inhibitory effect of Remodelin on OS cells, however, the mechanism of action has not yet been elucidated. We used network pharmacological analysis to quantify the therapeutic targets of Remodelin against OS. acRIP-seq and RNA-seq were performed to investigate the inhibitory activity of Remodelin on acetylation and its effect on the transcriptome after intervening in OS cells U2OS with Remodelin in vitro. Key target genes were deduced based on their pharmacological properties, combined with network pharmacology results and sequencing results. Finally, the deduced target genes were validated with vitro experiments. Network pharmacological analysis showed that 2291 OS-related target genes and 369 Remodelin-related target genes were obtained, and 116 overlapping genes were identified as Remodelin targets for OS treatment. Sequencing results showed that a total of 13,736 statistically significant ac4C modification peaks were detected by acRIP-seq, including 6938 hypoacetylation modifications and 6798 hyperacetylation modifications. A total of 2350 statistically significant mRNAs were detected by RNA-seq, of which 830 were up-regulated and 1520 were down-regulated. Association analyses identified a total of 382 genes that were Hypoacetylated-down, consistent with inhibition of mRNA acetylation and expression by Remodelin. Five genes, CASP3, ESR2, FGFR2, IGF1 and MAPK1, were identified as key therapeutic targets of Remodelin against OS. Finally, in vitro experiments, CCK-8 and qRT-PCR demonstrated that Remodelin indeed inhibited the proliferation of OS cells and reduced the expression of three genes: ESR2, IGF1, and MAPK1. In conclusion, ESR2, IGF1 and MAPK1 were identified as key therapeutic targets of Remodelin against OS. This reveals the target of Remodelin's pharmacological action on OS and provides new ideas for the treatment of OS.
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Affiliation(s)
- Jia Gao
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China
| | - Peili Xu
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China
| | - Feng Wang
- Department of Orthopedics, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China
| | - Wenjie Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China
| | - Meipeng Min
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China
| | - Rafi Urba
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China
| | - Lei Fan
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, People's Republic of China.
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24
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Yang HZ, Zhuo D, Huang Z, Luo G, Liang S, Fan Y, Zhao Y, Lv X, Qiu C, Zhang L, Liu Y, Sun T, Chen X, Li SS, Jin X. Deficiency of Acetyltransferase nat10 in Zebrafish Causes Developmental Defects in the Visual Function. Invest Ophthalmol Vis Sci 2024; 65:31. [PMID: 38381411 PMCID: PMC10893899 DOI: 10.1167/iovs.65.2.31] [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: 07/25/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Purpose N4-acetylcytidine (ac4C) is a post-transcriptional RNA modification catalyzed by N-acetyltransferase 10 (NAT10), a critical factor known to influence mRNA stability. However, the role of ac4C in visual development remains unexplored. Methods Analysis of public datasets and immunohistochemical staining were conducted to assess the expression pattern of nat10 in zebrafish. We used CRISPR/Cas9 and RNAi technologies to knockout (KO) and knockdown (KD) nat10, the zebrafish ortholog of human NAT10, and evaluated its effects on early development. To assess the impact of nat10 knockdown on visual function, we performed comprehensive histological evaluations and behavioral analyses. Transcriptome profiling and real-time (RT)-PCR were utilized to detect alterations in gene expression resulting from the nat10 knockdown. Dot-blot and RNA immunoprecipitation (RIP)-PCR analyses were conducted to verify changes in ac4C levels in both total RNA and opsin mRNA specifically. Additionally, we used the actinomycin D assay to examine the stability of opsin mRNA following the nat10 KD. Results Our study found that the zebrafish NAT10 protein shares similar structural properties with its human counterpart. We observed that the nat10 gene was prominently expressed in the visual system during early zebrafish development. A deficiency of nat10 in zebrafish embryos resulted in increased mortality and developmental abnormalities. Behavioral and histological assessments indicated significant vision impairment in nat10 KD zebrafish. Transcriptomic analysis and RT-PCR identified substantial downregulation of retinal transcripts related to phototransduction, light response, photoreceptors, and visual perception in the nat10 KD group. Dot-blot and RIP-PCR analyses confirmed a pronounced reduction in ac4C levels in both total RNA and specifically in opsin messenger RNA (mRNA). Additionally, by evaluating mRNA decay in zebrafish treated with actinomycin D, we observed a significant decrease in the stability of opsin mRNA in the nat10 KD group. Conclusions The ac4C-mediated mRNA modification plays an essential role in maintaining visual development and retinal function. The loss of NAT10-mediated ac4C modification results in significant disruptions to these processes, underlining the importance of this RNA modification in ocular development.
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Affiliation(s)
| | - Donghai Zhuo
- School of Medicine, Nankai University, Tianjin, China
| | | | - Gan Luo
- Tianjin Medical University, Tianjin, China
- Department of Spinal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Shuang Liang
- Tianjin Central Hospital of Gynecology and Obstetrics, Tianjin, China
| | - Yonggang Fan
- School of Medicine, Nankai University, Tianjin, China
| | - Ying Zhao
- School of Medicine, Nankai University, Tianjin, China
| | - Xinxin Lv
- School of Medicine, Nankai University, Tianjin, China
| | - Caizhen Qiu
- School of Medicine, Nankai University, Tianjin, China
| | - Lingzhu Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Yang Liu
- Department of Spinal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Tianwei Sun
- Tianjin Medical University, Tianjin, China
- Department of Spinal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Xu Chen
- Tianjin Central Hospital of Gynecology and Obstetrics, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
| | - Shan-Shan Li
- School of Medicine, Nankai University, Tianjin, China
| | - Xin Jin
- School of Medicine, Nankai University, Tianjin, China
- Tianjin Central Hospital of Gynecology and Obstetrics, Tianjin, China
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, China
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25
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Shen J, Sun Y, Zhuang Q, Xue D, He X. NAT10 promotes renal ischemia-reperfusion injury via activating NCOA4-mediated ferroptosis. Heliyon 2024; 10:e24573. [PMID: 38312597 PMCID: PMC10835180 DOI: 10.1016/j.heliyon.2024.e24573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/06/2024] Open
Abstract
Ischemia-reperfusion injury (IRI) is a significant contributor to acute kidney injury (AKI) and is associated with substantial morbidity and mortality rates. In this study, we aimed to investigate the role of NAT10 and its ac4C RNA modification in IRI-induced renal injury. Our findings revealed that both the expression level of NAT10 and the RNA ac4C level in the kidneys were elevated in the IRI group compared to the sham group. Functionally, we observed that inhibition of NAT10 activity with Remodelin or the specific knockout of NAT10 in the kidney led to a significant attenuation of IRI-induced renal injury. Furthermore, in vitro experiments demonstrated that NAT10 inhibition and specific knockout of NAT10 in the kidney markedly suppressed global ac4C RNA modification, providing protection against hypoxia/reoxygenation-induced tubular epithelial cell injury and ferroptosis. Mechanistically, our study uncovered that NAT10 promoted ac4C RNA modification of NCOA4 mRNA, thereby enhancing its stability and contributing to IRI-induced ferroptosis in tubular epithelial cells (TECs). These findings underscore the potential of NAT10 and ac4C RNA modification as promising therapeutic targets for the treatment of AKI. Overall, our study sheds light on the critical involvement of NAT10 and ac4C RNA modification in the pathogenesis of IRI-induced renal injury, offering valuable insights for the development of novel AKI treatment strategies.
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Affiliation(s)
- Jie Shen
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, People's Republic of China
| | - Yangyang Sun
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, People's Republic of China
| | - Qianfeng Zhuang
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, People's Republic of China
| | - Dong Xue
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, People's Republic of China
| | - Xiaozhou He
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, People's Republic of China
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26
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Wang X, Ling R, Peng Y, Qiu W, Chen D. RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac 4C modification. Int J Oral Sci 2024; 16:6. [PMID: 38246918 PMCID: PMC10800354 DOI: 10.1038/s41368-023-00276-7] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Existing studies have underscored the pivotal role of N-acetyltransferase 10 (NAT10) in various cancers. However, the outcomes of protein-protein interactions between NAT10 and its protein partners in head and neck squamous cell carcinoma (HNSCC) remain unexplored. In this study, we identified a significant upregulation of RNA-binding protein with serine-rich domain 1 (RNPS1) in HNSCC, where RNPS1 inhibits the ubiquitination degradation of NAT10 by E3 ubiquitin ligase, zinc finger SWIM domain-containing protein 6 (ZSWIM6), through direct protein interaction, thereby promoting high NAT10 expression in HNSCC. This upregulated NAT10 stability mediates the enhancement of specific tRNA ac4C modifications, subsequently boosting the translation process of genes involved in pathways such as IL-6 signaling, IL-8 signaling, and PTEN signaling that play roles in regulating HNSCC malignant progression, ultimately influencing the survival and prognosis of HNSCC patients. Additionally, we pioneered the development of TRMC-seq, leading to the discovery of novel tRNA-ac4C modification sites, thereby providing a potent sequencing tool for tRNA-ac4C research. Our findings expand the repertoire of tRNA ac4C modifications and identify a role of tRNA ac4C in the regulation of mRNA translation in HNSCC.
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Affiliation(s)
- Xiaochen Wang
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yurong Peng
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiqiong Qiu
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Demeng Chen
- Center For Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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27
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Qin G, Bai F, Hu H, Zhang J, Zhan W, Wu Z, Li J, Fu Y, Deng Y. Targeting the NAT10/NPM1 axis abrogates PD-L1 expression and improves the response to immune checkpoint blockade therapy. Mol Med 2024; 30:13. [PMID: 38243170 PMCID: PMC10799409 DOI: 10.1186/s10020-024-00780-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND PD-1/PD-L1 play a crucial role as immune checkpoint inhibitors in various types of cancer. Although our previous study revealed that NPM1 was a novel transcriptional regulator of PD-L1 and stimulated the transcription of PD-L1, the underlying regulatory mechanism remains incompletely characterized. METHODS Various human cancer cell lines were used to validate the role of NPM1 in regulating the transcription of PD-L1. The acetyltransferase NAT10 was identified as a facilitator of NPM1 acetylation by coimmunoprecipitation and mass spectrometry. The potential application of combined NAT10 inhibitor and anti-CTLA4 treatment was evaluated by an animal model. RESULTS We demonstrated that NPM1 enhanced the transcription of PD-L1 in various types of cancer, and the acetylation of NPM1 played a vital role in this process. In particular, NAT10 facilitated the acetylation of NPM1, leading to enhanced transcription and increased expression of PD-L1. Moreover, our findings demonstrated that Remodelin, a compound that inhibits NAT10, effectively reduced NPM1 acetylation, leading to a subsequent decrease in PD-L1 expression. In vivo experiments indicated that Remodelin combined with anti-CTLA-4 therapy had a superior therapeutic effect compared with either treatment alone. Ultimately, we verified that the expression of NAT10 exhibited a positive correlation with the expression of PD-L1 in various types of tumors, serving as an indicator of unfavorable prognosis. CONCLUSION This study suggests that the NAT10/NPM1 axis is a promising therapeutic target in malignant tumors.
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Affiliation(s)
- Ge Qin
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Fan Bai
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Huabin Hu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Jianwei Zhang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Weixiang Zhan
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Zehua Wu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Jianxia Li
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Yang Fu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China
| | - Yanhong Deng
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China.
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of China.
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-Sen University, Yuan Cun Er Rd No. 26, Guangzhou, 510655, People's Republic of 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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Hu Z, Lu Y, Cao J, Lin L, Chen X, Zhou Z, Pu J, Chen G, Ma X, Deng Q, Jin Y, Jiang L, Li Y, Li T, Liu J, Zhu S. N-acetyltransferase NAT10 controls cell fates via connecting mRNA cytidine acetylation to chromatin signaling. SCIENCE ADVANCES 2024; 10:eadh9871. [PMID: 38215194 PMCID: PMC10786415 DOI: 10.1126/sciadv.adh9871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Cell fate transition involves dynamic changes of gene regulatory network and chromatin landscape, requiring multiple levels of regulation, yet the cross-talk between epitranscriptomic modification and chromatin signaling remains largely unknown. Here, we uncover that suppression of N-acetyltransferase 10 (NAT10), the writer for mRNA N4-acetylcytidine (ac4C) modification, can notably affect human embryonic stem cell (hESC) lineage differentiation and pluripotent reprogramming. With integrative analysis, we identify that NAT10-mediated ac4C modification regulates the protein levels of a subset of its targets, which are strongly enriched for fate-instructive chromatin regulators, and among them, histone chaperone ANP32B is experimentally verified and functionally relevant. Furthermore, NAT10-ac4C-ANP32B axis can modulate the chromatin landscape of their downstream genes (e.g., key regulators of Wnt and TGFβ pathways). Collectively, we show that NAT10 is an essential regulator of cellular plasticity, and its catalyzed mRNA cytidine acetylation represents a critical layer of epitranscriptomic modulation and uncover a previously unrecognized, direct cross-talk between epitranscriptomic modification and chromatin signaling during cell fate transitions.
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Affiliation(s)
- Zhensheng Hu
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunkun Lu
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Lianyu Lin
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xi Chen
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ziyu Zhou
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiaqi Pu
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
- The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Guo Chen
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaojie Ma
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qian Deng
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Jin
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liling Jiang
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuhan Li
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Saiyong Zhu
- Life Sciences Institute, The Second Affiliated Hospital and School of Medicine, The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Ohira T, Suzuki T. Transfer RNA modifications and cellular thermotolerance. Mol Cell 2024; 84:94-106. [PMID: 38181765 DOI: 10.1016/j.molcel.2023.11.041] [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: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024]
Abstract
RNA molecules are modified post-transcriptionally to acquire their diverse functions. Transfer RNA (tRNA) has the widest variety and largest numbers of RNA modifications. tRNA modifications are pivotal for decoding the genetic code and stabilizing the tertiary structure of tRNA molecules. Alternation of tRNA modifications directly modulates the structure and function of tRNAs and regulates gene expression. Notably, thermophilic organisms exhibit characteristic tRNA modifications that are dynamically regulated in response to varying growth temperatures, thereby bolstering fitness in extreme environments. Here, we review the history and latest findings regarding the functions and biogenesis of several tRNA modifications that contribute to the cellular thermotolerance of thermophiles.
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Affiliation(s)
- Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Wang L, Tao Y, Zhai J, Xue M, Zheng C, Hu H. The emerging roles of ac4C acetylation "writer" NAT10 in tumorigenesis: A comprehensive review. Int J Biol Macromol 2024; 254:127789. [PMID: 37926318 DOI: 10.1016/j.ijbiomac.2023.127789] [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: 09/20/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
The quick progress of epigenetic study has kindled new hope for treating many cancers. When it comes to RNA epigenetics, the ac4C acetylation modification is showing promise, whereas N-acetyltransferase 10 plays a wide range of biological functions, has a significant impact on cellular life events, and is frequently highly expressed in many malignant tumors. N-acetyltransferase 10 is an acetyltransferase with important biological involvement in cellular processes and lifespan. Because it is highly expressed in many malignant tumors, it is considered a pro-carcinogenic gene. The review aims to introduce NAT10, summarize the effects of ac4C acetylation on tumor growth from multiple angles, and discuss the possible therapeutic targeting of NAT10 and the future directions of ac4C acetylation investigations.
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Affiliation(s)
- Leisheng Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu Province, China; Wuxi Medical College, Jiangnan University, Wuxi, 214122, China
| | - Yue Tao
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu Province, China; Wuxi Medical College, Jiangnan University, Wuxi, 214122, China
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, 2 Jingba Road, Zhengzhou, Henan, China, 450001
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
| | - Hao Hu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Jiangnan University, Wuxi, 214122, Jiangsu Province, China; Wuxi Medical College, Jiangnan University, Wuxi, 214122, China; Medical Oncology, Affiliated Hospital of Jiangnan University, Wuxi, 214122, China; Hepatobiliary and Pancreatic Surgery, The Third Hospital Affiliated to Nantong University, Wuxi, 214041, China; Medical School, Nantong University, Nantong, 226001, China; Wuxi Institute of Hepatobiliary Surgery, Wuxi, 214122, China
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Li Z, Jin B, Fang J. MetaAc4C: A multi-module deep learning framework for accurate prediction of N4-acetylcytidine sites based on pre-trained bidirectional encoder representation and generative adversarial networks. Genomics 2024; 116:110749. [PMID: 38008265 DOI: 10.1016/j.ygeno.2023.110749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/05/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
MOTIVATION N4-acetylcytidine (ac4C) is a highly conserved RNA modification that plays a crucial role in various biological processes. Accurately identifying ac4C sites is of paramount importance for gaining a deeper understanding of their regulatory mechanisms. Nevertheless, the existing experimental techniques for ac4C site identification are characterized by limitations in terms of cost-effectiveness, while the performance of current computational methods in accurately identifying ac4C sites requires further enhancement. RESULTS In this paper, we present MetaAc4C, an advanced deep learning model that leverages pre-trained bidirectional encoder representations from transformers (BERT). The model is based on a bi-directional long short-term memory network (BLSTM) architecture, incorporating attention mechanism and residual connection. To address the issue of data imbalance, we adapt generative adversarial networks to generate synthetic feature samples. On the independent test set, MetaAc4C surpasses the current state-of-the-art ac4C prediction model, exhibiting improvements in terms of ACC, MCC, and AUROC by 2.36%, 4.76%, and 3.11%, respectively, on the unbalanced dataset. When evaluated on the balanced dataset, MetaAc4C achieves improvements in ACC, MCC, and AUROC by 2.6%, 5.11%, and 1.01%, respectively. Notably, our approach of utilizing WGAN-GP augmented training RNA samples demonstrates even superior performance compared to the SMOTE oversampling method.
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Affiliation(s)
- Zutan Li
- College of Engineering, Westlake University, Hangzhou, China; College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bingbing Jin
- College of Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jingya Fang
- College of Science, China Pharmaceutical University, Nanjing, China.
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Zheng J, Lu Y, Lin Y, Si S, Guo B, Zhao X, Cui L. Epitranscriptomic modifications in mesenchymal stem cell differentiation: advances, mechanistic insights, and beyond. Cell Death Differ 2024; 31:9-27. [PMID: 37985811 PMCID: PMC10782030 DOI: 10.1038/s41418-023-01238-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
RNA modifications, known as the "epitranscriptome", represent a key layer of regulation that influences a wide array of biological processes in mesenchymal stem cells (MSCs). These modifications, catalyzed by specific enzymes, often termed "writers", "readers", and "erasers", can dynamically alter the MSCs' transcriptomic landscape, thereby modulating cell differentiation, proliferation, and responses to environmental cues. These enzymes include members of the classes METTL, IGF2BP, WTAP, YTHD, FTO, NAT, and others. Many of these RNA-modifying agents are active during MSC lineage differentiation. This review provides a comprehensive overview of the current understanding of different RNA modifications in MSCs, their roles in regulating stem cell behavior, and their implications in MSC-based therapies. It delves into how RNA modifications impact MSC biology, the functional significance of individual modifications, and the complex interplay among these modifications. We further discuss how these intricate regulatory mechanisms contribute to the functional diversity of MSCs, and how they might be harnessed for therapeutic applications. The review also highlights current challenges and potential future directions in the study of RNA modifications in MSCs, emphasizing the need for innovative tools to precisely map these modifications and decipher their context-specific effects. Collectively, this work paves the way for a deeper understanding of the role of the epitranscriptome in MSC biology, potentially advancing therapeutic strategies in regenerative medicine and MSC-based therapies.
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Affiliation(s)
- Jiarong Zheng
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Ye Lu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Yunfan Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Shanshan Si
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Bing Guo
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Xinyuan Zhao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
| | - Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, Los Angeles, 90095, CA, USA.
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Shi J, Yang C, Zhang J, Zhao K, Li P, Kong C, Wu X, Sun H, Zheng R, Sun W, Chen L, Kong X. NAT10 Is Involved in Cardiac Remodeling Through ac4C-Mediated Transcriptomic Regulation. Circ Res 2023; 133:989-1002. [PMID: 37955115 DOI: 10.1161/circresaha.122.322244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Heart failure, characterized by cardiac remodeling, is associated with abnormal epigenetic processes and aberrant gene expression. Here, we aimed to elucidate the effects and mechanisms of NAT10 (N-acetyltransferase 10)-mediated N4-acetylcytidine (ac4C) acetylation during cardiac remodeling. METHODS NAT10 and ac4C expression were detected in both human and mouse subjects with cardiac remodeling through multiple assays. Subsequently, acetylated RNA immunoprecipitation and sequencing, thiol-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), and ribosome sequencing (Ribo-seq) were employed to elucidate the role of ac4C-modified posttranscriptional regulation in cardiac remodeling. Additionally, functional experiments involving the overexpression or knockdown of NAT10 were conducted in mice models challenged with Ang II (angiotensin II) and transverse aortic constriction. RESULTS NAT10 expression and RNA ac4C levels were increased in in vitro and in vivo cardiac remodeling models, as well as in patients with cardiac hypertrophy. Silencing and inhibiting NAT10 attenuated Ang II-induced cardiomyocyte hypertrophy and cardiofibroblast activation. Next-generation sequencing revealed ac4C changes in both mice and humans with cardiac hypertrophy were associated with changes in global mRNA abundance, stability, and translation efficiency. Mechanistically, NAT10 could enhance the stability and translation efficiency of CD47 and ROCK2 transcripts by upregulating their mRNA ac4C modification, thereby resulting in an increase in their protein expression during cardiac remodeling. Furthermore, the administration of Remodelin, a NAT10 inhibitor, has been shown to prevent cardiac functional impairments in mice subjected to transverse aortic constriction by suppressing cardiac fibrosis, hypertrophy, and inflammatory responses, while also regulating the expression levels of CD47 and ROCK2 (Rho associated coiled-coil containing protein kinase 2). CONCLUSIONS Therefore, our data suggest that modulating epitranscriptomic processes, such as ac4C acetylation through NAT10, may be a promising therapeutic target against cardiac remodeling.
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Affiliation(s)
- Jing Shi
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Chuanxi Yang
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China (C.Y.)
| | - Jing Zhang
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Kun Zhao
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Peng Li
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Chuiyu Kong
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Jiangsu, China (C.K.)
| | - Xiaoguang Wu
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Haoliang Sun
- Department of Cardiovascular Surgery (H.S., R.Z.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Rui Zheng
- Department of Cardiovascular Surgery (H.S., R.Z.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Wei Sun
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
| | - Lianmin Chen
- Changzhou Medical Center of the Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University and Department of Cardiology of the First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China (L.C.)
| | - Xiangqing Kong
- Department of Cardiology (J.S., K.Z., J.Z., P.L., X.W., W.S., X.K.), The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, China
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China (X.K.)
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Zhang H, Shan W, Yang Z, Zhang Y, Wang M, Gao L, Zeng L, Zhao Q, Liu J. NAT10 mediated mRNA acetylation modification patterns associated with colon cancer progression and microsatellite status. Epigenetics 2023; 18:2188667. [PMID: 36908042 PMCID: PMC10026876 DOI: 10.1080/15592294.2023.2188667] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
N4-acetylcytidine (ac4C) is one type of RNA modification found in eukaryotes. RNA acetylation modifications are gradually expanding in oncology. However, the role of RNA acetylation modifications in colorectal cancer and its association with colorectal cancer microsatellite status remain unclear. Using public databases and in vitro experiments, we verified the expression and biological function of NAT10, as the key RNA acetylation modification enzyme, in colorectal cancer. The results showed that NAT10 was highly expressed in colorectal cancer, and significantly promoted colorectal cancer cell proliferation. NAT10 was also involved in several aspects of cell homoeostasis such as ion transport, calcium-dependent phospholipid binding, and RNA stability. NAT10 expression positively correlated with immune infiltration in colorectal cancer. We further constructed a risk regression model for mRNA acetylation in colorectal cancer using acetylation-related differential genes. We found that tumour immune infiltration, microsatellite instability (MSI) proportion, tumour immune mutation burden, and patient response to immunotherapy were positively correlated with risk scores. For the first time, our study showed that the level of mRNA acetylation modification level is elevated in colorectal cancer and positively correlates with immune infiltration and microsatellite status of patients. Based on our findings, NAT10 may be a new target for colorectal cancer treatment.
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Affiliation(s)
- Hailin Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Wenqing Shan
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Zhenwei Yang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Yangyang Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Meng Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Liping Gao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Lingxiu Zeng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan University, Wuhan, Hubei, 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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Lou LL, Qiu WR, Liu Z, Xu ZC, Xiao X, Huang SF. Stacking-ac4C: an ensemble model using mixed features for identifying n4-acetylcytidine in mRNA. Front Immunol 2023; 14:1267755. [PMID: 38094296 PMCID: PMC10716444 DOI: 10.3389/fimmu.2023.1267755] [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: 07/27/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
N4-acetylcytidine (ac4C) is a modification of cytidine at the nitrogen-4 position, playing a significant role in the translation process of mRNA. However, the precise mechanism and details of how ac4C modifies translated mRNA remain unclear. Since identifying ac4C sites using conventional experimental methods is both labor-intensive and time-consuming, there is an urgent need for a method that can promptly recognize ac4C sites. In this paper, we propose a comprehensive ensemble learning model, the Stacking-based heterogeneous integrated ac4C model, engineered explicitly to identify ac4C sites. This innovative model integrates three distinct feature extraction methodologies: Kmer, electron-ion interaction pseudo-potential values (PseEIIP), and pseudo-K-tuple nucleotide composition (PseKNC). The model also incorporates the robust Cluster Centroids algorithm to enhance its performance in dealing with imbalanced data and alleviate underfitting issues. Our independent testing experiments indicate that our proposed model improves the Mcc by 15.61% and the ROC by 5.97% compared to existing models. To test our model's adaptability, we also utilized a balanced dataset assembled by the authors of iRNA-ac4C. Our model showed an increase in Sn of 4.1%, an increase in Acc of nearly 1%, and ROC improvement of 0.35% on this balanced dataset. The code for our model is freely accessible at https://github.com/louliliang/ST-ac4C.git, allowing users to quickly build their model without dealing with complicated mathematical equations.
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Affiliation(s)
- Li-Liang Lou
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Wang-Ren Qiu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Zi Liu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Zhao-Chun Xu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Xuan Xiao
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Shun-Fa Huang
- School of Information Engineering , Jingdezhen University, Jingdezhen, China
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Jia J, Cao X, Wei Z. DLC-ac4C: A Prediction Model for N4-acetylcytidine Sites in Human mRNA Based on DenseNet and Bidirectional LSTM Methods. Curr Genomics 2023; 24:171-186. [PMID: 38178985 PMCID: PMC10761336 DOI: 10.2174/0113892029270191231013111911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 01/06/2024] Open
Abstract
Introduction N4 acetylcytidine (ac4C) is a highly conserved nucleoside modification that is essential for the regulation of immune functions in organisms. Currently, the identification of ac4C is primarily achieved using biological methods, which can be time-consuming and labor-intensive. In contrast, accurate identification of ac4C by computational methods has become a more effective method for classification and prediction. Aim To the best of our knowledge, although there are several computational methods for ac4C locus prediction, the performance of the models they constructed is poor, and the network structure they used is relatively simple and suffers from the disadvantage of network degradation. This study aims to improve these limitations by proposing a predictive model based on integrated deep learning to better help identify ac4C sites. Methods In this study, we propose a new integrated deep learning prediction framework, DLC-ac4C. First, we encode RNA sequences based on three feature encoding schemes, namely C2 encoding, nucleotide chemical property (NCP) encoding, and nucleotide density (ND) encoding. Second, one-dimensional convolutional layers and densely connected convolutional networks (DenseNet) are used to learn local features, and bi-directional long short-term memory networks (Bi-LSTM) are used to learn global features. Third, a channel attention mechanism is introduced to determine the importance of sequence characteristics. Finally, a homomorphic integration strategy is used to limit the generalization error of the model, which further improves the performance of the model. Results The DLC-ac4C model performed well in terms of sensitivity (Sn), specificity (Sp), accuracy (Acc), Mathews correlation coefficient (MCC), and area under the curve (AUC) for the independent test data with 86.23%, 79.71%, 82.97%, 66.08%, and 90.42%, respectively, which was significantly better than the prediction accuracy of the existing methods. Conclusion Our model not only combines DenseNet and Bi-LSTM, but also uses the channel attention mechanism to better capture hidden information features from a sequence perspective, and can identify ac4C sites more effectively.
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Affiliation(s)
- Jianhua Jia
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
| | - Xiaojing Cao
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
| | - Zhangying Wei
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
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Chillar K, Yin Y, Apostle A, Fang S. PEGylated Dmoc phosphoramidites for sensitive oligodeoxynucleotide synthesis. Org Biomol Chem 2023; 21:9005-9010. [PMID: 37921008 PMCID: PMC11288643 DOI: 10.1039/d3ob01495a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Sensitive oligodeoxynucleotides (ODNs) can be synthesized using Dmoc phosphoramidites, but only short ODNs were demonstrated. Here, we report the synthesis of much longer ODNs, which was made possible by the use of PEGylated Dmoc (pDmoc) phosphoramidites. The longer ODNs synthesized include those containing the sensitive 4acC epigenetic modification recently discovered in nature.
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Affiliation(s)
- Komal Chillar
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
| | - Yipeng Yin
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
| | - Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
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Sun X, Wang G, Luo W, Gu H, Ma W, Wei X, Liu D, Jia S, Cao S, Wang Y, Yuan Z. Small but strong: the emerging role of small nucleolar RNA in cardiovascular diseases. Front Cell Dev Biol 2023; 11:1292925. [PMID: 38033868 PMCID: PMC10682241 DOI: 10.3389/fcell.2023.1292925] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of mortality and disability worldwide. Numerous studies have demonstrated that non-coding RNAs (ncRNAs) play a primary role in CVD development. Therefore, studies on the mechanisms of ncRNAs are essential for further efforts to prevent and treat CVDs. Small nucleolar RNAs (snoRNAs) are a novel species of non-conventional ncRNAs that guide post-transcriptional modifications and the subsequent maturation of small nuclear RNA and ribosomal RNA. Evidently, snoRNAs are extensively expressed in human tissues and may regulate different illnesses. Particularly, as the next-generation sequencing techniques have progressed, snoRNAs have been shown to be differentially expressed in CVDs, suggesting that they may play a role in the occurrence and progression of cardiac illnesses. However, the molecular processes and signaling pathways underlying the function of snoRNAs remain unidentified. Therefore, it is of great value to comprehensively investigate the association between snoRNAs and CVDs. The aim of this review was to collate existing literature on the biogenesis, characteristics, and potential regulatory mechanisms of snoRNAs. In particular, we present a scientific update on these snoRNAs and their relevance to CVDs in an effort to cast new light on the functions of snoRNAs in the clinical diagnosis of CVDs.
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Affiliation(s)
- Xue Sun
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gebang Wang
- Department of Thoracic Surgery, Liaoning Cancer Hospital and Institute, Cancer Hospital of Dalian University of Technology, Shenyang, Liaoning, China
| | - Wenting Luo
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hui Gu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Ma
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaowei Wei
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Dan Liu
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shanshan Jia
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Songying Cao
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Wang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Chen X, Hao Y, Liu Y, Zhong S, You Y, Ao K, Chong T, Luo X, Yin M, Ye M, He H, Lu A, Chen J, Li X, Zhang J, Guo X. NAT10/ac4C/FOXP1 Promotes Malignant Progression and Facilitates Immunosuppression by Reprogramming Glycolytic Metabolism in Cervical Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302705. [PMID: 37818745 PMCID: PMC10646273 DOI: 10.1002/advs.202302705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/21/2023] [Indexed: 10/13/2023]
Abstract
Immunotherapy has recently emerged as the predominant therapeutic approach for cervical cancer (CCa), driven by the groundbreaking clinical achievements of immune checkpoint inhibitors (ICIs), such as anti-PD-1/PD-L1 antibodies. N4-acetylcytidine (ac4C) modification, catalyzed by NAT10, is an important posttranscriptional modification of mRNA in cancers. However, its impact on immunological dysregulation and the tumor immunotherapy response in CCa remains enigmatic. Here, a significant increase in NAT10 expression in CCa tissues is initially observed that is clinically associated with poor prognosis. Subsequently, it is found that HOXC8 activated NAT10 by binding to its promoter, thereby stimulating ac4C modification of FOXP1 mRNA and enhancing its translation efficiency, eventually leading to induction of GLUT4 and KHK expression. Moreover, NAT10/ac4C/FOXP1 axis activity resulted in increased glycolysis and a continuous increase in lactic acid secretion by CCa cells. The lactic acid-enriched tumor microenvironment (TME) further contributed to amplifying the immunosuppressive properties of tumor-infiltrating regulatory T cells (Tregs). Impressively, NAT10 knockdown enhanced the efficacy of PD-L1 blockade-mediated tumor regression in vivo. Taken together, the findings revealed the oncogenic role of NAT10 in initiating crosstalk between cancer cell glycolysis and immunosuppression, which can be a target for synergistic PD-1/PD-L1 blockade immunotherapy in CCa.
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Affiliation(s)
- Xiaona Chen
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yi Hao
- Department of UltrasoundSouth China Hospital of Shenzhen UniversityShenzhenGuangdongChina
| | - Yong Liu
- Department of Critical Care MedicineShenzhen Hospital, Southern Medical UniversityShenzhenGuangdongChina
| | - Sheng Zhong
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Yuehua You
- Department of StomatologyLonghua People's Hospital Affiliated with Southern Medical UniversityShenzhenGuangdongChina
- School of StomatologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Keyi Ao
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Tuotuo Chong
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Xiaomin Luo
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Minuo Yin
- Department of Obstetrics and GynecologyShenzhen Hospital of Southern Medical UniversityShenzhenGuangdongChina
| | - Ming Ye
- Department of PathologyAffiliated Tumour Hospital of Xinjiang Medical UniversityUrumqiXinjiangChina
| | - Hui He
- Department of PathologyShenzhen HospitalThe University of Hong KongShenzhenGuangdongChina
| | - Anwei Lu
- Department of Obstetrics and GynecologyShenzhen Hospital of Southern Medical UniversityShenzhenGuangdongChina
| | - Jianjun Chen
- School of Pharmaceutical SciencesGuangdong Provincial Key Laboratory of New Drug ScreeningSouthern Medical UniversityGuangzhouGuangdongChina
| | - Xin Li
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Jian Zhang
- School of MedicineSouthern University of Science and TechnologyShenzhenGuangdongChina
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease ResearchShenzhenGuangdongChina
| | - Xia Guo
- Shenzhen Key Laboratory of Viral Oncology; Ministry of Science and InnovationShenzhen HospitalSouthern Medical UniversityShenzhenGuangdongChina
- The Third School of Clinical MedicineSouthern Medical UniversityGuangzhouGuangdongChina
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Yang Z, Wilkinson E, Cui YH, Li H, He YY. NAT10 regulates the repair of UVB-induced DNA damage and tumorigenicity. Toxicol Appl Pharmacol 2023; 477:116688. [PMID: 37716414 PMCID: PMC10591715 DOI: 10.1016/j.taap.2023.116688] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Chemical modifications in messenger RNA (mRNA) regulate gene expression and play critical roles in stress responses and diseases. Recently we have shown that N6-methyladenosine (m6A), the most abundant mRNA modification, promotes the repair of UVB-induced DNA damage by regulating global genome nucleotide excision repair (GG-NER). However, the roles of other mRNA modifications in the UVB-induced damage response remain understudied. N4-acetylcytidine (ac4C) is deposited in mRNA by the RNA-binding acetyltransferase NAT10. This NAT10-mediated ac4C in mRNA has been reported to increase both mRNA stability and translation. However, the role of ac4C and NAT10 in the UVB-induced DNA damage response remains poorly understood. Here we show that NAT10 plays a critical role in the repair of UVB-induced DNA damage lesions through regulating the expression of the key GG-NER gene DDB2. We found that knockdown of NAT10 enhanced the repair of UVB-induced DNA damage lesions by promoting the mRNA stability of DDB2. Our findings are in contrast to the previously reported role of NAT10-mediated ac4C deposition in promoting mRNA stability and may represent a novel mechanism for ac4C in the UVB damage response. Furthermore, NAT10 knockdown in skin cancer cells decreased skin cancer cell proliferation in vitro and tumorigenicity in vivo. Chronic UVB irradiation increases NAT10 protein levels in mouse skin. Taken together, our findings demonstrate a novel role for NAT10 in the repair of UVB-induced DNA damage products by decreasing the mRNA stability of DDB2 and suggest that NAT10 is a potential novel target for preventing and treating skin cancer.
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Affiliation(s)
- Zizhao Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Emma Wilkinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Haixia Li
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USA.
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Wang C, Liu Y, Zhang Y, Wang D, Xu L, Li Z, Bai X, Wang Y. Targeting NAT10 protects against sepsis-induced skeletal muscle atrophy by inhibiting ROS/NLRP3. Life Sci 2023; 330:121948. [PMID: 37467885 DOI: 10.1016/j.lfs.2023.121948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023]
Abstract
AIMS To identify N-acetyltransferase 10 (NAT10) and its downstream signaling pathways in myocytes and skeletal muscle, and to investigate its role in inflammation-induced muscle atrophy. MATERIALS AND METHODS Cecal ligation and puncture models were used to induce sepsis in C57BL/6 mice, which were treated with either a NAT10 inhibitor or a control agent. The therapeutic effect of NAT10 inhibitor was investigated by evaluating the mass, morphology, and molecular characteristics of mouse skeletal muscle. C2C12 cells were stimulated with LPS, and the expression of the NAT10 gene, downstream protein content, and atrophy phenotype were analyzed using a NAT10 inhibitor, to further explore the atrophic effect of NAT10 on C2C12 differentiated myotubes. RESULTS Gene set enrichment analysis revealed that NAT10 expression was elevated in the Lateral femoris muscle of patients with ICUAW. In vitro and in vivo experiments showed that sepsis or LPS induced the upregulation of NAT10 expression in skeletal muscles and C2C12 myotubes. Skeletal muscle mass, tissue morphology, gene expression, and protein content were associated with atrophic response in sepsis models. Remodelin ameliorated the LPS-induced skeletal muscle weight loss, as well as muscular atrophy, and improved survival. Remodelin reversed the atrophy program that was induced by inflammation through the downregulation of the ROS/NLRP3 pathway, along with the inhibition of the expression of MuRF1 and Atrogin-1. CONCLUSION NAT10 is closely related to skeletal muscle atrophy during sepsis. Remodelin improves the survival rate of mice by improving the systemic inflammatory response and skeletal muscle atrophy by downregulating the ROS/NLRP3 signaling pathway.
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Affiliation(s)
- Chuntao Wang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Yukun Liu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Yongsheng Zhang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Dongfang Wang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Ligang Xu
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Zhanfei Li
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Xiangjun Bai
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.
| | - Yuchang Wang
- Trauma Center/Department of Emergency and Traumatic Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.
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44
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Wang F, Tessier AJ, Liang L, Wittenbecher C, Haslam DE, Fernández-Duval G, Heather Eliassen A, Rexrode KM, Tobias DK, Li J, Zeleznik O, Grodstein F, Martínez-González MA, Salas-Salvadó J, Clish C, Lee KH, Sun Q, Stampfer MJ, Hu FB, Guasch-Ferré M. Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals. Nat Commun 2023; 14:5744. [PMID: 37717037 PMCID: PMC10505179 DOI: 10.1038/s41467-023-41515-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023] Open
Abstract
Experimental studies reported biochemical actions underpinning aging processes and mortality, but the relevant metabolic alterations in humans are not well understood. Here we examine the associations of 243 plasma metabolites with mortality and longevity (attaining age 85 years) in 11,634 US (median follow-up of 22.6 years, with 4288 deaths) and 1878 Spanish participants (median follow-up of 14.5 years, with 525 deaths). We find that, higher levels of N2,N2-dimethylguanosine, pseudouridine, N4-acetylcytidine, 4-acetamidobutanoic acid, N1-acetylspermidine, and lipids with fewer double bonds are associated with increased risk of all-cause mortality and reduced odds of longevity; whereas L-serine and lipids with more double bonds are associated with lower mortality risk and a higher likelihood of longevity. We further develop a multi-metabolite profile score that is associated with higher mortality risk. Our findings suggest that differences in levels of nucleosides, amino acids, and several lipid subclasses can predict mortality. The underlying mechanisms remain to be determined.
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Affiliation(s)
- Fenglei Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne-Julie Tessier
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Clemens Wittenbecher
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- SciLifeLab, Division of Food Science and Nutrition, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Danielle E Haslam
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gonzalo Fernández-Duval
- Department of Preventive Medicine and Public Health, Navarra Health Research Institute (IDISNA), University of Navarra, Pamplona, Spain
| | - A Heather Eliassen
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kathryn M Rexrode
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Women's Health, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Deirdre K Tobias
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jun Li
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Oana Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Miguel A Martínez-González
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Preventive Medicine and Public Health, Navarra Health Research Institute (IDISNA), University of Navarra, Pamplona, Spain
- Consorcio CIBER, Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Jordi Salas-Salvadó
- Consorcio CIBER, Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
| | - Clary Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kyu Ha Lee
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qi Sun
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meir J Stampfer
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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45
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Liu R, Wubulikasimu Z, Cai R, Meng F, Cui Q, Zhou Y, Li Y. NAT10-mediated N4-acetylcytidine mRNA modification regulates self-renewal in human embryonic stem cells. Nucleic Acids Res 2023; 51:8514-8531. [PMID: 37497776 PMCID: PMC10484679 DOI: 10.1093/nar/gkad628] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 07/05/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023] Open
Abstract
NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. However, its role in mammalian development remains unclear. Here, we found that NAT10 expression positively correlates with pluripotency in vivo and in vitro. High throughput ac4C-targeted RNA immunoprecipitation sequencing (ac4C-RIP-seq), NaCNBH3-based chemical ac4C sequencing (ac4C-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays revealed noticeable ac4C modifications in transcriptome of hESCs, among which transcripts encoding core pluripotency transcription factors are favorable targets of ac4C modification. Further validation assays demonstrate that genetic inactivation of NAT10, the ac4C writer enzyme, led to ac4C level decrease on target genes, promoted the core pluripotency regulator OCT4 (POU5F1) transcript decay, and finally impaired self-renewal and promoted early differentiation in hESCs. Together, our work presented here elucidates a previously unrecognized interconnectivity between the core pluripotent transcriptional network for the maintenance of human ESC self-renewal and NAT10-catalyzed ac4C RNA epigenetic modification.
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Affiliation(s)
- Rucong Liu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
- Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Zibaguli Wubulikasimu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Runze Cai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Fanyi Meng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Qinghua Cui
- Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
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46
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Ma Y, Fan C, Wang Y, Li W, Jiang H, Yang W. Comprehensive analysis of mRNAs in the cerebral cortex in APP/PS1 double-transgenic mice with Alzheimer's disease based on high-throughput sequencing of N4-acetylcytidine. Funct Integr Genomics 2023; 23:267. [PMID: 37548859 DOI: 10.1007/s10142-023-01192-z] [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: 02/11/2023] [Revised: 07/12/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
N4-acetylcytidine (ac4C), a significant modified nucleoside, participates in the development of many diseases. Messenger RNAs (mRNAs) contain most of the information of the genome and are the molecules that transmit information from genes to proteins. Alzheimer's disease (AD) is a progressive neurodegenerative disease in which fibrillar amyloid plaques are present. However, it remains unknown how mRNA ac4C modification affects the development of AD. In the current study, ac4C-modified mRNAs were comprehensively analyzed in AD mice by ac4C-RIP-seq and RNA-seq. Next, a protein-protein interaction (PPI) network was constructed to examine the relationships between the genes with differential ac4C modification levels and their RNA expression levels. The differentially expressed genes (DEGs) acquired above were subjected to Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to further analyze the molecular mechanisms in AD. In total, 3312 significant ac4C peaks were found on 2512 mRNAs, 1241 of which were hyperacetylated and 1271 of which were hypoacetylated. In addition, 956 mRNAs with differential expression were found, including 520 upregulated mRNAs and 436 downregulated mRNAs. Overall, 134 mRNAs with simultaneous changes at the ac4C levels as well as RNA expression levels were identified via joint analysis. Then, through PPI network construction and functional enrichment analysis, 37 key mRNAs were screened, which were predominantly enriched in GABAergic synapses and the PI3K/AKT signaling pathway. The significant difference in the abundance of mRNA ac4C modification indicates that this modification is associated with AD progression, which may provide insight for more investigations of the potential mechanisms.
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Affiliation(s)
- Yanzhen Ma
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Anhui, China
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Anhui, China
| | - Yongzhong Wang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Anhui, China
| | - Weizu Li
- Department of Pharmacology, Basic Medicine College, Key Laboratory of Anti-Inflammatory and Immunopharmacology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Anhui, China.
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China.
| | - Wenming Yang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China.
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Anhui, China.
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47
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Zheng N, Liu X, Yang Y, Liu Y, Yan F, Zeng Y, Cheng Y, Wu D, Chen C, Wang X. Regulatory roles of NAT10 in airway epithelial cell function and metabolism in pathological conditions. Cell Biol Toxicol 2023; 39:1237-1256. [PMID: 35877022 DOI: 10.1007/s10565-022-09743-z] [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: 03/08/2022] [Accepted: 06/20/2022] [Indexed: 12/01/2022]
Abstract
N-acetyltransferase 10 (NAT10), a nuclear acetyltransferase and a member of the GNAT family, plays critical roles in RNA stability and translation processes as well as cell proliferation. Little is known about regulatory effects of NAT10 in lung epithelial cell proliferation. We firstly investigated NTA10 mRNA expression in alveolar epithelial types I and II, basal, ciliated, club, and goblet/mucous epithelia from heathy and patients with chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung adenocarcinoma, para-tumor tissue, and systemic sclerosis, respectively. We selected A549 cells for representative of alveolar epithelia or H1299 and H460 cells as airway epithelia with different genetic backgrounds and studied dynamic responses of NAT10-down-regulated epithelia to high temperature, lipopolysaccharide, cigarette smoking extract (CSE), drugs, radiation, and phosphoinositide 3-kinase (PI3K) inhibitors at various doses. We also compared transcriptomic profiles between alveolar and airway epithelia, between cells with or without NAT10 down-regulation, between early and late stages, and between challenges. The present study demonstrated that NAT10 expression increased in human lung epithelia and varied among epithelial types, challenges, and diseases. Knockdown of NAT10 altered epithelial mitochondrial functions, dynamic responses to LPS, CSE, or PI3K inhibitors, and transcriptomic phenomes. NAT10 regulates biological phenomes, and behaviors are more complex and are dependent upon multiple signal pathways. Thus, NAT10-associated signal pathways can be a new alternative for understanding the disease and developing new biomarkers and targets.
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Affiliation(s)
- Nannan Zheng
- Department of Respiratory Medicine, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Xuanqi Liu
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Ying Yang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Yifei Liu
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Furong Yan
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Yiming Zeng
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Yunfeng Cheng
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Duojiao Wu
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.
| | - Chengshui Chen
- Department of Respiratory Medicine, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
- Quzhou Hospital of Wenzhou Medical University, Quzhou, Zhejiang Province, China.
| | - Xiangdong Wang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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48
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Wei W, Zhang S, Han H, Wang X, Zheng S, Wang Z, Yang C, Wang L, Ma J, Guo S, Wang J, Liu L, Choe J, Lin S. NAT10-mediated ac4C tRNA modification promotes EGFR mRNA translation and gefitinib resistance in cancer. Cell Rep 2023; 42:112810. [PMID: 37463108 DOI: 10.1016/j.celrep.2023.112810] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/22/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
Aberrant RNA modifications are frequently associated with cancers, while the underlying mechanisms and clinical significance remain poorly understood. Here, we find that the ac4C RNA acetyltransferase NAT10 is significantly upregulated in esophageal cancers (ESCAs) and associated with poor ESCA prognosis. In addition, using ESCA cell lines and mouse models, we confirm the critical functions of NAT10 in promoting ESCA tumorigenesis and progression in vitro and in vivo. Mechanistically, NAT10 depletion reduces the abundance of ac4C-modified tRNAs and decreases the translation efficiencies of mRNAs enriched for ac4C-modified tRNA-decoded codons. We further identify EGFR as a key downstream target that facilitates NAT10's oncogenic functions. In terms of clinical significance, we demonstrate that NAT10 depletion and gefitinib treatment synergistically inhibit ESCA progression in vitro and in vivo. Our data indicate the mechanisms underlying ESCA progression at the layer of mRNA translation control and provide molecular insights for the development of effective cancer therapeutic strategies.
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Affiliation(s)
- Wei Wei
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Shuishen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Hui Han
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaochen Wang
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Siyi Zheng
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zhaoyu Wang
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Chunlong Yang
- Clinical Research Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
| | - Lu Wang
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Jieyi Ma
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Siyao Guo
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, 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
| | - Junho Choe
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Shuibin Lin
- Department of Otolaryngology, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China.
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Jia J, Wei Z, Cao X. EMDL-ac4C: identifying N4-acetylcytidine based on ensemble two-branch residual connection DenseNet and attention. Front Genet 2023; 14:1232038. [PMID: 37519885 PMCID: PMC10372626 DOI: 10.3389/fgene.2023.1232038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/29/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction: N4-acetylcytidine (ac4C) is a critical acetylation modification that has an essential function in protein translation and is associated with a number of human diseases. Methods: The process of identifying ac4C sites by biological experiments is too cumbersome and costly. And the performance of several existing computational models needs to be improved. Therefore, we propose a new deep learning tool EMDL-ac4C to predict ac4C sites, which uses a simple one-hot encoding for a unbalanced dataset using a downsampled ensemble deep learning network to extract important features to identify ac4C sites. The base learner of this ensemble model consists of a modified DenseNet and Squeeze-and-Excitation Networks. In addition, we innovatively add a convolutional residual structure in parallel with the dense block to achieve the effect of two-layer feature extraction. Results: The average accuracy (Acc), mathews correlation coefficient (MCC), and area under the curve Area under curve of EMDL-ac4C on ten independent testing sets are 80.84%, 61.77%, and 87.94%, respectively. Discussion: Multiple experimental comparisons indicate that EMDL-ac4C outperforms existing predictors and it greatly improved the predictive performance of the ac4C sites. At the same time, EMDL-ac4C could provide a valuable reference for the next part of the study. The source code and experimental data are available at: https://github.com/13133989982/EMDLac4C.
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Affiliation(s)
- Jianhua Jia
- *Correspondence: Jianhua Jia, ; Zhangying Wei,
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50
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Luo J, Cao J, Chen C, Xie H. Emerging role of RNA acetylation modification ac4C in diseases: Current advances and future challenges. Biochem Pharmacol 2023; 213:115628. [PMID: 37247745 DOI: 10.1016/j.bcp.2023.115628] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
The oldest known highly conserved modification of RNA, N4-acetylcytidine, is widely distributed from archaea to eukaryotes and acts as a posttranscriptional chemical modification of RNA, contributing to the correct reading of specific nucleotide sequences during translation, stabilising mRNA and improving transcription efficiency. Yeast Kre33 and human NAT10, the only known authors of ac4C, modify tRNA with the help of the Tan1/THUMPD1 adapter to stabilise its structure. Currently, the mRNA for N4-acetylcytidine (ac4C), catalysed by NAT10 (N-acetyltransferase 10), has been implicated in a variety of human diseases, particularly cancer. This article reviews advances in the study of ac4C modification of RNA and the ac4C-related gene NAT10 in normal physiological cell development, cancer, premature disease and viral infection and discusses its therapeutic promise and future research challenges.
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Affiliation(s)
- Jie Luo
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jingsong Cao
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Institute of Clinical Medicine, University of South China, Hengyang 421001, China
| | - Cong Chen
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Haitao Xie
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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