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Lian Z, Chen R, Xian M, Huang P, Xu J, Xiao X, Ning X, Zhao J, Xie J, Duan J, Li B, Wang W, Shi X, Wang X, Jia N, Chen X, Li J, Yang Z. Targeted inhibition of m6A demethylase FTO by FB23 attenuates allergic inflammation in the airway epithelium. FASEB J 2024; 38:e23846. [PMID: 39093041 DOI: 10.1096/fj.202400545r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/02/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024]
Abstract
Epithelial cells play a crucial role in asthma, contributing to chronic inflammation and airway hyperresponsiveness. m6A modification, which involves key proteins such as the demethylase fat mass and obesity-associated protein (FTO), is crucial in the regulation of various diseases, including asthma. However, the role of FTO in epithelial cells and the development of asthma remains unclear. In this study, we investigated the demethylase activity of FTO using a small-molecule inhibitor FB23 in epithelial cells and allergic inflammation in vivo and in vitro. We examined the FTO-regulated transcriptome-wide m6A profiling by methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-seq under FB23 treatment and allergic inflammation conditions. Immunofluorescence staining was performed to assess the tissue-specific expression of FTO in asthmatic bronchial mucosa. We demonstrated that FB23 alleviated allergic inflammation in IL-4/IL-13-treated epithelial cells and house dust mite (HDM)-induced allergic airway inflammation mouse model. The demethylase activity of FTO contributed to the regulation of TNF-α signaling via NF-κB and epithelial-mesenchymal transition-related pathways under allergic inflammation conditions in epithelial cells. FTO was expressed in epithelial, submucosal gland, and smooth muscle cells in human bronchial mucosa. In conclusion, FB23-induced inhibition of FTO alleviates allergic inflammation in epithelial cells and HDM-induced mice, potentially through diverse cellular processes and epithelial-mesenchymal transition signaling pathways, suggesting that FTO is a potential therapeutic target in asthma management.
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Affiliation(s)
- Zexuan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Mo Xian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Peiying Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Jiahan Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Xiaojun Xiao
- State Key Laboratory of Respiratory Disease Allergy Division at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University, Shenzhen, Guangdong, P.R. China
| | - Xiaoping Ning
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Jin Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Jianlei Xie
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Jielin Duan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Bizhou Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Wanjun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Xu Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Xinru Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Nan Jia
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Xuepeng Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, P.R. China
| | - Jing Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Zhaowei Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
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Chen Q, Ao L, Zhao Q, Tang L, Xiong Y, Yuan Y, Wu X, Xing W, Li Z, Guo W, Liang H, Zheng SG, Lian Q, Lu D, Wan W, Xu X. WTAP/YTHDF1-mediated m 6A modification amplifies IFN-γ-induced immunosuppressive properties of human MSCs. J Adv Res 2024:S2090-1232(24)00256-X. [PMID: 38944238 DOI: 10.1016/j.jare.2024.06.019] [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: 05/14/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
INTRODUCTION The immunosuppressive capacity of mesenchymal stem cells (MSCs) is dependent on the "license" of several pro-inflammatory factors to express immunosuppressive molecular profiles, which determines the therapeutic efficacy of MSCs in immune-mediated inflammatory diseases. Of those, interferon-γ (IFN-γ) is a key inducer for the expression of immunosuppressive molecular profiles; however, the mechanism underlying this effect is unknown. OBJECTIVES To elucidate the regulation mechanism and biological functions of N6-methyladenosine (m6A) modification in the immunosuppressive functions by the IFN-γ-licensing MSCs. METHODS Epitranscriptomic microarray analysis and MeRIP-qPCR assay were performed to identify the regulatory effect of WTAP in the IFN-γ-licensing MSCs. RIP-qPCR, western blot, qRT-PCR and RNA stability assays were used to determine the regulation of WTAP/m6A/YTHDF1 signaling axis in the expression of immunosuppressive molecules. Further, functional capacity of T cells was tested using flow cytometry, and both DSS-induced colitis mice and CIA mice were constructed to clarify the effect of WTAP and YTHDF1 in MSC-mediated immunosuppression. RESULTS We identified that IFN-γ increased the m6A methylation levels of immunosuppressive molecules, while WTAP deficiency abolished the IFN-γ-induced promotion of m6A modification. IFN-γ activated ERK signaling, which induced WTAP phosphorylation. Additionally, the stabilization of WTAP post-transcriptionally increased the mRNA expression of immunosuppressive molecules (IDO1, PD-L1, ICAM1, and VCAM1) in an m6A-YTHDF1-dependent manner; this effect further impacted the immunosuppressive capacity of IFN-γ licensing MSCs on activated T cells. Notably, WTAP/YTHDF1 overexpression enhanced the therapeutic efficacy of IFN-γ licensing MSCs and restructures the ecology of inflammation in both colitis and arthritis models. CONCLUSION Our results showed that m6A modification of IDO1, PD-L1, ICAM1, and VCAM1 mRNA mediated by WTAP-YTHDF1 is involved in the regulation of IFN-γ licensing MSCs immunosuppressive abilities, and shed a light to enhance the clinical therapeutic potential of IFN-γ-licensing MSCs.
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Affiliation(s)
- Quan Chen
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Luoquan Ao
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Qing Zhao
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Lu Tang
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yanli Xiong
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China; Cancer Center, Daping Hospital, Army Medical University, Chongqing, China, No.10 Changjiang Zhi Rd, Yuzhong District, Chongqing 400042, China
| | - Yuchuan Yuan
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Xiaofeng Wu
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Wei Xing
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Zhan Li
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Wei Guo
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Huaping Liang
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Song Guo Zheng
- Department of Immunology, School of Cell and Gene Therapy, Songjiang Research Institute, Shanghai Songjiang District Central Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 201600, China
| | - Qizhou Lian
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China; Cord Blood Bank, Guangzhou Institute of Eugenics and Perinatology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510000, China; State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Di Lu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Weijun Wan
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China.
| | - Xiang Xu
- State Key Laboratory of Trauma and Chemical Poisoning, Department of Stem Cell and Regenerative Medicine, Daping Hospital, Army Medical University, Chongqing 400042, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China; Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing 400038, China.
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Xie S, Kuang W, Guo M, Yang F, Jin H, Chen X, Yi L, Huo C, Xu Z, Lin A, Liu W, Mao J, Shu Q, Zhou T. m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression. J Cell Biol 2024; 223:e202307002. [PMID: 38526325 PMCID: PMC10965392 DOI: 10.1083/jcb.202307002] [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: 07/07/2023] [Revised: 01/07/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
N6, 2'-O-dimethyladenosine (m6Am) is a widespread RNA modification catalyzed by the methyltransferase PCIF1 (phosphorylated CTD interacting factor 1). Despite its prevalence, the biological functions of m6Am in RNA remain largely elusive. Here, we report a critical role of PCIF1-dependent m6Am RNA modification in ciliogenesis in RPE-1 cells. Our findings demonstrate that PCIF1 acts as a negative regulator of ciliation through its m6Am methyltransferase activity. A quantitative proteomic analysis identifies BICD2 as a downstream target of PCIF1, with PCIF1 depletion resulting in a significant increase in BICD2 levels. BICD2 depletion leads to a significant reduction in ciliation. Crucially, the ciliary phenotype in PCIF1-depleted cells is reversed upon BICD2 knockdown. Further investigations reveal that PCIF1 regulates BICD2 protein levels through its m6Am catalytic activity, which reduces the stability and translation efficiency of BICD2 mRNA. Single-base resolution LC-MS analysis identifies the m6Am site on BICD2 mRNA modified by PCIF1. These findings establish the essential involvement of PCIF1-dependent m6Am modification in ciliogenesis.
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Affiliation(s)
- Shanshan Xie
- Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenjun Kuang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Mengzhe Guo
- School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Feng Yang
- Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Jin
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiying Chen
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Li Yi
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Chunxiao Huo
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhangqi Xu
- Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Liu
- Metabolic Medicine Center, International Institutes of Medicine and the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Jianhua Mao
- Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Shu
- Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianhua Zhou
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
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Qian W, Yang L, Li T, Li W, Zhou J, Xie S. RNA modifications in pulmonary diseases. MedComm (Beijing) 2024; 5:e546. [PMID: 38706740 PMCID: PMC11068158 DOI: 10.1002/mco2.546] [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: 06/26/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 05/07/2024] Open
Abstract
Threatening public health, pulmonary disease (PD) encompasses diverse lung injuries like chronic obstructive PD, pulmonary fibrosis, asthma, pulmonary infections due to pathogen invasion, and fatal lung cancer. The crucial involvement of RNA epigenetic modifications in PD pathogenesis is underscored by robust evidence. These modifications not only shape cell fates but also finely modulate the expression of genes linked to disease progression, suggesting their utility as biomarkers and targets for therapeutic strategies. The critical RNA modifications implicated in PDs are summarized in this review, including N6-methylation of adenosine, N1-methylation of adenosine, 5-methylcytosine, pseudouridine (5-ribosyl uracil), 7-methylguanosine, and adenosine to inosine editing, along with relevant regulatory mechanisms. By shedding light on the pathology of PDs, these summaries could spur the identification of new biomarkers and therapeutic strategies, ultimately paving the way for early PD diagnosis and treatment innovation.
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Affiliation(s)
- Weiwei Qian
- Emergency Department of Emergency MedicineLaboratory of Emergency Medicine, West China Hospital, And Disaster Medical, Sichuan UniversityChengduSichuanChina
- Emergency DepartmentShangjinnanfu Hospital, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Lvying Yang
- The Department of Respiratory and Critical Care MedicineThe First Veterans Hospital of Sichuan ProvinceChengduSichuanChina
| | - Tianlong Li
- Department of Critical Care Medicine Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Wanlin Li
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's HospitalShenzhenGuangdongChina
| | - Jian Zhou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National‐Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical SchoolShenzhenChina
- Department of ImmunologyInternational Cancer Center, Shenzhen University Health Science CenterShenzhenGuangdongChina
| | - Shenglong Xie
- Department of Thoracic SurgerySichuan Provincial People's Hospital, University of Electronic Science and Technology of ChinaChengduSichuanChina
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Yao Y, Liu P, Li Y, Wang W, Jia H, Bai Y, Yuan Z, Yang Z. Regulatory role of m 6A epitranscriptomic modifications in normal development and congenital malformations during embryogenesis. Biomed Pharmacother 2024; 173:116171. [PMID: 38394844 DOI: 10.1016/j.biopha.2024.116171] [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: 10/18/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
The discovery of N6-methyladenosine (m6A) methylation and its role in translation has led to the emergence of a new field of research. Despite accumulating evidence suggesting that m6A methylation is essential for the pathogenesis of cancers and aging diseases by influencing RNA stability, localization, transformation, and translation efficiency, its role in normal and abnormal embryonic development remains unclear. An increasing number of studies are addressing the development of the nervous and gonadal systems during embryonic development, but only few are assessing that of the immune, hematopoietic, urinary, and respiratory systems. Additionally, these studies are limited by the requirement for reliable embryonic animal models and the difficulty in collecting tissue samples of fetuses during development. Multiple studies on the function of m6A methylation have used suitable cell lines to mimic the complex biological processes of fetal development or the early postnatal phase; hence, the research is still in the primary stage. Herein, we discuss current advances in the extensive biological functions of m6A methylation in the development and maldevelopment of embryos/fetuses and conclude that m6A modification occurs extensively during fetal development. Aberrant expression of m6A regulators is probably correlated with single or multiple defects in organogenesis during the intrauterine life. This comprehensive review will enhance our understanding of the pivotal role of m6A modifications involved in fetal development and examine future research directions in embryogenesis.
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Affiliation(s)
- Yifan Yao
- Department of Pediatric Surgery, 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
| | - Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, 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.
| | - Zhonghua Yang
- Department of Pediatric Surgery, 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.
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6
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Wesselman HM, Arceri L, Nguyen TK, Lara CM, Wingert RA. Genetic mechanisms of multiciliated cell development: from fate choice to differentiation in zebrafish and other models. FEBS J 2023. [PMID: 37997009 DOI: 10.1111/febs.17012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
Multiciliated cells (MCCS) form bundles of cilia and their activities are essential for the proper development and physiology of many organ systems. Not surprisingly, defects in MCCs have profound consequences and are associated with numerous disease states. Here, we discuss the current understanding of MCC formation, with a special focus on the genetic and molecular mechanisms of MCC fate choice and differentiation. Furthermore, we cast a spotlight on the use of zebrafish to study MCC ontogeny and several recent advances made in understanding MCCs using this vertebrate model to delineate mechanisms of MCC emergence in the developing kidney.
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Affiliation(s)
| | - Liana Arceri
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Caroline M Lara
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, IN, USA
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Xu L, Zhou L, Yan C, Li L. Emerging role of N6-methyladenosine RNA methylation in lung diseases. Exp Biol Med (Maywood) 2022; 247:1862-1872. [PMID: 36278325 PMCID: PMC9679358 DOI: 10.1177/15353702221128564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In recent years, with the increase of air pollution, smoking, aging, and respiratory infection, the incidence rate and mortality of lung diseases are increasing annually, which has become a major hazard to human health. N6-methyladenosine (m6A) RNA methylation is the most abundant modifications in eukaryotes, and such modified RNA can be specifically recognized and combined by m6A recognition proteins and then mediate RNA splicing, maturation, enucleation, degradation, and translation. More and more studies have revealed that the m6A modification is involved in the pathogenesis and development of some diseases; however, the mechanisms of m6A in lung diseases are poorly understood. In this review, we summarize the latest progress in the biological function of m6A modifications in lung diseases and discuss the potential therapeutic and prognostic strategies. The dysregulation of global m6A levels and m6A regulators may affect the occurrence and development of asthma, chronic obstructive pulmonary disease, lung cancer, and other lung diseases through inflammation and immune function. In lung cancer, this modification has an important impact on malignant cell proliferation, migration, invasion, and drug resistance. In addition, abnormally changed m6A-modified proteins in lung cancer tissue samples and circulating tumor cells (CTCs) may be used as diagnostic and prognostic markers of lung cancer. Models composed of multiple m6A regulators can be used to evaluate the risk prediction or prognosis of asthma and pulmonary fibrosis. In general, the in-depth study of m6A modifications is a frontier direction in disease research. It provides novel insights for understanding of the molecular mechanisms underlying disease occurrence, development, and drug resistance, as well as for the development of effective novel therapeutics.
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Affiliation(s)
- Limin Xu
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China
| | - Lingyan Zhou
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China
| | - Chenxin Yan
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Liqin Li
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China,Liqin Li.
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8
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Critical role of m 6A modification in T-helper cell disorders. Mol Immunol 2022; 151:1-10. [PMID: 36058047 DOI: 10.1016/j.molimm.2022.08.015] [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: 05/12/2022] [Revised: 08/08/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022]
Abstract
Diseases with T-helper cell subset imbalance involve multiple systems and organs. In addition to this, the pathogenesis of these diseases is always complex, and involves Th1, Th2, Th9, Th17, Th22, and Tfh cells. T-helper cell subset imbalance mediates immune responses to various pathogenic factors, by secreting specific cytokines. Although several studies have revealed the specific mechanisms of the occurrence and development of these diseases from different aspects, there is still a need for more comprehensive and in-depth studies that can compensate for the corresponding gaps in the diagnosis, targeted therapy, and prognosis of these diseases. N6-methyladenosine(m6A) modification is the most prevalent and abundant post-transcriptional modification in eukaryotic RNAs. In recent years, the critical role of m6A modification has been confirmed in multiple diseases with T-helper cell subset imbalance. m6A modification affects the immune cell development, inflammatory processes, biological behaviour of tumours, and immune response in these diseases. In this review, we focussed on how the enzymes involved in m6A modification, directly or indirectly, influence the pathogenesis and phenotype of various diseases with T-helper cell subset imbalance, and could therefore, serve as potential diagnostic markers and therapeutic targets for these diseases. In addition, this review also discusses the focus of future research in this area. Finally, we summarise the prospects of m6A modification in immunotherapy and chemotherapy.
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9
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Murakami S, Jaffrey SR. Hidden codes in mRNA: Control of gene expression by m 6A. Mol Cell 2022; 82:2236-2251. [PMID: 35714585 DOI: 10.1016/j.molcel.2022.05.029] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022]
Abstract
Information in mRNA has largely been thought to be confined to its nucleotide sequence. However, the advent of mapping techniques to detect modified nucleotides has revealed that mRNA contains additional information in the form of chemical modifications. The most abundant modified nucleotide is N6-methyladenosine (m6A), a methyl modification of adenosine. Although early studies viewed m6A as a dynamic and tissue-specific modification, it is now clear that the mRNAs that contain m6A and the location of m6A in those transcripts are largely universal and are influenced by gene architecture, i.e., the size and location of exons and introns. m6A can affect nuclear processes such as splicing and epigenetic regulation, but the major effect of m6A on mRNAs is to promote degradation in the cytoplasm. m6A marks a functionally related cohort of mRNAs linked to certain biological processes, including cell differentiation and cell fate determination. m6A is also enriched in other cohorts of mRNAs and can therefore affect their respective cellular processes and pathways. Future work will focus on understanding how the m6A pathway is regulated to achieve control of m6A-containing mRNAs.
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Affiliation(s)
- Shino Murakami
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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10
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Lin Q, Ni H, Zheng Z, Zhong J, Nie H. Cross-talk of four types of RNA modification writers defines the immune microenvironment in severe asthma. Ann N Y Acad Sci 2022; 1514:93-103. [PMID: 35506887 DOI: 10.1111/nyas.14782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Adenine modifications, including m6 A, m1 A, APA, and A-to-I modifications, are the most impactful RNA modifications. These modifications are primarily produced by enzymes called writers. The main purpose of this study was to explore the cross-talk and potential roles of these writers in severe asthma. We found 13 RNA writers potentially related to severe asthma and three RNA modification patterns. Cluster 3 showed predominant neutrophil infiltration and C-type lectin receptor signaling; cluster 1 showed predominant innate immune cell infiltration and ubiquitin-proteasome system activation; and cluster 2 did not show obvious immune infiltration characteristics. We found that RNA modification writers modified immune cell-related genes and led to both accumulation of different immune cells in the airways and activation of a series of biological processes, which ultimately leads to severe asthma. TRMT6, WTAP, and TRMT6A were included in a random forest model as predictors. Cromoglicic acid, thioperamide, and fluvastatin were potential drugs for clusters 1, 2, and 3, respectively. We found that cross-talk of RNA modifications is significant in severe asthma, which provides insight into severe asthma pathogenesis and possible treatment avenues.
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Affiliation(s)
- Qibin Lin
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Haiyang Ni
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhishui Zheng
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jieying Zhong
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hanxiang Nie
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, China
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11
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ALKBH3-dependent m1A demethylation of Aurora A mRNA inhibits ciliogenesis. Cell Discov 2022; 8:25. [PMID: 35277482 PMCID: PMC8917145 DOI: 10.1038/s41421-022-00385-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
Primary cilia are antenna-like subcellular structures to act as signaling platforms to regulate many cellular processes and embryonic development. m1A RNA modification plays key roles in RNA metabolism and gene expression; however, the physiological function of m1A modification remains largely unknown. Here we find that the m1A demethylase ALKBH3 significantly inhibits ciliogenesis in mammalian cells by its demethylation activity. Mechanistically, ALKBH3 removes m1A sites on mRNA of Aurora A, a master suppressor of ciliogenesis. Depletion of ALKBH3 enhances Aurora A mRNA decay and inhibits its translation. Moreover, alkbh3 morphants exhibit ciliary defects, including curved body, pericardial edema, abnormal otoliths, and dilation in pronephric ducts in zebrafish embryos, which are significantly rescued by wild-type alkbh3, but not by its catalytically inactive mutant. The ciliary defects caused by ALKBH3 depletion in both vertebrate cells and embryos are also significantly reversed by ectopic expression of Aurora A mRNA. Together, our data indicate that ALKBH3-dependent m1A demethylation has a crucial role in the regulation of Aurora A mRNA, which is essential for ciliogenesis and cilia-associated developmental events in vertebrates.
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12
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Kim H, Jang S, Lee YS. The m6A(m)-independent role of FTO in regulating WNT signaling pathways. Life Sci Alliance 2022; 5:5/5/e202101250. [PMID: 35169043 PMCID: PMC8860091 DOI: 10.26508/lsa.202101250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 01/02/2023] Open
Abstract
FTO and ALKBH5 are the two enzymes responsible for mRNA demethylation. Hence, the functional study of FTO has been focused on its mechanistic role in dynamic mRNA modification, and how this post-transcriptional regulation modulates signaling pathways. Here, we report that the functional landscape of FTO is largely associated with WNT signaling pathways but in a manner that is independent of its enzymatic activity. Re-analyses of public datasets identified the bifurcation of canonical and noncanonical WNT pathways as the major role of FTO. In FTO-depleted cells, we find that the canonical WNT/β-Catenin signaling is attenuated in a non-cell autonomous manner via the up-regulation of DKK1. Simultaneously, this up-regulation of DKK1 promotes cell migration via activating the noncanonical WNT/PCP pathway. Unexpectedly, this regulation of DKK1 is independent of its RNA methylation status but operates at the transcriptional level, revealing a noncanonical function of FTO in gene regulation. In conclusion, this study places the functional context of FTO at the branch point of multiple WNT signaling pathways and extends its mechanistic role in gene regulation.
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Affiliation(s)
- Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul, Korea .,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Soohyun Jang
- Center for RNA Research, Institute for Basic Science, Seoul, Korea.,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Young-Suk Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
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13
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Teng F, Tang W, Wuniqiemu T, Qin J, Zhou Y, Huang X, Wang S, Zhu X, Tang Z, Yi L, Wei Y, Dong J. N 6-Methyladenosine Methylomic Landscape of Lung Tissues in Murine Acute Allergic Asthma. Front Immunol 2021; 12:740571. [PMID: 34737744 PMCID: PMC8560743 DOI: 10.3389/fimmu.2021.740571] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Allergic asthma is well known as a common respiratory disorder comprising an allergic inflammatory nature and excessive immune characteristic. N 6-methyladenosine (m6A) methylation is an RNA epigenetic modification that post-transcriptionally regulates gene expression and function by affecting the RNA fate. Currently, m6A methylation is gaining attention as a mechanism of immunoregulation. However, whether m6A methylation engages the pathological process of asthma remains uncertain. Here, we present the m6A methylomic landscape in the lung tissues of ovalbumin-induced acute asthma mice using MeRIP-seq and RNA-seq. We identified 353 hypermethylated m6A peaks within 329 messenger RNAs (mRNAs) and 150 hypomethylated m6A peaks within 143 mRNAs in the lung tissues of asthmatic mice. These differentially methylated mRNAs were found to be involved in several immune function-relevant signaling pathways. In addition, we predicted 25 RNA-binding proteins that recognize the differentially methylated peak sites by exploring public databases, and the roles of these proteins are mostly related to mRNA biogenesis and metabolism. To further investigate the expression levels of the differentially methylated genes, we performed combined analysis of the m6A methylome and transcriptome data and identified 127 hypermethylated mRNAs (107 high and 20 low expression) and 43 hypomethylated mRNAs with differential expressions (9 high and 34 low expression). Of these, there are a list of mRNAs involved in immune function and regulation. The present results highlight the essential role of m6A methylation in the pathogenesis of asthma.
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Affiliation(s)
- Fangzhou Teng
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Weifeng Tang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Tulake Wuniqiemu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Jingjing Qin
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Yaolong Zhou
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Xi Huang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Shiyuan Wang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Xueyi Zhu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Zhao Tang
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - La Yi
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Ying Wei
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Institutes of Integrative Medicine, Fudan University, Shanghai, China
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14
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RNA m6A Methyltransferase Mettl3 Regulates Spatial Neural Patterning in Xenopus laevis. Mol Cell Biol 2021; 41:e0010421. [PMID: 33972392 DOI: 10.1128/mcb.00104-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most prevalent internal RNA modification and has a widespread impact on mRNA stability and translation. Methyltransferase-like 3 (Mettl3) is a methyltransferase responsible for RNA m6A modification, and it is essential for early embryogenesis before or during gastrulation in mice and zebrafish. However, due to the early embryonic lethality, loss-of-function phenotypes of Mettl3 beyond gastrulation, especially during neurulation stages when spatial neural patterning takes place, remain elusive. Here, we address multiple roles of Mettl3 during Xenopus neurulation in anteroposterior neural patterning, neural crest specification, and neuronal cell differentiation. Knockdown of Mettl3 causes anteriorization of neurulae and tailbud embryos along with the loss of neural crest and neuronal cells. Knockdown of the m6A reader Ythdf1 and mRNA degradation factors, such as 3' to 5' exonuclease complex component Lsm1 or mRNA uridylation enzyme Tut7, also show similar neural patterning defects, suggesting that m6A-dependent mRNA destabilization regulates spatial neural patterning in Xenopus. We also address that canonical WNT signaling is inhibited in Mettl3 morphants, which may underlie the neural patterning defects of the morphants. Altogether, this study reveals functions of Mettl3 during spatial neural patterning in Xenopus.
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