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Modi AD, Zahid H, Southerland AC, Modi DM. Epitranscriptomics and cervical cancer: the emerging role of m 6A, m 5C and m 1A RNA modifications. Expert Rev Mol Med 2024; 26:e20. [PMID: 39377535 PMCID: PMC11488341 DOI: 10.1017/erm.2024.20] [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: 07/01/2023] [Revised: 04/18/2024] [Accepted: 06/25/2024] [Indexed: 10/09/2024]
Abstract
Cervical cancer (CC), one of the most prevalent and detrimental gynaecologic cancers, evolves through genetic and epigenetic alterations resulting in the promotion of oncogenic activity and dysfunction of tumour-suppressing mechanisms. Despite medical advancement, the prognosis for advanced-stage patients remains extremely low due to high recurrence rates and resistance to existing treatments. Thereby, the search for potential prognostic biomarkers is heightened to unravel new modalities of CC pathogenesis and to develop novel anti-cancer therapies. Epitranscriptomic modifications, reversible epigenetic RNA modifications, regulate various biological processes by deciding RNA fate to mediating RNA interactions. This narrative review provides insight into the cellular and molecular roles of endogenous RNA-editing proteins and their associated epitranscriptomic modifications, especially N6-methyladenosine (m6A), 5-methylcytosine (m5C) and N1-methyladenosine (m1A), in governing the development, progression and metastasis of CC. We discussed the in-depth epitranscriptomic mechanisms underlying the regulation of over 50 RNAs responsible for tumorigenesis, proliferation, migration, invasion, survival, autophagy, stemness, epithelial-mesenchymal transition, metabolism (glucose, lipid, glutamate and glutamine), resistance (drug and radiation), angiogenesis and recurrence of CC. Additionally, we provided a concise overview of the therapeutic potential of targeting the altered expression of endogenous RNA-editing proteins and aberrant deposition of RNA modifications on both coding and non-coding RNAs in CC.
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Affiliation(s)
- Akshat D. Modi
- Department of Biological Sciences, University of Toronto, Scarborough, Canada
| | - Hira Zahid
- Department of Biology, University of Toronto, Mississauga, Canada
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2
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Yang W, Zhao Y, Yang Y. Dynamic RNA methylation modifications and their regulatory role in mammalian development and diseases. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2084-2104. [PMID: 38833084 DOI: 10.1007/s11427-023-2526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/15/2023] [Indexed: 06/06/2024]
Abstract
Among over 170 different types of chemical modifications on RNA nucleobases identified so far, RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs, and has been demonstrated to participate in the entire process of RNA metabolism, including transcription, pre-mRNA alternative splicing and maturation, mRNA nucleus export, mRNA degradation and stabilization, mRNA translation. Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins, mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear. Here, we particularly focus on three types of RNA methylations: N6-methylcytosine (m6A), 5-methylcytosine (m5C), and N7-methyladenosine (m7G). We summarize the elements related to their dynamic installment and removal, specific binding proteins, and the development of high-throughput detection technologies. Then, for a comprehensive understanding of their biological significance, we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis, embryonic development, immune system development, as well as disease and tumor progression.
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Affiliation(s)
- Wenlan Yang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Yongliang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Yungui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China.
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3
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Deng Y, Zhou J, Li HB. The physiological and pathological roles of RNA modifications in T cells. Cell Chem Biol 2024; 31:1578-1592. [PMID: 38986618 DOI: 10.1016/j.chembiol.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/20/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
RNA molecules undergo dynamic chemical modifications in response to various external or cellular stimuli. Some of those modifications have been demonstrated to post-transcriptionally modulate the RNA transcription, localization, stability, translation, and degradation, ultimately tuning the fate decisions and function of mammalian cells, particularly T cells. As a crucial part of adaptive immunity, T cells play fundamental roles in defending against infections and tumor cells. Recent findings have illuminated the importance of RNA modifications in modulating T cell survival, proliferation, differentiation, and functional activities. Therefore, understanding the epi-transcriptomic control of T cell biology enables a potential avenue for manipulating T cell immunity. This review aims to elucidate the physiological and pathological roles of internal RNA modifications in T cell development, differentiation, and functionality drawn from current literature, with the goal of inspiring new insights for future investigations and providing novel prospects for T cell-based immunotherapy.
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Affiliation(s)
- Yu Deng
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Zhou
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Geriatrics, Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Chongqing International Institute for Immunology, Chongqing 401320, China.
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4
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Kuszczynska A, Bors M, Podskoczyj K, Leszczynska G. Chemistry of installing epitranscriptomic 5-modified cytidines in RNA oligomers. Org Biomol Chem 2024; 22:7271-7286. [PMID: 39177469 DOI: 10.1039/d4ob01098a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Studies of 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C) and 5-carboxycytidine (ca5C) modifications as products of the 5-methylcytidine (m5C) oxidative demethylation pathway in cellular mRNAs constitute an important element of the new epitranscriptomic field of research. The dynamic process of m5C conversion and final turnover to the parent cytidine is considered a post-transcriptional layer of gene-expression regulation. However, the regulatory mechanism associated with epitranscriptomic cytidine modifications remains largely unknown. Therefore, oligonucleotides containing m5C oxidation products are of great value for the next generation of biochemical, biophysical, and structural studies on their function, metabolism, and contribution to human diseases. Herein, we summarize the synthetic strategies developed for the incorporation of hm5C, f5C and ca5C into RNA oligomers by phosphoramidite chemistry, including post-synthetic C5-cytidine functionalization and enzymatic methods.
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Affiliation(s)
- Anna Kuszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
| | - Milena Bors
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
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Wang F, Mei X, Yang Y, Zhang H, Li Z, Zhu L, Deng S, Wang Y. Non-coding RNA and its network in the pathogenesis of Myasthenia Gravis. Front Mol Biosci 2024; 11:1388476. [PMID: 39318549 PMCID: PMC11420011 DOI: 10.3389/fmolb.2024.1388476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 08/21/2024] [Indexed: 09/26/2024] Open
Abstract
Myasthenia Gravis (MG) is a chronic autoimmune disease that primarily affects the neuromuscular junction, leading to muscle weakness in patients with this condition. Previous studies have identified several dysfunctions in thymus and peripheral blood mononuclear cells (PBMCs), such as the formation of ectopic germinal centers in the thymus and an imbalance of peripheral T helper cells and regulatory T cells, that contribute to the initiation and development of MG. Recent evidences suggest that noncoding RNA, including miRNA, lncRNA and circRNA may play a significant role in MG progression. Additionally, the network between these noncoding RNAs, such as the competing endogenous RNA regulatory network, has been found to be involved in MG progression. In this review, we summarized the roles of miRNA, lncRNA, and circRNA, highlighted their potential application as biomarkers in diagnosing MG, and discussed their potential regulatory networks in the abnormal thymus and PBMCs during MG development.
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Affiliation(s)
- Fuqiang Wang
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoli Mei
- Department of Thoracic Surgery, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, China
| | - Yunhao Yang
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Hanlu Zhang
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Zhiyang Li
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Lei Zhu
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Senyi Deng
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Wang
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
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Teng S, Han C, Zhou J, He Z, Qian W. m 5C RNA methylation: a potential mechanism for infectious Alzheimer's disease. Front Cell Dev Biol 2024; 12:1440143. [PMID: 39175875 PMCID: PMC11338875 DOI: 10.3389/fcell.2024.1440143] [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: 05/30/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder caused by a variety of factors, including age, genetic susceptibility, cardiovascular disease, traumatic brain injury, and environmental factors. The pathogenesis of AD is largely associated with the overproduction and accumulation of amyloid-β peptides and the hyperphosphorylation of tau protein in the brain. Recent studies have identified the presence of diverse pathogens, including viruses, bacteria, and parasites, in the tissues of AD patients, underscoring the critical role of central nervous system infections in inducing pathological changes associated with AD. Nevertheless, it remains unestablished about the specific mechanism by which infections lead to the occurrence of AD. As an important post-transcriptional RNA modification, RNA 5-methylcytosine (m5C) methylation regulates a wide range of biological processes, including RNA splicing, nuclear export, stability, and translation, therefore affecting cellular function. Moreover, it has been recently demonstrated that multiple pathogenic microbial infections are associated with the m5C methylation of the host. However, the role of m5C methylation in infectious AD is still uncertain. Therefore, this review discusses the mechanisms of pathogen-induced AD and summarizes research on the molecular mechanisms of m5C methylation in infectious AD, thereby providing new insight into exploring the mechanism underlying infectious AD.
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Affiliation(s)
- Sisi Teng
- Department of Neurology, Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cunqiao Han
- Department of Emergency, Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Zhou
- Department of Immunology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, Guangdong, China
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Zhenyan He
- Department of Neurosurgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Weiwei Qian
- Department of Emergency, Shangjinnanfu Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Emergency Medicine, Laboratory of Emergency Medicine, West China Hospital, and Disaster Medical Center, Sichuan University, Chengdu, Sichuan, China
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7
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Li Y, Jin H, Li Q, Shi L, Mao Y, Zhao L. The role of RNA methylation in tumor immunity and its potential in immunotherapy. Mol Cancer 2024; 23:130. [PMID: 38902779 PMCID: PMC11188252 DOI: 10.1186/s12943-024-02041-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 06/10/2024] [Indexed: 06/22/2024] Open
Abstract
RNA methylation, a prevalent post-transcriptional modification, has garnered considerable attention in research circles. It exerts regulatory control over diverse biological functions by modulating RNA splicing, translation, transport, and stability. Notably, studies have illuminated the substantial impact of RNA methylation on tumor immunity. The primary types of RNA methylation encompass N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G), and 3-methylcytidine (m3C). Compelling evidence underscores the involvement of RNA methylation in regulating the tumor microenvironment (TME). By affecting RNA translation and stability through the "writers", "erasers" and "readers", RNA methylation exerts influence over the dysregulation of immune cells and immune factors. Consequently, RNA methylation plays a pivotal role in modulating tumor immunity and mediating various biological behaviors, encompassing proliferation, invasion, metastasis, etc. In this review, we discussed the mechanisms and functions of several RNA methylations, providing a comprehensive overview of their biological roles and underlying mechanisms within the tumor microenvironment and among immunocytes. By exploring how these RNA modifications mediate tumor immune evasion, we also examine their potential applications in immunotherapy. This review aims to provide novel insights and strategies for identifying novel targets in RNA methylation and advancing cancer immunotherapy efficacy.
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Affiliation(s)
- Yan Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Qingling Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Liangrong Shi
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Deng T, Wang Z, Geng Q, Wang Z, Jiao Y, Diao W, Xu J, Deng T, Luo J, Tao Q, Xiao C. Methylation of T and B Lymphocytes in Autoimmune Rheumatic Diseases. Clin Rev Allergy Immunol 2024; 66:401-422. [PMID: 39207646 DOI: 10.1007/s12016-024-09003-4] [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] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
The role of abnormal epigenetic modifications, particularly DNA methylation, in the pathogenesis of autoimmune rheumatic diseases (ARDs) has garnered increasing attention. Lymphocyte dysfunction is a significant contributor to the pathogenesis of ARDs. Methylation is crucial for maintaining normal immune system function, and aberrant methylation can hinder lymphocyte differentiation, resulting in functional abnormalities that disrupt immune tolerance, leading to the excessive expression of inflammatory cytokines, thereby exacerbating the onset and progression of ARDs. Recent studies suggest that methylation-related factors have the potential to serve as biomarkers for monitoring the activity of ARDs. This review summarizes the current state of research on the impact of DNA and RNA methylation on the development, differentiation, and function of T and B cells and examines the progress of these epigenetic modifications in studies of six specific ARDs: systemic lupus erythematosus, rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, juvenile idiopathic arthritis, and ankylosing spondylitis. Additionally, we propose that exploring the interplay between RNA methylation and DNA methylation may represent a novel direction for understanding the pathogenesis of ARDs and developing novel treatment strategies.
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Affiliation(s)
- Tiantian Deng
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Zihan Wang
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Qishun Geng
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhaoran Wang
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yi Jiao
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Wenya Diao
- Beijing University of Chinese Medicine, School of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jiahe Xu
- China-Japan Friendship Hospital, Peking University, Beijing, 100029, China
| | - Tingting Deng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Luo
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Qingwen Tao
- Department of TCM Rheumatology, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
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Li L, Xia X, Yang T, Sun Y, Liu X, Xu W, Lu M, Cui D, Wu Y. RNA methylation: A potential therapeutic target in autoimmune disease. Int Rev Immunol 2024; 43:160-177. [PMID: 37975549 DOI: 10.1080/08830185.2023.2280544] [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: 01/19/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and inflammatory bowel disease (IBD) are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is unclear. Numerous studies have demonstrated that RNA methylation plays a key role in disease progression, which is essential for post-transcriptional regulation and has gradually become a broad regulatory mechanism that controls gene expression in various physiological processes, including RNA nuclear output, translation, splicing, and noncoding RNA processing. Here, we outline the writers, erasers, and readers of RNA methylation, including N6-methyladenosine (m6A), 2'-O-methylation (Nm), 2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytidine (m5C) and N7-methylguanosine (m7G). As the role of RNA methylation modifications in the immune system and diseases is explained, the potential treatment value of these modifications has also been demonstrated. This review reports the relationship between RNA methylation and autoimmune diseases, highlighting the need for future research into the therapeutic potential of RNA modifications.
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Affiliation(s)
- Lele Li
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaoping Xia
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Tian Yang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yuchao Sun
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xueke Liu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Wei Xu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mei Lu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Dawei Cui
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
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Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024; 9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.
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Affiliation(s)
- Wei-Wei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Clinical Medicine, Shandong University, Jinan, China
| | - Si-Qing Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Tian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Yun-Fei Fei
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Chen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Shuang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
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11
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Yu T, Nie FQ, Zhang Q, Yu SK, Zhang ML, Wang Q, Wang EX, Lu KH, Sun M. Effects of methionine deficiency on B7H3-DAP12-CAR-T cells in the treatment of lung squamous cell carcinoma. Cell Death Dis 2024; 15:12. [PMID: 38182561 PMCID: PMC10770166 DOI: 10.1038/s41419-023-06376-w] [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: 02/20/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024]
Abstract
Lung squamous cell carcinoma (LUSC) is a subtype of lung cancer for which precision therapy is lacking. Chimeric antigen receptor T-cells (CAR-T) have the potential to eliminate cancer cells by targeting specific antigens. However, the tumor microenvironment (TME), characterized by abnormal metabolism could inhibit CAR-T function. Therefore, the aim of this study was to improve CAR-T efficacy in solid TME by investigating the effects of amino acid metabolism. We found that B7H3 was highly expressed in LUSC and developed DAP12-CAR-T targeting B7H3 based on our previous findings. When co-cultured with B7H3-overexpressing LUSC cells, B7H3-DAP12-CAR-T showed significant cell killing effects and released cytokines including IFN-γ and IL-2. However, LUSC cells consumed methionine (Met) in a competitive manner to induce a Met deficiency. CAR-T showed suppressed cell killing capacity, reduced cytokine release and less central memory T phenotype in medium with lower Met, while the exhaustion markers were up-regulated. Furthermore, the gene NKG7, responsible for T cell cytotoxicity, was downregulated in CAR-T cells at low Met concentration due to a decrease in m5C modification. NKG7 overexpression could partially restore the cytotoxicity of CAR-T in low Met. In addition, the anti-tumor efficacy of CAR-T was significantly enhanced when co-cultured with SLC7A5 knockdown LUSC cells at low Met concentration. In conclusion, B7H3 is a prospective target for LUSC, and B7H3-DAP12-CAR-T cells are promising for LUSC treatment. Maintaining Met levels in CAR-T may help overcome TME suppression and improve its clinical application potential.
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Affiliation(s)
- Tao Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - Feng-Qi Nie
- Department of Oncology, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Qi Zhang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Shao-Kun Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - Mei-Ling Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - Qian Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China
| | - En-Xiu Wang
- Nanjing CART Medical Technology Co., Ltd, Nanjing, China
| | - Kai-Hua Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, China.
| | - Ming Sun
- Suzhou Cancer Center Core Laboratory, Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
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12
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Shan Y, Chen W, Li Y. The role of m 6A RNA methylation in autoimmune diseases: Novel therapeutic opportunities. Genes Dis 2024; 11:252-267. [PMID: 37588214 PMCID: PMC10425809 DOI: 10.1016/j.gendis.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/02/2022] [Accepted: 02/08/2023] [Indexed: 03/29/2023] Open
Abstract
N6-methyladenosine (m6A) modifications, as one of the most common forms of internal RNA chemical modifications in eukaryotic cells, have gained increasing attention in recent years. The m6A RNA modifications exert various crucial roles in various biological processes, such as embryonic development, neurogenesis, circadian rhythms, and tumorigenesis. Recent advances have highlighted that m6A RNA modification plays an important role in immune response, especially in the initiation and progression of autoimmune diseases. In this review, we summarized the regulatory mechanisms of m6A methylation and its biological functions in the immune system and mainly focused on recent progress in research on the potential role of m6A RNA methylation in the pathogenesis of autoimmune diseases, thus providing possible biomarkers and potential targets for the prevention and treatment of autoimmune diseases.
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Affiliation(s)
- Yunan Shan
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, China
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Neuroimmunology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong 250013, China
| | - Wei Chen
- Department of Gastroenterology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Yanbin Li
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Neuroimmunology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong 250013, China
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13
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Liu Y, Zhu E, Lei Y, Luo A, Yan Y, Cai M, Liu S, Huang Y, Guan H, Zhong M, Li W, Lin L, Hultstöm M, Lai E, Zheng Z, Liu X, Tang C. Diagnostic Values of METTL1-Related Genes and Immune Characteristics in Systemic Lupus Erythematosus. J Inflamm Res 2023; 16:5367-5383. [PMID: 38026241 PMCID: PMC10661937 DOI: 10.2147/jir.s431628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Methyltransferase like 1 (METTL1) regulates epitranscriptomes via the m7G modification in mammalian mRNA and microRNA. Systemic lupus erythematosus (SLE) is caused by abnormal immune reactivity and has diverse clinical manifestations. RNA methylation as a mechanism to regulate gene expression is widely implicated in immune regulation. However, the role of m7G in immune response of SLE has not been extensively studied. Patients and Methods Expression of METTL1 was identified in the public dataset GSE122459 and validated in an independent cohort of SLE patients. We investigated the association between METTL1-expression and clinical manifestations of SLE. Subsequently, differentially expressed genes (DEG) that were correlated with METTL1-expression in GSE122459 were used for functional enrichment analysis. The correlation between infiltrating immune cells and METTL1, as well as candidate biomarkers identified to be correlated with either METTL1 or immune cell infiltration were assessed by single-sample GSEA. Potential mechanisms were explored with Gene ontology and KEGG pathway enrichment. Diagnostic performances of candidate biomarkers in SLE were analyzed. Results The mRNA and protein expression of METTL1 in SLE patients were significantly decreased in both datasets. METTL1-coexpressed DEGs were enriched in several key immune-related pathways. Activated CD8 T cells, activated CD4 T cells, memory B cells and type 2 helper T cells were different between patients with high and low METTL1 expression. Further, activated CD8 T-cells, activated CD4 T-cells, memory B-cells were correlated with METTL1. The genes of LAMP3, CD83, PDCD1LG2, IGKVD3D-20, IGKV5-2, IGKV2D-30, IGLV3-19 and IGLV4-60 were identified as candidate targets that were correlated with immune cell proportion. Moreover, LAMP3, CD83, and PDCD1LG2 expression were of diagnostic value in SLE as indicated by ROC analysis. Conclusion Our findings suggested that METTL1 and its candidate targets LAMP3, CD83, PDCD1LG2 may be used for diagnosing SLE and could be explored for developing targeted molecular therapy for SLE.
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Affiliation(s)
- Yu Liu
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Enyi Zhu
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Yan Lei
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Ailing Luo
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Yaping Yan
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Mansi Cai
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Shanshan Liu
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Yan Huang
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, People’s Republic of China
| | - Hui Guan
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Ming Zhong
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Weinian Li
- Department of Rheumatology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, 510623, People’s Republic of China
| | - Lian Lin
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Michael Hultstöm
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Uppsala, Sweden
- Department of Medical Cell Biology, Unit for Integrative Physiology, Uppsala University, Uppsala, Sweden
| | - Enyin Lai
- Department of Physiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, 310058, People’s Republic of China
| | - Zhihua Zheng
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Xiaoping Liu
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Chun Tang
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
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Yu Y, Liang C, Wang X, Shi Y, Shen L. The potential role of RNA modification in skin diseases, as well as the recent advances in its detection methods and therapeutic agents. Biomed Pharmacother 2023; 167:115524. [PMID: 37722194 DOI: 10.1016/j.biopha.2023.115524] [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: 07/04/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023] Open
Abstract
RNA modification is considered as an epigenetic modification that plays an indispensable role in biological processes such as gene expression and genome editing without altering nucleotide sequence, but the molecular mechanism of RNA modification has not been discussed systematically in the development of skin diseases. This article mainly presents the whole picture of theoretical achievements on the potential role of RNA modification in dermatology. Furthermore, this article summarizes the latest advances in clinical practice related with RNA modification, including its detection methods and drug development. Based on this comprehensive review, we aim to illustrate the current blind spots and future directions of RNA modification, which may provide new insights for researchers in this field.
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Affiliation(s)
- Yue Yu
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China; Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Chen Liang
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xin Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China; Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Yuling Shi
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China; Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China.
| | - Liangliang Shen
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China.
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15
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Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [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: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
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Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
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16
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Huang Y, Xue Q, Chang J, Wang Y, Cheng C, Xu S, Wang X, Miao C. M6A methylation modification in autoimmune diseases, a promising treatment strategy based on epigenetics. Arthritis Res Ther 2023; 25:189. [PMID: 37784134 PMCID: PMC10544321 DOI: 10.1186/s13075-023-03149-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/24/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) methylation modification is involved in the regulation of various biological processes, including inflammation, antitumor, and antiviral immunity. However, the role of m6A modification in the pathogenesis of autoimmune diseases has been rarely reported. METHODS Based on a description of m6A modification and the corresponding research methods, this review systematically summarizes current insights into the mechanism of m6A methylation modification in autoimmune diseases, especially its contribution to rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). RESULTS By regulating different biological processes, m6A methylation is involved in the pathogenesis of autoimmune diseases and provides a promising biomarker for the diagnosis and treatment of such diseases. Notably, m6A methylation modification is involved in regulating a variety of immune cells and mitochondrial energy metabolism. In addition, m6A methylation modification plays a role in the pathological processes of RA, and m6A methylation-related genes can be used as potential targets in RA therapy. CONCLUSIONS M6A methylation modification plays an important role in autoimmune pathological processes such as RA and SLE and represents a promising new target for clinical diagnosis and treatment, providing new ideas for the treatment of autoimmune diseases by targeting m6A modification-related pathways.
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Affiliation(s)
- Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, Anhui Province, China
| | - Qiuyun Xue
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, Anhui Province, China
| | - Jun Chang
- Department of Orthopaedics, the First Affiliated Hospital, Anhui Medical University, Hefei, 230032, China.
- Anhui Public Health Clinical Center, Hefei, China.
| | - Yuting Wang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, Anhui Province, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, Anhui Province, China
| | - Suowen Xu
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230027, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, China.
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, Anhui Province, China.
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Zhang Q, Bao X, Cui M, Wang C, Ji J, Jing J, Zhou X, Chen K, Tang L. Identification and validation of key biomarkers based on RNA methylation genes in sepsis. Front Immunol 2023; 14:1231898. [PMID: 37701433 PMCID: PMC10493392 DOI: 10.3389/fimmu.2023.1231898] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Background RNA methylation is closely involved in immune regulation, but its role in sepsis remains unknown. Here, we aim to investigate the role of RNA methylation-associated genes (RMGs) in classifying and diagnosing of sepsis. Methods Five types of RMGs (m1A, m5C, m6Am, m7G and Ψ) were used to identify sepsis subgroups based on gene expression profile data obtained from the GEO database (GSE57065, GSE65682, and GSE95233). Unsupervised clustering analysis was used to identify distinct RNA modification subtypes. The CIBERSORT, WGCNA, GO and KEGG analysis were performed to explore immune infiltration pattern and biological function of each cluster. RF, SVM, XGB, and GLM algorithm were applied to identify the diagnostic RMGs in sepsis. Finally, the expression levels of the five key RMGs were verified by collecting PBMCs from septic patients using qRT-PCR, and their diagnostic efficacy for sepsis was verified in combination with clinical data using ROC analysis. Results Sepsis was divided into three subtypes (cluster 1 to 3). Cluster 1 highly expressed NSUN7 and TRMT6, with the characteristic of neutrophil activation and upregulation of MAPK signaling pathways. Cluster 2 highly expressed NSUN3, and was featured by the regulation of mRNA stability and amino acid metabolism. NSUN5 and NSUN6 were upregulated in cluster 3 which was involved in ribonucleoprotein complex biogenesis and carbohydrate metabolism pathways. In addition, we identified that five RMGs (NSUN7, NOP2, PUS1, PUS3 and FTO) could function as biomarkers for clinic diagnose of sepsis. For validation, we determined that the relative expressions of NSUN7, NOP2, PUS1 and PUS3 were upregulated, while FTO was downregulated in septic patients. The area under the ROC curve (AUC) of NSUN7, NOP2, PUS1, PUS3 and FTO was 0.828, 0.707, 0.846, 0.834 and 0.976, respectively. Conclusions Our study uncovered that dysregulation of RNA methylation genes (m1A, m5C, m6Am, m7G and Ψ) was closely involved in the pathogenesis of sepsis, providing new insights into the classification of sepsis endotypes. We also revealed that five hub RMGs could function as novel diagnostic biomarkers and potential targets for treatment.
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Affiliation(s)
- Qianqian Zhang
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaowei Bao
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Mintian Cui
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chunxue Wang
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Jinlu Ji
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Jiongjie Jing
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaohui Zhou
- Research Center for Translational Medicine, Shanghai Heart Failure Research Center, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
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Abstract
Chemical modifications on mRNA represent a critical layer of gene expression regulation. Research in this area has continued to accelerate over the last decade, as more modifications are being characterized with increasing depth and breadth. mRNA modifications have been demonstrated to influence nearly every step from the early phases of transcript synthesis in the nucleus through to their decay in the cytoplasm, but in many cases, the molecular mechanisms involved in these processes remain mysterious. Here, we highlight recent work that has elucidated the roles of mRNA modifications throughout the mRNA life cycle, describe gaps in our understanding and remaining open questions, and offer some forward-looking perspective on future directions in the field.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA;
| | - Sigrid Nachtergaele
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA;
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Gu X, Ma X, Chen C, Guan J, Wang J, Wu S, Zhu H. Vital roles of m 5C RNA modification in cancer and immune cell biology. Front Immunol 2023; 14:1207371. [PMID: 37325635 PMCID: PMC10264696 DOI: 10.3389/fimmu.2023.1207371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
RNA modification plays an important role in epigenetics at the posttranscriptional level, and 5-methylcytosine (m5C) has attracted increasing attention in recent years due to the improvement in RNA m5C site detection methods. By influencing transcription, transportation and translation, m5C modification of mRNA, tRNA, rRNA, lncRNA and other RNAs has been proven to affect gene expression and metabolism and is associated with a wide range of diseases, including malignant cancers. RNA m5C modifications also substantially impact the tumor microenvironment (TME) by targeting different groups of immune cells, including B cells, T cells, macrophages, granulocytes, NK cells, dendritic cells and mast cells. Alterations in immune cell expression, infiltration and activation are highly linked to tumor malignancy and patient prognosis. This review provides a novel and holistic examination of m5C-mediated cancer development by examining the exact mechanisms underlying the oncogenicity of m5C RNA modification and summarizing the biological effects of m5C RNA modification on tumor cells as well as immune cells. Understanding methylation-related tumorigenesis can provide useful insights for the diagnosis as well as the treatment of cancer.
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Affiliation(s)
- Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Ma
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Guan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haihong Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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20
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Akhil A, Bansal R, Anupam K, Tandon A, Bhatnagar A. Systemic lupus erythematosus: latest insight into etiopathogenesis. Rheumatol Int 2023:10.1007/s00296-023-05346-x. [PMID: 37226016 DOI: 10.1007/s00296-023-05346-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disorder of unknown etiology. Multifactorial interaction among various susceptible factors such as environmental, hormonal, and genetic factors makes it more heterogeneous and complex. Genetic and epigenetic modifications have been realized to regulate the immunobiology of lupus through environmental modifications such as diet and nutrition. Although these interactions may vary from population to population, the understanding of these risk factors can enhance the perception of the mechanistic basis of lupus etiology. To recognize the recent advances in lupus, an electronic search was conducted among search engines such as Google Scholar and PubMed, where we found about 30.4% publications of total studies related to genetics and epigenetics, 33.5% publications related to immunobiology and 34% related to environmental factors. These outcomes suggested that management of diet and lifestyle have a direct relationship with the severity of lupus that influence via modulating the complex interaction among genetics and immunobiology. The present review emphasizes the knowledge about the multifactorial interactions between various susceptible factors based on recent advances that will further update the understanding of mechanisms involved in disease pathoetiology. Knowledge of these mechanisms will further assist in the creation of novel diagnostic and therapeutic options.
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Affiliation(s)
- Akhil Akhil
- Department of Biochemistry, BMS-Block II, South Campus, Panjab University, Chandigarh, 160014, India
| | - Rohit Bansal
- Department of Biochemistry, BMS-Block II, South Campus, Panjab University, Chandigarh, 160014, India
| | - Kumari Anupam
- Department of Pathology, Saint Louis University, St. Louis, MO, 63103, USA
| | - Ankit Tandon
- Department of Endocrinology, PGIMER, Chandigarh, 160012, India
| | - Archana Bhatnagar
- Department of Biochemistry, BMS-Block II, South Campus, Panjab University, Chandigarh, 160014, India.
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Zhao Z, Zhang L, Ocansey DKW, Wang B, Mao F. The role of mesenchymal stem cell-derived exosome in epigenetic modifications in inflammatory diseases. Front Immunol 2023; 14:1166536. [PMID: 37261347 PMCID: PMC10227589 DOI: 10.3389/fimmu.2023.1166536] [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: 02/15/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
Epigenetic modification is a complex process of reversible and heritable alterations in gene function, and the combination of epigenetic and metabolic alterations is recognized as an important causative factor in diseases such as inflammatory bowel disease (IBD), osteoarthritis (OA), systemic lupus erythematosus (SLE), and even tumors. Mesenchymal stem cell (MSC) and MSC-derived exosome (MSC-EXO) are widely studied in the treatment of inflammatory diseases, where they appear to be promising therapeutic agents, partly through the potent regulation of epigenetic modifications such as DNA methylation, acetylation, phosphorylation, and expression of regulatory non-coding RNAs, which affects the occurrence and development of inflammatory diseases. In this review, we summarize the current research on the role of MSC-EXO in inflammatory diseases through their modulation of epigenetic modifications and discuss its potential application in the treatment of inflammatory diseases.
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Affiliation(s)
- Zihan Zhao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Li Zhang
- Nanjing Lishui People’s Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
- Directorate of University Health Services, University of Cape Coast, Cape Coast, Ghana
| | - Bo Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, China
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Ao C, Ye X, Sakurai T, Zou Q, Yu L. m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation. BMC Biol 2023; 21:93. [PMID: 37095510 PMCID: PMC10127088 DOI: 10.1186/s12915-023-01596-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND RNA 5-methyluridine (m5U) modifications are obtained by methylation at the C5 position of uridine catalyzed by pyrimidine methylation transferase, which is related to the development of human diseases. Accurate identification of m5U modification sites from RNA sequences can contribute to the understanding of their biological functions and the pathogenesis of related diseases. Compared to traditional experimental methods, computational methods developed based on machine learning with ease of use can identify modification sites from RNA sequences in an efficient and time-saving manner. Despite the good performance of these computational methods, there are some drawbacks and limitations. RESULTS In this study, we have developed a novel predictor, m5U-SVM, based on multi-view features and machine learning algorithms to construct predictive models for identifying m5U modification sites from RNA sequences. In this method, we used four traditional physicochemical features and distributed representation features. The optimized multi-view features were obtained from the four fused traditional physicochemical features by using the two-step LightGBM and IFS methods, and then the distributed representation features were fused with the optimized physicochemical features to obtain the new multi-view features. The best performing classifier, support vector machine, was identified by screening different machine learning algorithms. Compared with the results, the performance of the proposed model is better than that of the existing state-of-the-art tool. CONCLUSIONS m5U-SVM provides an effective tool that successfully captures sequence-related attributes of modifications and can accurately predict m5U modification sites from RNA sequences. The identification of m5U modification sites helps to understand and delve into the related biological processes and functions.
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Affiliation(s)
- Chunyan Ao
- School of Computer Science and Technology, Xidian University, Xi'an, China
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Tetsuya Sakurai
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, China.
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23
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Construction of a m5C-related long non-coding RNA signature for the prognosis of hepatocellular carcinoma. Hum Cell 2023; 36:712-724. [PMID: 36520346 DOI: 10.1007/s13577-022-00845-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
RNA modification serves as a kind of posttranscriptional modification. Besides N6-methyladenosine (m6A), 5-methylcytosine(m5C) is also an important RNA modification. Long non-coding RNAs (lncRNAs) play an important role in tumor progression. Thus, we performed bioinformatic analysis to establish a m5C-related lncRNA signature(m5ClncSig) for hepatocellular carcinoma (HCC). The RNA sequencing data and clinical data were obtained from The Cancer Genome Atlas (TCGA) database. Pearson correlation coefficient analysis was applied to conduct m5C-related genes and m5C-related lncRNAs co-expressing network. Univariate Cox regression was used to screen the m5C-related lncRNAs with prognosis value. LASSO regression was applied to establish m5ClncSig. Functional analysis including KEGG and GO were performed. The relation between m5ClncSig and immunity was assessed by CIBERSORT and ESTIMATE. RP11-498C9.15 was selected for in vitro validation. A m5ClncSig was established containing 8 lncRNAs with significantly prognosis value. According to risk score calculated by m5ClncSig, high-risk group had worse clinical outcomes than low-risk group. The risk score was validated as an independent prognosis factor. Moreover, the abundances of 11 types of immune cells were significantly different between high-risk group and low-risk group while 8 immune-related genes expressed differently between these two groups. RP11-498C9.15 was validated as a risk factor in HCC progression.
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24
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Yang WL, Qiu W, Zhang T, Xu K, Gu ZJ, Zhou Y, Xu HJ, Yang ZZ, Shen B, Zhao YL, Zhou Q, Yang Y, Li W, Yang PY, Yang YG. Nsun2 coupling with RoRγt shapes the fate of Th17 cells and promotes colitis. Nat Commun 2023; 14:863. [PMID: 36792629 PMCID: PMC9932167 DOI: 10.1038/s41467-023-36595-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
T helper 17 (Th17) cells are a subset of CD4+ T helper cells involved in the inflammatory response in autoimmunity. Th17 cells secrete Th17 specific cytokines, such as IL-17A and IL17-F, which are governed by the master transcription factor RoRγt. However, the epigenetic mechanism regulating Th17 cell function is still not fully understood. Here, we reveal that deletion of RNA 5-methylcytosine (m5C) methyltransferase Nsun2 in mouse CD4+ T cells specifically inhibits Th17 cell differentiation and alleviates Th17 cell-induced colitis pathogenesis. Mechanistically, RoRγt can recruit Nsun2 to chromatin regions of their targets, including Il17a and Il17f, leading to the transcription-coupled m5C formation and consequently enhanced mRNA stability. Our study demonstrates a m5C mediated cell intrinsic function in Th17 cells and suggests Nsun2 as a potential therapeutic target for autoimmune disease.
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Affiliation(s)
- Wen-Lan Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Weinan Qiu
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.,Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Zhang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Kai Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zi-Juan Gu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yu Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Heng-Ji Xu
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Zhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University Medical School, 210093, Nanjing, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Peng-Yuan Yang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China. .,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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25
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Li J, Liu D, Ren J, Li G, Zhao Z, Zhao H, Yan Q, Duan J, Liu Z. Integrated analysis of RNA methylation regulators crosstalk and immune infiltration for predictive and personalized therapy of diabetic nephropathy. Hum Genomics 2023; 17:6. [PMID: 36765416 PMCID: PMC9912588 DOI: 10.1186/s40246-023-00457-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND RNA methylation is a widely known post-transcriptional regulation which exists in many cancer and immune system diseases. However, the potential role and crosstalk of five types RNA methylation regulators in diabetic nephropathy (DN) and immune microenvironment remain unclear. METHODS The mRNA expression of 37 RNA modification regulators and RNA modification regulators related genes were identified in 112 samples from 5 Gene Expression Omnibus datasets. Nonnegative Matrix Factorization clustering method was performed to determine RNA modification patterns. The ssGSEA algorithms and the expression of human leukocyte antigen were employed to assess the immune microenvironment characteristics. Risk model based on differentially expression genes responsible for the modification regulators was constructed to evaluate its predictive capability in DN patients. Furthermore, the results were validated by using immunofluorescence co-localizations and protein experiments in vitro. RESULTS We found 24 RNA methylation regulators were significant differently expressed in glomeruli in DN group compared with control group. Four methylation-related genes and six RNA regulators were introduced into riskScore model using univariate Logistic regression and integrated LASSO regression, which could precisely distinguish the DN and healthy individuals. Group with high-risk score was associated with high immune infiltration. Three distinct RNA modification patterns were identified, which has significant differences in immune microenvironment, biological pathway and eGFR. Validation analyses showed the METTL3, ADAR1, DNMT1 were upregulated whereas YTHDC1 was downregulated in DN podocyte cell lines comparing with cells cultured by the normal glucose. CONCLUSION Our study reveals that RNA methylation regulators and immune infiltration regulation play critical roles in the pathogenesis of DN. The bioinformatic analyses combine with verification in vitro could provide robust evidence for identification of predictive RNA methylation regulators in DN.
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Affiliation(s)
- Jia Li
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Dongwei Liu
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Jingjing Ren
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Guangpu Li
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Zihao Zhao
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Huanhuan Zhao
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Qianqian Yan
- grid.207374.50000 0001 2189 3846Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,grid.412633.10000 0004 1799 0733Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 People’s Republic of China ,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052 People’s Republic of China ,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052 People’s Republic of China
| | - Jiayu Duan
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, People's Republic of China.
| | - Zhangsuo Liu
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Traditional Chinese Medicine Integrated Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China. .,Henan Province Research Center for Kidney Disease, Zhengzhou, 450052, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, 450052, People's Republic of China.
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26
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Mei X, Zhang B, Zhao M, Lu Q. An update on epigenetic regulation in autoimmune diseases. J Transl Autoimmun 2022; 5:100176. [PMID: 36544624 PMCID: PMC9762196 DOI: 10.1016/j.jtauto.2022.100176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 10/09/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Autoimmune diseases (AIDs) generally manifest as chronic immune disorders characterized by significant heterogeneity and complex symptoms. The discordant incidence of AIDs between monozygotic twins guided people to attach importance to environmental factors. Epigenetics is one of the major ways to be influenced, some of them can even occur years before clinical diagnosis. With the advent of high-throughput omics times, the mysterious veil of epigenetic modification in AIDs has been gradually unraveled, and some progress has been made in utilizing it as indicators of diagnosis and disease activity. For example, the hypomethylated IFI44L promoter in diagnosing systematic lupus erythematosus (SLE). More recently, newly identified noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), are also believed to be involved in the etiology of AIDs while the initial factor behind those epigenetic alterations can be diverse from metabolism to microbiota. Update and comprehensive insights into epigenetics in AIDs can help us understand the pathogenesis and further orchestrate it to benefit patients in the future. Therefore, we reviewed the latest epigenetic findings in SLE, rheumatoid arthritis (RA), Type 1 diabetes (T1D), systemic sclerosis (SSc) primarily from cellular levels.
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Affiliation(s)
- Xiaole Mei
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China,Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, Hunan, China
| | - Bo Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China,Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, Hunan, China,Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, Hunan, China,Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China,Corresponding author. Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, Hunan, China.
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China,Institute of Dermatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, Hunan, China,Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China,Corresponding author. Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China.
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27
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:13851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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28
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Zhang Q, Sun X, Sun J, Lu J, Gao X, Shen K, Qin X. RNA m 5C regulator-mediated modification patterns and the cross-talk between tumor microenvironment infiltration in gastric cancer. Front Immunol 2022; 13:905057. [PMID: 36389669 PMCID: PMC9646743 DOI: 10.3389/fimmu.2022.905057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/11/2022] [Indexed: 02/22/2024] Open
Abstract
The effect of immunotherapy strategy has been affirmed in the treatment of various tumors. Nevertheless, the latent role of RNA 5-methylcytosine (m5C) modification in gastric cancer (GC) tumor microenvironment (TME) cell infiltration is still unclear. We systematically explore the m5C modification patterns of 2,122 GC patients from GEO and TCGA databases by 16 m5C regulators and related these patterns to TME characteristics. LASSO Cox regression was employed to construct the m5Cscore based on the expression of regulators and DEGs, which was used to evaluate the prognosis. All the GC patients were divided into three m5C modification clusters with distinct gene expression characteristics and TME patterns. GSVA, ssGSEA, and TME cell infiltration analysis showed that m5C clusters A, B, and C were classified as immune-desert, immune-inflamed, and immune-excluded phenotype, respectively. The m5Cscore system based on the expression of eight genes could effectively predict the prognosis of individual GC patients, with AUC 0.766. Patients with a lower m5Cscore were characterized by the activation of immunity and experienced significantly longer PFS and OS. Our study demonstrated the non-negligible role of m5C modification in the development of TME complexity and inhomogeneity. Assessing the m5C modification pattern for individual GC patients will help recognize the infiltration characterization and guide more effective immunotherapy treatment.
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Affiliation(s)
- Qiang Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Gastrointestinal Surgery, the Second People’s Hospital of Lianyungang Affiliated to Kangda College, Nanjing Medical University, Lianyungang, Jiangsu, China
| | - Xiangfei Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianyi Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiangshen Lu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kuntang Shen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinyu Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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29
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Zha L, Wang J, Cheng X. The effects of
RNA
methylation on immune cells development and function. FASEB J 2022; 36:e22552. [DOI: 10.1096/fj.202200716r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ling‐Feng Zha
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Jing‐Lin Wang
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Xiang Cheng
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
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30
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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RNA methylation in immune cells. Adv Immunol 2022; 155:39-94. [PMID: 36357012 DOI: 10.1016/bs.ai.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Ren H, Liu C, Wu H, Wang Z, Chen S, Zhang X, Ren J, Qiu H, Zhou L. m5C Regulator-mediated methylation modification clusters contribute to the immune microenvironment regulation of multiple myeloma. Front Genet 2022; 13:920164. [PMID: 36092897 PMCID: PMC9453209 DOI: 10.3389/fgene.2022.920164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Multiple myeloma (MM) is a hematological malignancy in which plasma cells proliferate abnormally. 5-methylcytosine (m5C) methylation modification is the primary epigenetic modification and is involved in regulating the occurrence, development, invasion, and metastasis of various tumors; however, its immunological functions have not been systematically described in MM. Thus, this study aimed to clarify the significance of m5C modifications and how the immune microenvironment is linked to m5C methylation in MM.Method: A total of 483 samples (60 healthy samples, 423 MM samples) from the Gene Expression Omnibus dataset were acquired to assess the expression of m5C regulators. A nomogram model was established to predict the occurrence of MM. We investigated the impact of m5C modification on immune microenvironment characteristics, such as the infiltration of immunocytes and immune response reactions. We then systematically evaluated three different m5C expression patterns to assess immune characteristics and metabolic functional pathways and established m5C-related differentially expressed genes (DEGs). In addition, biological process analysis was performed and an m5C score was constructed to identify potentially significant immunological functions in MM.Result: Differential expressions of m5C regulators were identified between healthy and MM samples. The nomogram revealed that m5C regulators could predict higher disease occurrence of MM. We identified three distinct m5C clusters with unique immunological and metabolic characteristics. Among the three different m5C clusters, cluster C had more immune characteristics and more metabolism-related pathways than clusters A and B. We analyzed 256 m5C-related DEGs and classified the samples into three different m5C gene clusters. Based on the m5C and m5C gene clusters, we calculated m5C scores and classified each patient into high- and low-m5C score groups.Conclusion: Our study demonstrated that m5C modification is involved in and contributes to the diversity and complexity of the immune microenvironment, which offers promise for the development of accurate therapeutic strategies.
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Affiliation(s)
- Hefei Ren
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Chang Liu
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Hongkun Wu
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhenhua Wang
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Sai Chen
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiaomin Zhang
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jigang Ren
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Huiying Qiu
- Department of Hematology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Lin Zhou, ; Huiying Qiu,
| | - Lin Zhou
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Lin Zhou, ; Huiying Qiu,
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Zhou H, Mao L, Xu H, Wang S, Tian J. The functional roles of m 6A modification in T lymphocyte responses and autoimmune diseases. Cytokine Growth Factor Rev 2022; 65:51-60. [PMID: 35490098 DOI: 10.1016/j.cytogfr.2022.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/14/2022]
Abstract
RNA N6-methyladenosine (m6A) modification is abundant in eukaryotes, bacteria and archaea. It is an RNA modification mainly existing in messenger RNA (mRNAs) and has a significant effect on the metabolism and function of mRNAs. m6A modification is controlled by three types of proteins, namely methyltransferase as the "writers", demethylase as the "erasers", and specific m6A recognized protein (YTHDF1-3) as the "readers". Recent studies have shown that m6A modification plays an important role in cancer, viral infection and autoimmune diseases. In this review, we will elaborate on the m6A modifications in the homeostasis and differentiation of T cells. Then we will further summarize the effects of m6A modification on the T cell responses and T cell-mediated autoimmune diseases. This will advance T cell epigenetics research and provide potential biomarkers and therapeutic targets for autoimmune diseases.
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Affiliation(s)
- Huimin Zhou
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China.
| | - Huaxi Xu
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shengjun Wang
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Jie Tian
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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Wang R, Guo Y, Ma P, Song Y, Min J, Zhao T, Hua L, Zhang C, Yang C, Shi J, Zhu L, Gan D, Li S, Li J, Su H. Comprehensive Analysis of 5-Methylcytosine (m 5C) Regulators and the Immune Microenvironment in Pancreatic Adenocarcinoma to Aid Immunotherapy. Front Oncol 2022; 12:851766. [PMID: 35433474 PMCID: PMC9009261 DOI: 10.3389/fonc.2022.851766] [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: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
Background Pancreatic adenocarcinoma (PAAD) is one of the most malignant cancers and has a poor prognosis. As a critical RNA modification, 5-methylcytosine (m5C) has been reported to regulate tumor progression, including PAAD progression. However, a comprehensive analysis of m5C regulators in PAAD is lacking. Methods In the present study, PAAD datasets were obtained from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and ArrayExpress databases. The expression pattern of m5C regulators were analyzed and patients were divided into different m5C clusters according to consensus clustering based on m5C regulators. Additionally, m5C differentially expressed genes (DEGs) were determined using Limma package. Based on m5C DEGs, patients were divided into m5C gene clusters. Moreover, m5C gene signatures were derived from m5C DEGs and a quantitative indicator, the m5C score, was developed from the m5C gene signatures. Results Our study showed that m5C regulators were differentially expressed in patients with PAAD. The m5C clusters and gene clusters based on m5C regulators and m5C DEGs were related to immune cell infiltration, immune-related genes and patient survival status, indicating that m5C modification play a central role in regulating PAAD development partly by modulating immune microenvironment. Additionally, a quantitative indicator, the m5C score, was also developed and was related to a series of immune-related indicators. Moreover, the m5C score precisely predicted the immunotherapy response and prognosis of patients with PAAD. Conclusion In summary, we confirmed that m5C regulators regulate PAAD development by modulating the immune microenvironment. In addition, a quantitative indicator, the m5C score, was developed to predict immunotherapy response and prognosis and assisted in identifying PAAD patients suitable for tailored immunotherapy strategies.
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Affiliation(s)
- Ronglin Wang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yongdong Guo
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Peixiang Ma
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yang Song
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jie Min
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Ting Zhao
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Lei Hua
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Chao Zhang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Cheng Yang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jingjie Shi
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Liaoliao Zhu
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Dongxue Gan
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Shanshan Li
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Junqiang Li
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Haichuan Su
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
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Song H, Zhang J, Liu B, Xu J, Cai B, Yang H, Straube J, Yu X, Ma T. Biological roles of RNA m 5C modification and its implications in Cancer immunotherapy. Biomark Res 2022; 10:15. [PMID: 35365216 PMCID: PMC8973801 DOI: 10.1186/s40364-022-00362-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetics including DNA and RNA modifications have always been the hotspot field of life sciences in the post-genome era. Since the first mapping of N6-methyladenosine (m6A) and the discovery of its widespread presence in mRNA, there are at least 160-170 RNA modifications have been discovered. These methylations occur in different RNA types, and their distribution is species-specific. 5-methylcytosine (m5C) has been found in mRNA, rRNA and tRNA of representative organisms from all kinds of species. As reversible epigenetic modifications, m5C modifications of RNA affect the fate of the modified RNA molecules and play important roles in various biological processes including RNA stability control, protein synthesis, and transcriptional regulation. Furthermore, accumulative evidence also implicates the role of RNA m5C in tumorigenesis. Here, we review the latest progresses in the biological roles of m5C modifications and how it is regulated by corresponding "writers", "readers" and "erasers" proteins, as well as the potential molecular mechanism in tumorigenesis and cancer immunotherapy.
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Affiliation(s)
- Hang Song
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Jianye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Bin Liu
- Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Jing Xu
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Biao Cai
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Hai Yang
- Division of Surgical Research, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Julia Straube
- Division of Molecular and Experimental Surgery, Department of Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Xiyong Yu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Teng Ma
- Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
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5-methylcytosine modification by Plasmodium NSUN2 stabilizes mRNA and mediates the development of gametocytes. Proc Natl Acad Sci U S A 2022; 119:2110713119. [PMID: 35210361 PMCID: PMC8892369 DOI: 10.1073/pnas.2110713119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2022] [Indexed: 11/18/2022] Open
Abstract
5-methylcytosine (m5C) is an important epitranscriptomic modification involved in messenger RNA (mRNA) stability and translation efficiency in various biological processes. However, it remains unclear if m5C modification contributes to the dynamic regulation of the transcriptome during the developmental cycles of Plasmodium parasites. Here, we characterize the landscape of m5C mRNA modifications at single nucleotide resolution in the asexual replication stages and gametocyte sexual stages of rodent (Plasmodium yoelii) and human (Plasmodium falciparum) malaria parasites. While different representations of m5C-modified mRNAs are associated with the different stages, the abundance of the m5C marker is strikingly enhanced in the transcriptomes of gametocytes. Our results show that m5C modifications confer stability to the Plasmodium transcripts and that a Plasmodium ortholog of NSUN2 is a major mRNA m5C methyltransferase in malaria parasites. Upon knockout of P. yoelii nsun2 (pynsun2), marked reductions of m5C modification were observed in a panel of gametocytogenesis-associated transcripts. These reductions correlated with impaired gametocyte production in the knockout rodent malaria parasites. Restoration of the nsun2 gene in the knockout parasites rescued the gametocyte production phenotype as well as m5C modification of the gametocytogenesis-associated transcripts. Together with the mRNA m5C profiles for two species of Plasmodium, our findings demonstrate a major role for NSUN2-mediated m5C modifications in mRNA transcript stability and sexual differentiation in malaria parasites.
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Tong J, Zhang W, Chen Y, Yuan Q, Qin NN, Qu G. The Emerging Role of RNA Modifications in the Regulation of Antiviral Innate Immunity. Front Microbiol 2022; 13:845625. [PMID: 35185855 PMCID: PMC8851159 DOI: 10.3389/fmicb.2022.845625] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Posttranscriptional modifications have been implicated in regulation of nearly all biological aspects of cellular RNAs, from stability, translation, splicing, nuclear export to localization. Chemical modifications also have been revealed for virus derived RNAs several decades before, along with the potential of their regulatory roles in virus infection. Due to the dynamic changes of RNA modifications during virus infection, illustrating the mechanisms of RNA epigenetic regulations remains a challenge. Nevertheless, many studies have indicated that these RNA epigenetic marks may directly regulate virus infection through antiviral innate immune responses. The present review summarizes the impacts of important epigenetic marks on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytidine (m5C), 2ʹ-O-methylation (2ʹ-O-Methyl), and a few uncanonical nucleotides (A-to-I editing, pseudouridine), on antiviral innate immunity and relevant signaling pathways, while highlighting the significance of antiviral innate immune responses during virus infection.
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Affiliation(s)
- Jie Tong
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuran Chen
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Qiaoling Yuan
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Ning-Ning Qin
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guosheng Qu
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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38
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Adams DE, Shao WH. Epigenetic Alterations in Immune Cells of Systemic Lupus Erythematosus and Therapeutic Implications. Cells 2022; 11:cells11030506. [PMID: 35159315 PMCID: PMC8834103 DOI: 10.3390/cells11030506] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder that is characterized by autoantibody production and dysregulated immune cell activation. Although the exact etiology of SLE remains unknown, genetic, hormonal, and complex environmental factors are known to be critical for pathologic immune activation. In addition to the inherited genetic predisposition, epigenetic processes that do not change the genomic code, such as DNA methylation, histone modification, and noncoding RNAs are increasingly appreciated to play important roles in lupus pathogenesis. We herein focus on the up-to-date findings of lupus-associated epigenetic alterations and their pathophysiology in lupus development. We also summarize the therapeutic potential of the new findings. It is likely that advances in the epigenetic study will help to predict individual disease outcomes, promise diagnostic accuracy, and design new target-directed immunotherapies.
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Zhou M, Liu W, Zhang J, Sun N. RNA m 6A Modification in Immunocytes and DNA Repair: The Biological Functions and Prospects in Clinical Application. Front Cell Dev Biol 2022; 9:794754. [PMID: 34988083 PMCID: PMC8722703 DOI: 10.3389/fcell.2021.794754] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
As the most prevalent internal modification in mRNA, N6-methyladenosine (m6A) plays broad biological functions via fine-tuning gene expression at the post-transcription level. Such modifications are deposited by methyltransferases (i.e., m6A Writers), removed by demethylases (i.e., m6A Erasers), and recognized by m6A binding proteins (i.e., m6A Readers). The m6A decorations regulate the stability, splicing, translocation, and translation efficiency of mRNAs, and exert crucial effects on proliferation, differentiation, and immunologic functions of immunocytes, such as T lymphocyte, B lymphocyte, dendritic cell (DC), and macrophage. Recent studies have revealed the association of dysregulated m6A modification machinery with various types of diseases, including AIDS, cancer, autoimmune disease, and atherosclerosis. Given the crucial roles of m6A modification in activating immunocytes and promoting DNA repair in cells under physiological or pathological states, targeting dysregulated m6A machinery holds therapeutic potential in clinical application. Here, we summarize the biological functions of m6A machinery in immunocytes and the potential clinical applications via targeting m6A machinery.
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Affiliation(s)
- Mingjie Zhou
- Department of Blood Transfusion, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China.,Department of Immunology, Hebei Medical University, Shijiazhuang, China.,Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Liu
- Department of Immunology, Hebei Medical University, Shijiazhuang, China
| | - Jieyan Zhang
- Department of Orthopaedics, Wuxi Branch of Zhongda Hospital Southeast University, Wuxi, China
| | - Nan Sun
- Department of Blood Transfusion, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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Guo G, Pan K, Fang S, Ye L, Tong X, Wang Z, Xue X, Zhang H. Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:575-593. [PMID: 34631286 PMCID: PMC8479277 DOI: 10.1016/j.omtn.2021.08.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-methylcytosine (m5C) post-transcriptional modifications affect the maturation, stability, and translation of the mRNA molecule. These modifications play an important role in many physiological and pathological processes, including stress response, tumorigenesis, tumor cell migration, embryogenesis, and viral replication. Recently, there has been a better understanding of the biological implications of m5C modification owing to the rapid development and optimization of detection technologies, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-BisSeq. Further, predictive models (such as PEA-m5C, m5C-PseDNC, and DeepMRMP) for the identification of potential m5C modification sites have also emerged. In this review, we summarize the current experimental detection methods and predictive models for mRNA m5C modifications, focusing on their advantages and limitations. We systematically surveyed the latest research on the effectors related to mRNA m5C modifications and their biological functions in multiple species. Finally, we discuss the physiological effects and pathological significance of m5C modifications in multiple diseases, as well as their therapeutic potential, thereby providing new perspectives for disease treatment and prognosis.
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Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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41
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Zhou W, Wang X, Chang J, Cheng C, Miao C. The molecular structure and biological functions of RNA methylation, with special emphasis on the roles of RNA methylation in autoimmune diseases. Crit Rev Clin Lab Sci 2021; 59:203-218. [PMID: 34775884 DOI: 10.1080/10408363.2021.2002256] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic vasculitis are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is complex. RNA methylation is known to play a key role in disease progression as it regulates almost all aspects of RNA processing, including RNA nuclear export, translation, splicing, and noncoding RNA processing. This review summarizes the mechanisms, molecular structures of RNA methylations and their roles in biological functions. Similar to the roles of RNA methylation in cancers, RNA methylation in RA and SLE involves "writers" that deposit methyl groups to form N6-methyladenosine (m6A) and 5-methylcytosine (m5C), "erasers" that remove these modifications, and "readers" that further affect mRNA splicing, export, translation, and degradation. Recent advances in detection methods have identified N1-methyladenosine (m1A), N6,2-O-dimethyladenosine (m6Am), and 7-methylguanosine (m7G) RNA modifications, and their roles in RA and SLE need to be further studied. The relationship between RNA methylation and other autoimmune diseases has not been reported, and the roles and mechanisms of RNA modifications in these diseases need to be explored in the future.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jun Chang
- Department of Orthopaedics, Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Institute of Prevention and Treatment of Rheumatoid Arthritis, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Pharmacy, School of Life and Health Sciences, Anhui University of Science and Technology, Fengyang, Anhui Province, China
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42
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Pan K, Guo G, Xue X. Messenger RNA modifications: clinical clarification and significance. Epigenomics 2021; 13:1901-1903. [PMID: 34676794 DOI: 10.2217/epi-2021-0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, 325035, China
| | - Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research & Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens & Immunity, Department of Microbiology & Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research & Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens & Immunity, Department of Microbiology & Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
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Hu Y, Chen C, Tong X, Chen S, Hu X, Pan B, Sun X, Chen Z, Shi X, Hu Y, Shen X, Xue X, Lu M. NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation. Cell Death Dis 2021; 12:842. [PMID: 34504059 PMCID: PMC8429414 DOI: 10.1038/s41419-021-04127-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/08/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
The 5-methylcytosine (m5C) RNA methyltransferase NSUN2 is involved in the regulation of cell proliferation and metastasis formation and is upregulated in multiple cancers. However, the biological significance of NSUN2 in gastric cancer (GC) and the modification of NSUN2 itself have not been fully investigated. Here, we analyzed the expression level of NSUN2 in tissue microarrays containing 403 GC tissues by immunohistochemistry. NSUN2 was upregulated in GC, and that it was a predictor of poor prognosis. NSUN2 promotes the proliferation, migration, and invasion of GC cells in vitro. We also demonstrated that small ubiquitin-like modifier (SUMO)-2/3 interacts directly with NSUN2 by stabilizing it and mediating its nuclear transport. This facilitates the carcinogenic activity of NSUN2. Furthermore, m5C bisulfite sequencing (Bis-seq) in NSUN2-deficient GC cells showed that m5C-methylated genes are involved in multiple cancer-related signaling pathways. PIK3R1 and PCYT1A may be the target genes that participate in GC progression. Our findings revealed a novel mechanism by which NSUN2 functions in GC progression. This may provide new treatment options for GC patients.
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Affiliation(s)
- Yuanbo Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Chenbin Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Xinya Tong
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Sian Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Xianjing Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Bujian Pan
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Xiangwei Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Zhiyuan Chen
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Xinyu Shi
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
| | - Yingying Hu
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xian Shen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Xiangyang Xue
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Wenzhou Medical University, Wenzhou, China.
| | - Mingdong Lu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.
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44
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Lv X, Liu X, Zhao M, Wu H, Zhang W, Lu Q, Chen X. RNA Methylation in Systemic Lupus Erythematosus. Front Cell Dev Biol 2021; 9:696559. [PMID: 34307373 PMCID: PMC8292951 DOI: 10.3389/fcell.2021.696559] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with complicated clinical manifestations. Although our understanding of the pathogenesis of SLE has greatly improved, the understanding of the pathogenic mechanisms of SLE is still limited by disease heterogeneity, and targeted therapy is still unavailable. Substantial evidence shows that RNA methylation plays a vital role in the mechanisms of the immune response, prompting speculation that it might also be related to the occurrence and development of SLE. RNA methylation has been a hot topic in the field of epigenetics in recent years. In addition to revealing the modification process, relevant studies have tried to explore the relationship between RNA methylation and the occurrence and development of various diseases. At present, some studies have provided evidence of a relationship between RNA methylation and SLE pathogenesis, but in-depth research and analysis are lacking. This review will start by describing the specific mechanism of RNA methylation and its relationship with the immune response to propose an association between RNA methylation and SLE pathogenesis based on existing studies and then discuss the future direction of this field.
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Affiliation(s)
- Xinyi Lv
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaomin Liu
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wuiguang Zhang
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiangmei Chen
- Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
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45
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Paredes JL, Fernandez-Ruiz R, Niewold TB. T Cells in Systemic Lupus Erythematosus. Rheum Dis Clin North Am 2021; 47:379-393. [PMID: 34215369 DOI: 10.1016/j.rdc.2021.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
T-cell dysregulation has been implicated in the loss of tolerance and overactivation of B cells in systemic lupus erythematosus (SLE). Recent studies have identified T-cell subsets and genetic, epigenetic, and environmental factors that contribute to pathogenic T-cell differentiation, as well as disease pathogenesis and clinical phenotypes in SLE. Many therapeutics targeting T-cell pathways are under development, and although many have not progressed in clinical trials, the recent approval of the calcineurin inhibitor voclosporin is encouraging. Further study of T-cell subsets and biomarkers of T-cell action may pave the way for specific targeting of pathogenic T-cell populations in SLE.
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Affiliation(s)
- Jacqueline L Paredes
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, 550 1st Avenue, New York, NY 10016, USA
| | - Ruth Fernandez-Ruiz
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, 550 1st Avenue, New York, NY 10016, USA; Division of Rheumatology, NYU Grossman School of Medicine, 550 1st Avenue, New York, NY 10016, USA
| | - Timothy B Niewold
- Colton Center for Autoimmunity, NYU Grossman School of Medicine, 550 1st Avenue, New York, NY 10016, USA.
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46
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Chen H, Ge XL, Zhang ZY, Liu M, Wu RY, Zhang XF, Xu LP, Cheng HY, Sun XC, Zhu HC. M 5C regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in lung adenocarcinoma. Transl Lung Cancer Res 2021; 10:2172-2192. [PMID: 34164268 PMCID: PMC8182725 DOI: 10.21037/tlcr-21-351] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background In recent years, immunotherapy has made great progress, and the regulatory role of epigenetics has been verified. However, the role of 5-methylcytosine (m5C) in the tumor microenvironment (TME) and immunotherapy response remains unclear. Methods Based on 11 m5C regulators, we evaluated the m5C modification patterns of 572 lung adenocarcinoma (LUAD) patients. The m5C score was constructed by principal component analysis (PCA) algorithms in order to quantify the m5C modification pattern of individual LUAD patients. Results Two m5C methylation modification patterns were identified according to 11 m5C regulators. The two patterns had a remarkably distinct TME immune cell infiltration characterization. Next, 226 differentially expressed genes (DEGs) related to the m5C phenotype were screened. Patients were divided into three different gene cluster subtypes based on these genes, which had different TME immune cell infiltration and prognosis characteristics. The m5C score was constructed to quantify the m5C modification pattern of individual LUAD patients. We found that the high m5C score group had a better prognosis. The role of the m5C score in predicting prognosis was also verified in the dataset GSE31210. Conclusions Our study revealed that m5C modification played a significant role in TME regulation of LUAD. Investigation of the m5C regulation mode may have some implications for tumor immunotherapy in the future.
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Affiliation(s)
- Hui Chen
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao-Lin Ge
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhao-Yue Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Liu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Rui-Yan Wu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Xiao-Fei Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
| | - Li-Ping Xu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Yan Cheng
- Department of Synthetic Internal Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin-Chen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Cheng Zhu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Radiation Oncology, Shanghai, China
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47
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Epigenetics: Roles and therapeutic implications of non-coding RNA modifications in human cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:67-82. [PMID: 34188972 PMCID: PMC8217334 DOI: 10.1016/j.omtn.2021.04.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As next-generation sequencing (NGS) is leaping forward, more than 160 covalent RNA modification processes have been reported, and they are widely present in every organism and overall RNA type. Many modification processes of RNA introduce a new layer to the gene regulation process, resulting in novel RNA epigenetics. The commonest RNA modification includes pseudouridine (Ψ), N 7-methylguanosine (m7G), 5-hydroxymethylcytosine (hm5C), 5-methylcytosine (m5C), N 1-methyladenosine (m1A), N 6-methyladenosine (m6A), and others. In this study, we focus on non-coding RNAs (ncRNAs) to summarize the epigenetic consequences of RNA modifications, and the pathogenesis of cancer, as diagnostic markers and therapeutic targets for cancer, as well as the mechanisms affecting the immune environment of cancer. In addition, we summarize the current status of epigenetic drugs for tumor therapy based on ncRNA modifications and the progress of bioinformatics methods in elucidating RNA modifications in recent years.
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48
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Han Z, Yang B, Wang Y, Zeng X, Tian Z. Identification of Expression Patterns and Potential Prognostic Significance of m 5C-Related Regulators in Head and Neck Squamous Cell Carcinoma. Front Oncol 2021; 11:592107. [PMID: 33912441 PMCID: PMC8072008 DOI: 10.3389/fonc.2021.592107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
5-Methylcytosine (m5C) methylation is a major epigenetic technique of RNA modification and is dynamically mediated by m5C “writers,” “erasers,” and “readers.” m5C RNA modification and its regulators are implicated in the onset and development of many tumors, but their roles in head and neck squamous cell carcinoma (HNSCC) have not yet been completely elucidated. In this study, we examined expression patterns of core m5C regulators in the publicly available HNSCC cohort via bioinformatic methods. The differentially expressed m5C regulators could divide the HNSCC cohort into four subgroups with distinct prognostic characteristics. Furthermore, a three-gene expression signature model, comprised of NSUN5, DNMT1, and DNMT3A, was established to identify individuals with a high or low risk of HNSCC. To explore the underlying mechanism in the prognosis of HNSCC, screening of differentially expressed genes, followed by the analysis of functional and pathway enrichment, from individuals with high- or low-risk HNSCC was performed. The results revealed a critical role for m5C RNA modification in two aspects of HNSCC: (1) dynamic m5C modification contributes to the regulation of HNSCC progression and (2) expression patterns of NSUN5, DNMT1, and DNMT3A help to predict the prognosis of HNSCC.
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Affiliation(s)
- Zhenyuan Han
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China
| | - Biao Yang
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Yu Wang
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China
| | - Xiuxia Zeng
- Department of Stomatology, Putian Hanjiang Hospital, Putian, China
| | - Zhen Tian
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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49
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Chao Y, Li HB, Zhou J. Multiple Functions of RNA Methylation in T Cells: A Review. Front Immunol 2021; 12:627455. [PMID: 33912158 PMCID: PMC8071866 DOI: 10.3389/fimmu.2021.627455] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/22/2021] [Indexed: 01/10/2023] Open
Abstract
RNA modification represents one of the most ubiquitous mechanisms of epigenetic regulation and plays an essential role in modulating cell proliferation, differentiation, fate determination, and other biological activities. At present, over 170 types of RNA modification have been discovered in messenger RNA (mRNA) and noncoding RNA (ncRNA). RNA methylation, as an abundant and widely studied epigenetic modification, is crucial for regulating various physiological or pathological states, especially immune responses. Considering the biological significance of T cells as a defense against viral infection and tumor challenge, in this review, we will summarize recent findings of how RNA methylation regulates T cell homeostasis and function, discuss the open questions in this rapidly expanding field of RNA modification, and provide the theoretical basis and potential therapeutic strategies involving targeting of RNA methylation to orchestrate beneficial T cell immune responses.
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Affiliation(s)
- Yinong Chao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhou
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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50
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Yang H, Chen Y, Xu W, Shao M, Deng J, Xu S, Gao X, Guan S, Wang J, Xu S, Shuai Z, Pan F. Epigenetics of ankylosing spondylitis: Recent developments. Int J Rheum Dis 2021; 24:487-493. [PMID: 33608999 DOI: 10.1111/1756-185x.14080] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory autoimmune disease which mainly affects the spine, sacroiliac joint and peripheral joints. To date, the exact causes and pathogenesis of AS still remain unknown. It is considered that the pathogenesis of AS is associated with genetic, infection, environment, immunity and other factors. Among them, the role of genetic factors in the pathogenesis of AS has been studied most deeply. However, over the past few years, the function of environmental predisposition and epigenetic modification in the pathogenesis of AS has received extensive attention. This paper summarizes the recent progress in the epigenetics of AS, including abnormal epigenetic modifications at AS-associated genomic loci, such as DNA methylation, histone modification, microRNA, and so on. In summary, the findings of this review attempt to explain the role of epigenetic modification in the occurrence and development of AS. Nevertheless, there are still unknown and complicated aspects worth exploring to deepen our understanding of the pathogenesis of AS.
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Affiliation(s)
- Hui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Yuting Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Wei Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Ming Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Jixiang Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Shanshan Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Shiyang Guan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Jinian Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Shengqian Xu
- Department of Rheumatism and Immunity, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zongwen Shuai
- Department of Rheumatism and Immunity, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
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