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Yin J, Fu J, Xu J, Chen C, Zhu H, Wang B, Yu C, Yang X, Cai R, Li M, Ji K, Wu W, Zhao Y, Zheng Z, Pu Y, Zheng L. Integrated analysis of m6A regulator-mediated RNA methylation modification patterns and immune characteristics in Sjögren's syndrome. Heliyon 2024; 10:e28645. [PMID: 38596085 PMCID: PMC11002070 DOI: 10.1016/j.heliyon.2024.e28645] [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: 01/23/2023] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
The epigenetic modifier N6-methyladenosine (m6A), recognized as the most prevalent internal modification in messenger RNA (mRNA), has recently emerged as a pivotal player in immune regulation. Its dysregulation has been implicated in the pathogenesis of various autoimmune conditions. However, the implications of m6A modification within the immune microenvironment of Sjögren's syndrome (SS), a chronic autoimmune disorder characterized by exocrine gland dysfunction, remain unexplored. Herein, we leverage an integrative analysis combining public database resources and novel sequencing data to investigate the expression profiles of m6A regulatory genes in SS. Our cohort comprised 220 patients diagnosed with SS and 62 healthy individuals, enabling a comprehensive evaluation of peripheral blood at the transcriptomic level. We report a significant association between SS and altered expression of key m6A regulators, with these changes closely tied to the activation of CD4+ T cells. Employing a random forest (RF) algorithm, we identified crucial genes contributing to the disease phenotype, which facilitated the development of a robust diagnostic model via multivariate logistic regression analysis. Further, unsupervised clustering revealed two distinct m6A modification patterns, which were significantly associated with variations in immunocyte infiltration, immune response activity, and biological function enrichment in SS. Subsequently, we proceeded with a screening process aimed at identifying genes that were differentially expressed (DEGs) between the two groups distinguished by m6A modification. Leveraging these DEGs, we employed weight gene co-expression network analysis (WGCNA) to uncover sets of genes that exhibited strong co-variance and hub genes that were closely linked to m6A modification. Through rigorous analysis, we identified three critical m6A regulators - METTL3, ALKBH5, and YTHDF1 - alongside two m6A-related hub genes, COMMD8 and SRP9. These elements collectively underscore a complex but discernible pattern of m6A modification that appears to be integrally linked with SS's pathogenesis. Our findings not only illuminate the significant correlation between m6A modification and the immune microenvironment in SS but also lay the groundwork for a deeper understanding of m6A regulatory mechanisms. More importantly, the identification of these key regulators and hub genes opens new avenues for the diagnosis and treatment of SS, presenting potential targets for therapeutic intervention.
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Affiliation(s)
- Junhao Yin
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Jiayao Fu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Jiabao Xu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Changyu Chen
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Hanyi Zhu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Baoli Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Chuangqi Yu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Xiujuan Yang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Ruiyu Cai
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Mengyang Li
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Kaihan Ji
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanning Wu
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yijie Zhao
- Department of Oral and Maxillofacial Surgery, Shanghai Stomatological Hospital, Fudan University, 1258 Fuxin Zhong Road, Shanghai 200031, China
| | - Zhanglong Zheng
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Yiping Pu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
| | - Lingyan Zheng
- Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Disease, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
- Shanghai Institute of Stomatology, Shanghai, China
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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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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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Li S, Liu H, Ruan Z, Guo R, Sun C, Tang Y, Huang X, Gao T, Hao S, Li H, Song N, Su Y, Ning F, Li Z, Chang T. Landscape analysis of m6A modification regulators related biological functions and immune characteristics in myasthenia gravis. J Transl Med 2023; 21:166. [PMID: 36864526 PMCID: PMC9983271 DOI: 10.1186/s12967-023-03947-5] [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: 12/26/2022] [Accepted: 02/01/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification has been recognized to play fundamental roles in the development of autoimmune diseases. However, the implication of m6A modification in myasthenia gravis (MG) remains largely unknown. Thus, we aimed to systematically explore the potential functions and related immune characteristics of m6A regulators in MG. METHODS The GSE85452 dataset with MG and healthy samples was downloaded from Gene Expression Omnibus (GEO) database. m6A modification regulators were manually curated. The targets of m6A regulators were obtained from m6A2Target database. The differential expressed m6A regulators in GSE85452 dataset were identified by "limma" package and were validated by RT-PCR. Function enrichment analysis of dysregulated m6A regulators was performed using "clusterProfiler" package. Correlation analysis was applied for analyzing the relationships between m6A regulators and immune characteristics. Unsupervised clustering analysis was used to identify distinct m6A modification subtypes. The differences between subtypes were analyzed, including the expression level of all genes and the enrichment degree of immune characteristics. Weighted gene co-expression network analysis (WGCNA) was conducted to obtain modules associated with m6A modification subtypes. RESULTS We found that CBLL1, RBM15 and YTHDF1 were upregulated in MG samples of GSE85452 dataset, and the results were verified by RT-PCR in blood samples from19 MG patients and 19 controls. The targeted genes common modified by CBLL1, RBM15, and YTHDF1 were mainly enriched in histone modification and Wnt signaling pathway. Correlation analysis showed that three dysregulated m6A regulators were closely associated with immune characteristics. Among them, RBM15 possessed the strongest correlation with immune characteristics, including CD56dim natural killer cell (r = 0.77, P = 0.0023), T follicular helper cell (r = - 0.86, P = 0.0002), Interferon Receptor (r = 0.78, P = 0.0017), and HLA-DOA (r = 0.64, P = 0.0200). Further two distinct m6A modification patterns mediated by three dysregulated m6A regulators was identified. Bioinformatics analysis found that there were 3029 differentially expressed genes and different immune characteristics between two m6A modification patterns. Finally, WGCNA analysis obtained a total of 12 modules and yellow module was the most positively correlated to subtype-2. CONCLUSION Our findings suggested that m6A RNA modification had an important effect on immunity molecular mechanism of MG and provided a new perspective into understanding the pathogenesis of MG.
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Affiliation(s)
- Shuang Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Hui Liu
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.,Xi'an Medical University, Xi'an, 710021, Shaanxi, China
| | - Zhe Ruan
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Rongjing Guo
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Chao Sun
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yonglan Tang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiaoxi Huang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Gao
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Sijia Hao
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Huanhuan Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Na Song
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yue Su
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Fan Ning
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Zhuyi Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.
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Zhang TP, Li R, Wang LJ, Li HM. Impact of m6A demethylase (ALKBH5, FTO) genetic polymorphism and expression levels on the development of pulmonary tuberculosis. Front Cell Infect Microbiol 2022; 12:1074380. [PMID: 36619747 PMCID: PMC9817133 DOI: 10.3389/fcimb.2022.1074380] [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: 10/19/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Objective The m6A methylation was involved in the pathogenesis of pulmonary tuberculosis (PTB), and our study aimed to reveal the potential association of m6A demethylase (ALKBH5, FTO) genes variation, expression levels and PTB. Methods Eight SNPs (ALKBH5 gene rs8400, rs9913266, rs12936694, rs4925144 and FTO gene rs6499640, rs8047395, rs1121980, rs9939609) were selected for genotyping by SNPscan technique in 449 PTB patients and 463 healthy controls. Results The mRNA expression levels of ALKBH5, FTO were detected by qRT-PCR. There were no significant differences in genotype, allele distributions of all SNPs between PTB patients and healthy controls. Haplotype analysis demonstrated that the frequency of FTO gene GAAA haplotype was significantly reduced in PTB patients when compared to controls. ALKBH5 rs8400 AA genotype, A allele frequencies were associated with the decreased risk of sputum smear-positive, while AA genotype frequency was related to the increased risk of hypoproteinemia in PTB patients. In addition, rs9913266 variant was linked to the occurrence of drug-induced liver injury, sputum smear-positive, and rs4925144 variant was associated with leukopenia among PTB patients. In FTO gene, rs8047395 GG genotype and G allele frequencies were significantly higher in the PTB patients with drug resistance than that in the PTB patients without drug resistance. The ALKBH5, FTO expression levels were significantly decreased in PTB patients in comparison to controls. Moreover, ALKBH5 level was increased in PTB patients with drug resistance, and FTO level was decreased in PTB patients with sputum smear-positive. Conclusion FTO gene polymorphisms might be associated with PTB susceptibility, and ALKBH5, FTO levels were decreased in PTB patients, suggesting that these m6A demethylase played important roles in PTB.
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Affiliation(s)
- Tian-Ping Zhang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Rui Li
- Department of Nosocomial Infection Management, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li-Jun Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hong-Miao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China,*Correspondence: Hong-Miao Li,
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Critical role of m 6A modification in T-helper cell disorders. Mol Immunol 2022; 151:1-10. [PMID: 36058047 DOI: 10.1016/j.molimm.2022.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/08/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022]
Abstract
Diseases with T-helper cell subset imbalance involve multiple systems and organs. In addition to this, the pathogenesis of these diseases is always complex, and involves Th1, Th2, Th9, Th17, Th22, and Tfh cells. T-helper cell subset imbalance mediates immune responses to various pathogenic factors, by secreting specific cytokines. Although several studies have revealed the specific mechanisms of the occurrence and development of these diseases from different aspects, there is still a need for more comprehensive and in-depth studies that can compensate for the corresponding gaps in the diagnosis, targeted therapy, and prognosis of these diseases. N6-methyladenosine(m6A) modification is the most prevalent and abundant post-transcriptional modification in eukaryotic RNAs. In recent years, the critical role of m6A modification has been confirmed in multiple diseases with T-helper cell subset imbalance. m6A modification affects the immune cell development, inflammatory processes, biological behaviour of tumours, and immune response in these diseases. In this review, we focussed on how the enzymes involved in m6A modification, directly or indirectly, influence the pathogenesis and phenotype of various diseases with T-helper cell subset imbalance, and could therefore, serve as potential diagnostic markers and therapeutic targets for these diseases. In addition, this review also discusses the focus of future research in this area. Finally, we summarise the prospects of m6A modification in immunotherapy and chemotherapy.
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Song RH, Gao CQ, Zhao J, Zhang JA. An Update Evolving View of Copy Number Variations in Autoimmune Diseases. Front Genet 2022; 12:794348. [PMID: 35126462 PMCID: PMC8810490 DOI: 10.3389/fgene.2021.794348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023] Open
Abstract
Autoimmune diseases (AIDs) usually share possible common mechanisms, i.e., a defect in the immune tolerance exists due to diverse causes from central and peripheral tolerance mechanisms. Some genetic variations including copy number variations (CNVs) are known to link to several AIDs and are of importance in the susceptibility to AIDs and the potential therapeutic responses to medicines. As an important source of genetic variants, DNA CNVs have been shown to be very common in AIDs, implying these AIDs may possess possible common mechanisms. In addition, some CNVs are differently distributed in various diseases in different ethnic populations, suggesting that AIDs may have their own different phenotypes and different genetic and/or environmental backgrounds among diverse populations. Due to the continuous advancement in genotyping technology, such as high-throughput whole-genome sequencing method, more susceptible variants have been found. Moreover, further replication studies should be conducted to confirm the results of studies with different ethnic cohorts and independent populations. In this review, we aim to summarize the most relevant data that emerged in the past few decades on the relationship of CNVs and AIDs and gain some new insights into the issue.
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Chen Y, Shen M, Ji C, Huang Y, Shi Y, Ji L, Qin Y, Gu Y, Fu Q, Chen H, Xu K, Yang T. Genome-Wide Identification of N6-Methyladenosine Associated SNPs as Potential Functional Variants for Type 1 Diabetes. Front Endocrinol (Lausanne) 2022; 13:913345. [PMID: 35784577 PMCID: PMC9243540 DOI: 10.3389/fendo.2022.913345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES N6-methyladenosine (m6A) is essential in the regulation of the immune system, but the role that its single nucleotide polymorphisms (SNPs) play in the pathogenesis of type 1 diabetes (T1D) remains unknown. This study demonstrated the association between genetic variants in m6A regulators and T1D risk based on a case-control study in a Chinese population. METHODS The tagging SNPs in m6A regulators were genotyped in 1005 autoantibody-positive patients with T1D and 1257 controls using the Illumina Human OmniZhongHua-8 platform. Islet-specific autoantibodies were examined by radioimmunoprecipitation in all the patients. The mixed-meal glucose tolerance test was performed on 355 newly diagnosed patients to evaluate their residual islet function. The functional annotations for the identified SNPs were performed in silico. Using 102 samples from a whole-genome expression microarray, key signaling pathways associated with m6A regulators in T1D were comprehendingly evaluated. RESULTS Under the additive model, we observed three tag SNPs in the noncoding region of the PRRC2A (rs2260051, rs3130623) and YTHDC2 (rs1862315) gene are associated with T1D risk. Although no association was found between these SNPs and islet function, patients carrying risk variants had a higher positive rate for ZnT8A, GADA, and IA-2A. Further analyses showed that rs2260051[T] was associated with increased expression of PRRC2A mRNA (P = 7.0E-13), and PRRC2A mRNA was significantly higher in peripheral blood mononuclear cell samples from patients with T1D compared to normal samples (P = 0.022). Enrichment analyses indicated that increased PRRC2A expression engages in the most significant hallmarks of cytokine-cytokine receptor interaction, cell adhesion and chemotaxis, and neurotransmitter regulation pathways. The potential role of increased PRRC2A in disrupting immune homeostasis is through the PI3K/AKT pathway and neuro-immune interactions. CONCLUSION This study found intronic variants in PRRC2A and YTHDC2 associated with T1D risk in a Chinese Han population. PRRC2A rs2260051[T] may be implicated in unbalanced immune homeostasis by affecting the expression of PRRC2A mRNA. These findings enriched our understanding of m6A regulators and their intronic SNPs that underlie the pathogenesis of T1D.
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Affiliation(s)
- Yang Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Shen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen Ji
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yanqian Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yun Shi
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Ji
- Department of Emergency Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Qin
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Gu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Fu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Chen
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kuanfeng Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tao Yang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Tao Yang,
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Wang Y, Li L, Li J, Zhao B, Huang G, Li X, Xie Z, Zhou Z. The Emerging Role of m6A Modification in Regulating the Immune System and Autoimmune Diseases. Front Cell Dev Biol 2021; 9:755691. [PMID: 34869344 PMCID: PMC8635162 DOI: 10.3389/fcell.2021.755691] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/28/2021] [Indexed: 12/30/2022] Open
Abstract
Over the past several decades, RNA modifications have rapidly emerged as an indispensable topic in epitranscriptomics. N6-methyladenosine (m6A), namely, methylation at the sixth position of an adenine base in an RNA molecule, is the most prevalent RNA modification in both coding and noncoding RNAs. m6A has emerged as a crucial posttranscriptional regulator involved in both physiological and pathological processes. Based on accumulating evidence, m6A participates in the pathogenesis of immune-related diseases by regulating both innate and adaptive immune cells through various mechanisms. Autoimmune diseases are caused by a self-destructive immune response in the setting of genetic and environmental factors, and recent studies have discovered that m6A may play an essential role in the development of autoimmune diseases. In this review, we focus on the important role of m6A modification in biological functions and highlight its contributions to immune cells and the development of autoimmune diseases, thereby providing promising epitranscriptomic targets for preventing and treating autoimmune disorders.
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Affiliation(s)
- Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Bin Zhao
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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