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Xia X, Qu R. The Roles of RNA N6-methyladenosine Modifications in Systemic Lupus Erythematosus. Cell Biochem Biophys 2024:10.1007/s12013-024-01464-w. [PMID: 39095568 DOI: 10.1007/s12013-024-01464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
N6-methyladenosine (m6A) modification is the most widespread RNA internal modification involved in RNA metabolism. M6A regulators consist of writers, erasers and readers. They exert their function by methylation, demethylation and recognization respectively, participating in cell biology and immune responses. Previously, the focus of m6A modification is its effect on tumor progress. Currently, extensive m6A-related studies have been performed in autoimmune diseases, such as RA, IBD and SLE, revealing that the unique influence of m6A modification in autoimmunity is undeniable. In this review, we summarize the function of m6A regulators, analyze their roles in pathogenic immune cells, summarize the m6A modification in SLE, and provide the potential m6A-targeting therapies for autoimmune diseases.
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Affiliation(s)
- Xin Xia
- School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Rui Qu
- Faculty of Civil Engineering and Mechanics, Jiangsu University, Zhenjiang, 212013, China.
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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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Li D, Li Y, Zhu K, Yuan Y, He Z, Sun Q, Jin M. Analysis of m6A-regulated genes and subtype classification in lupus nephritis. BMC Nephrol 2024; 25:119. [PMID: 38570749 PMCID: PMC10988804 DOI: 10.1186/s12882-024-03549-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/18/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Lupus nephritis (LN) is the most common and severe clinical manifestation of systemic lupus erythematosus (SLE). N6-methyladenosine (m6A) is a reversible RNA modification and has been implicated in various biological processes. However, the roles of m6A regulators in LN are not fully demonstrated. METHODS We downloaded the kidney tissue transcriptome dataset of LN patients and normal controls from the GEO database and extracted the expression levels of m6A regulators. We constructed and compared Random Forest (RF) and Support Vector Machine (SVM) models, and subsequently selected featured genes to develop nomogram models. The m6A subtypes were identified based on significantly differentially expressed m6A regulators, and the m6A gene subtypes were identified based on m6A-associated differential genes, and the two m6A modification patterns were comprehensively evaluated. RESULTS We obtained the GSE32591 and GSE112943 datasets from the GEO database, including 78 LN samples and 36 normal control samples. We extracted the expression levels of 20 m6A regulators. By RF analysis we identified 7 characteristic m6A regulators and constructed nomogramh models with these 7 genes. We identified two m6A subtypes based on these seven important m6A regulators, and the immune cell infiltration levels of the two subtype clusters were significantly different. We identified two more m6A gene subtypes based on m6A-associated DEGs. We calculated the m6A scores using the principal component analysis (PCA) algorithm and found that the m6A scores of m6A cluster A and gene cluster A were lower than those of m6A cluster B and gene cluster B. In addition, we found that the levels of inflammatory factors were also significantly different between m6A clusters and gene clusters. CONCLUSION This study confirms that m6A regulators are involved in the LN process through different modes of action and provide new diagnostic and therapeutic targets for LN.
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Affiliation(s)
- Diangeng Li
- Department of Nephrology, Beijing-Chaoyang Hospital, Capital Medical University, 100020, Beijing, China.
| | - Yanchun Li
- Department of Nephrology, Beijing-Chaoyang Hospital, Capital Medical University, 100020, Beijing, China
| | - Kaiyi Zhu
- Department of Nephrology, Beijing-Chaoyang Hospital, Capital Medical University, 100020, Beijing, China
| | - Yuqing Yuan
- Department of Nephrology, Beijing-Chaoyang Hospital, Capital Medical University, 100020, Beijing, China
| | - Zheng He
- Department of Clinical Laboratory, Chinese PLA General Hospital, 100853, Beijing, China
| | - Qianmei Sun
- Department of Nephrology, Beijing-Chaoyang Hospital, Capital Medical University, 100020, Beijing, China.
| | - Meiling Jin
- Department of Nephrology, Beijing-Chaoyang Hospital, Capital Medical University, 100020, Beijing, China.
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Qi S, Song J, Chen L, Weng H. The role of N-methyladenosine modification in acute and chronic kidney diseases. Mol Med 2023; 29:166. [PMID: 38066436 PMCID: PMC10709953 DOI: 10.1186/s10020-023-00764-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
N6-methyladenosine (m6A) modification is a kind of RNA modification in which methylation occurs at the sixth N position in adenosine in RNA, which can occur in various RNAs such as mRNAs, lncRNAs and miRNAs. This is one of the most prominent and frequent posttranscriptional modifications within organisms and has been shown to function dynamically and reversibly in a variety of ways, including splicing, export, attenuation and translation initiation efficiency to regulate RNA expression. There are three main enzymes associated with m6A modification: writers, readers and erasers. Increasing evidence has shown that m6A modification is associated with the onset and development of kidney disease. In this article, we address the important physiological and pathological roles of m6A modification in kidney diseases (uremia, ischemia-reperfusion kidney injury, drug-induced kidney injury, and diabetic nephropathy) and its molecular mechanisms to provide reference for the diagnosis and clinical management of kidney diseases.
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Affiliation(s)
- Saiqi Qi
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, People's Republic of China
| | - Jie Song
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, People's Republic of China
| | - Linjun Chen
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, People's Republic of China.
| | - Huachun Weng
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Highway, Pudong New Area, Shanghai, 201318, People's Republic of China.
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Sun Y, Jin D, Zhang Z, Ji H, An X, Zhang Y, Yang C, Sun W, Zhang Y, Duan Y, Kang X, Jiang L, Zhao X, Lian F. N6-methyladenosine (m6A) methylation in kidney diseases: Mechanisms and therapeutic potential. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194967. [PMID: 37553065 DOI: 10.1016/j.bbagrm.2023.194967] [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: 03/27/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The N6-methyladenosine (m6A) modification is regulated by methylases, commonly referred to as "writers," and demethylases, known as "erasers," leading to a dynamic and reversible process. Changes in m6A levels have been implicated in a wide range of cellular processes, including nuclear RNA export, mRNA metabolism, protein translation, and RNA splicing, establishing a strong correlation with various diseases. Both physiologically and pathologically, m6A methylation plays a critical role in the initiation and progression of kidney disease. The methylation of m6A may also facilitate the early diagnosis and treatment of kidney diseases, according to accumulating research. This review aims to provide a comprehensive overview of the potential role and mechanism of m6A methylation in kidney diseases, as well as its potential application in the treatment of such diseases. There will be a thorough examination of m6A methylation mechanisms, paying particular attention to the interplay between m6A writers, m6A erasers, and m6A readers. Furthermore, this paper will elucidate the interplay between various kidney diseases and m6A methylation, summarize the expression patterns of m6A in pathological kidney tissues, and discuss the potential therapeutic benefits of targeting m6A in the context of kidney diseases.
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Affiliation(s)
- Yuting Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - De Jin
- Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Ziwei Zhang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Hangyu Ji
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuedong An
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuehong Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cunqing Yang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenjie Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Duan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaomin Kang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Jiang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuefei Zhao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengmei Lian
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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Yakupova EI, Abramicheva PA, Bocharnikov AD, Andrianova NV, Plotnikov EY. Biomarkers of the End-Stage Renal Disease Progression: Beyond the GFR. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1622-1644. [PMID: 38105029 DOI: 10.1134/s0006297923100164] [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: 04/22/2023] [Revised: 07/20/2023] [Accepted: 08/20/2023] [Indexed: 12/19/2023]
Abstract
Chronic kidney disease can progress to the end-stage renal disease (ESRD) characterized by a high risk of morbidity and mortality. ESRD requires immediate therapy or even dialysis or kidney transplantation, therefore, its timely diagnostics is critical for many patients. ESRD is associated with pathological changes, such as inflammation, fibrosis, endocrine disorders, and epigenetic changes in various cells, which could serve as ESRD markers. The review summarizes information on conventional and new ESRD biomarkers that can be assessed in kidney tissue, blood, and urine. Some biomarkers are specific to a particular pathology, while others are more universal. Here, we suggest several universal inflammatory, fibrotic, hormonal, and epigenetic markers indicative of severe deterioration of renal function and ESRD progression for improvement of ESRD diagnostics.
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Affiliation(s)
- Elmira I Yakupova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Polina A Abramicheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexey D Bocharnikov
- International School of Medicine of the Future, Sechenov First Moscow State Medical University, Moscow, 119992, Russia
| | - Nadezda V Andrianova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Egor Y Plotnikov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Moscow, 117997, Russia
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You L, Han Z, Chen H, Chen L, Lin Y, Wang B, Fan Y, Zhang M, Luo J, Peng F, Ma Y, Wang Y, Yuan L, Han Z. The role of N6-methyladenosine (m 6A) in kidney diseases. Front Med (Lausanne) 2023; 10:1247690. [PMID: 37841018 PMCID: PMC10569431 DOI: 10.3389/fmed.2023.1247690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/01/2023] [Indexed: 10/17/2023] Open
Abstract
Chemical modifications are a specific and efficient way to regulate the function of biological macromolecules. Among them, RNA molecules exhibit a variety of modifications that play important regulatory roles in various biological processes. More than 170 modifications have been identified in RNA molecules, among which the most common internal modifications include N6-methyladenine (m6A), n1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanine nucleotide (m7G). The most widely affected RNA modification is m6A, whose writers, readers, and erasers all have regulatory effects on RNA localization, splicing, translation, and degradation. These functions, in turn, affect RNA functionality and disease development. RNA modifications, especially m6A, play a unique role in renal cell carcinoma disease. In this manuscript, we will focus on the biological roles of m6A in renal diseases such as acute kidney injury, chronic kidney disease, lupus nephritis, diabetic kidney disease, and renal cancer.
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Affiliation(s)
- Luling You
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhongyu Han
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Haoran Chen
- Science and Education Department, Chengdu Xinhua Hospital, Chengdu, China
| | - Liuyan Chen
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yumeng Lin
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Binjian Wang
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yiyue Fan
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Meiqi Zhang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ji Luo
- School of Medical Information Engineering, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fang Peng
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yue Ma
- School of Clinical Medicine, Southeast University, Nanjing, China
| | - Yanmei Wang
- Institute of Traditional Chinese Medicine, Sichuan College of Traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu, China
| | - Lan Yuan
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhongyu Han
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Lu Y, Zhang H, Pan H, Zhang Z, Zeng H, Xie H, Yin J, Tang W, Lin R, Zeng C, Cai D. Expression pattern analysis of m6A regulators reveals IGF2BP3 as a key modulator in osteoarthritis synovial macrophages. J Transl Med 2023; 21:339. [PMID: 37217897 PMCID: PMC10204300 DOI: 10.1186/s12967-023-04173-9] [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: 02/22/2023] [Accepted: 04/30/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Disruption of N6 methyl adenosine (m6A) modulation hampers gene expression and cellular functions, leading to various illnesses. However, the role of m6A modification in osteoarthritis (OA) synovitis remains unclear. This study aimed to explore the expression patterns of m6A regulators in OA synovial cell clusters and identify key m6A regulators that mediate synovial macrophage phenotypes. METHODS The expression patterns of m6A regulators in the OA synovium were illustrated by analyzing bulk RNA-seq data. Next, we built an OA LASSO-Cox regression prediction model to identify the core m6A regulators. Potential target genes of these m6A regulators were identified by analyzing data from the RM2target database. A molecular functional network based on core m6A regulators and their target genes was constructed using the STRING database. Single-cell RNA-seq data were collected to verify the effects of m6A regulators on synovial cell clusters. Conjoint analyses of bulk and single-cell RNA-seq data were performed to validate the correlation between m6A regulators, synovial clusters, and disease conditions. After IGF2BP3 was screened as a potential modulator in OA macrophages, the IGF2BP3 expression level was tested in OA synovium and macrophages, and its functions were further tested by overexpression and knockdown in vitro. RESULTS OA synovium showed aberrant expression patterns of m6A regulators. Based on these regulators, we constructed a well-fitting OA prediction model comprising six factors (FTO, YTHDC1, METTL5, IGF2BP3, ZC3H13, and HNRNPC). The functional network indicated that these factors were closely associated with OA synovial phenotypic alterations. Among these regulators, the m6A reader IGF2BP3 was identified as a potential macrophage mediator. Finally, IGF2BP3 upregulation was verified in the OA synovium, which promoted macrophage M1 polarization and inflammation. CONCLUSIONS Our findings revealed the functions of m6A regulators in OA synovium and highlighted the association between IGF2BP3 and enhanced M1 polarization and inflammation in OA macrophages, providing novel molecular targets for OA diagnosis and treatment.
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Affiliation(s)
- Yuheng Lu
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Hongbo Zhang
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Haoyan Pan
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhicheng Zhang
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Hua Zeng
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Haoyu Xie
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jianbin Yin
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Wen Tang
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Rengui Lin
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chun Zeng
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China.
| | - Daozhang Cai
- Department of Orthopedics, Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.
- Department of Joint Surgery, Center for Orthopedic Surgery, Orthopedic Hospital of Guangdong Province, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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9
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Ni WJ, Lu H, Ma NN, Hou BB, Zeng J, Zhou H, Shao W, Meng XM. RNA N 6 -methyladenosine modifications and potential targeted therapeutic strategies in kidney disease. Br J Pharmacol 2023; 180:5-24. [PMID: 36196023 DOI: 10.1111/bph.15968] [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: 05/29/2022] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications have received increasing attention and have been shown to be extensively involved in kidney development and disease progression. Among them, the most common RNA modification, N6 -methyladenosine (m6 A), has been shown to dynamically and reversibly exert its functions in multiple ways, including splicing, export, decay and translation initiation efficiency to regulate mRNA fate. Moreover, m6 A has also been reported to exert biological effects by destabilizing base pairing to modulate various functions of RNAs. Most importantly, an increasing number of kidney diseases, such as renal cell carcinoma, acute kidney injury and chronic kidney disease, have been found to be associated with aberrant m6 A patterns. In this review, we comprehensively review the critical roles of m6 A in kidney diseases and discuss the possibilities and relevance of m6 A-targeted epigenetic therapy, with an integrated comprehensive description of the detailed alterations in specific loci that contribute to cellular processes that are associated with kidney diseases.
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Affiliation(s)
- Wei-Jian Ni
- Department of Pharmacy, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China.,Anhui Provincial Hospital, Anhui Medical University, Hefei, Anhui, 230001, China
| | - Hao Lu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Nan-Nan Ma
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230601, China
| | - Bing-Bing Hou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Jing Zeng
- Anhui Provincial Hospital, Anhui Medical University, Hefei, Anhui, 230001, China
| | - Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230031, China
| | - Wei Shao
- School of Basic Medicine, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
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10
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Luan J, Kopp JB, Zhou H. N6-methyladenine RNA Methylation Epigenetic Modification and Kidney Diseases. Kidney Int Rep 2022; 8:36-50. [PMID: 36644366 PMCID: PMC9831943 DOI: 10.1016/j.ekir.2022.10.009] [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: 07/31/2022] [Revised: 10/01/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
RNA methylation modification is a rapidly developing field in epigenetics. N6-methyladensine (m6A) is the most common internal modification in eukaryotic mRNA. m6A group regulates RNA splicing, stability, translocation, and translation. Enzymes catalyzing this process were termed as writers, erasers, and readers. Recent studies have focused on exploring the role of RNA methylation in human diseases. RNA methylation modifications, particularly m6A, play important roles in the pathogenesis of kidney diseases. In this review, we provide a brief description of m6A and summarize the impact of m6A on acute and chronic kidney disease (CKD) and possible future study directions for this research.
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Affiliation(s)
- Junjun Luan
- Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jeffrey B. Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health, Bethesda, Maryland, USA,Jeffrey B. Kopp, Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases/National Institutes of Health, 10 Center Drive, 3N116, Bethesda, Maryland 20892-1268, USA.
| | - Hua Zhou
- Department of Nephrology, Shengjing Hospital of China Medical University, Shenyang, China,Correspondence: Hua Zhou, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Shenyang, Liaoning 110004, China.
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11
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Li Y, Zhang W, Dai Y, Chen K. Identification and verification of IGFBP3 and YTHDC1 as biomarkers associated with immune infiltration and mitophagy in hypertrophic cardiomyopathy. Front Genet 2022; 13:986995. [PMID: 36267414 PMCID: PMC9577180 DOI: 10.3389/fgene.2022.986995] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022] Open
Abstract
Background: Hypertrophic cardiomyopathy (HCM) is the main cause of sudden cardiac death among young adults, yet its pathogenesis remains vague. N6-methyladenosine (m6A) methylation modification was involved in various cardiovascular diseases such as coronary heart disease and heart failure, although its influence on HCM remains unclear. This study aimed to explore the potential role of m6A in the diagnosis and pathogenesis of HCM. Methods: GSE36961 including 106 HCM and 39 controls was used in the study. The HCM-related m6A regulators were selected using support vector machine recursive feature elimination and random forest algorithm. A significant gene signature was then established using least absolute shrinkage and selection operator and then verified by GSE130036. Subgroup classification of HCM was performed based on the expression of m6A biomarkers. Gene set variation analysis was employed to explore the functional difference between distinct subgroups. Weighted gene co-expression network analysis was used to determine the m6A-related hub module. Single-sample gene set enrichment analysis was conducted to assess the immune and mitophagy features between subgroups. Besides, transfection of recombinant plasmids with targeted genes into H9c2 cells was performed to further verify the function of the significant biomarkers. Results: Significant difference existed in m6A landscape between HCM and control patients, among which IGFBP3 and YTHDC1 were identified as the independent biomarkers of HCM. Highly infiltrated immune cells (MDSC, macrophages, etc.), more enriched immune-related pathways (TNFα signaling via NFκB and IL6-JAK-STAT3 signaling) and cardiac remodeling-associated pathways (epithelial mesenchymal transition, angiogenesis, etc.) were identified in the subgroup with higher IGFBP3. Consistently, overexpression of IGFBP3 in H9c2 cells led to upregulation of extracellular-matrix-related genes (COL1A2, COL3A1 and MMP9) and inflammation-related genes (TNFα and IL6). Besides, higher YTHDC1 expression seemed to be consistent with less-activated mitophagy (PINK1-PRKN mediated mitophagy) and energy metabolism. Further experiments demonstrated that overexpression of YTHDC1 resulted in up-regulation of PINK and PRKN in cardiomyocytes, which are essential genes mediating mitophagy. Conclusion: Two m6A readers (IGFBP3 and YTHDC1) well distinguished HCM and may facilitate clinical diagnosis. IGFBP3 may play a role in the immune-microenvironments and remodeling of cardiac tissues, while YTHDC1 may influence mitophagy and energy metabolism in HCM.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Dai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yan Dai, ; Keping Chen,
| | - Keping Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yan Dai, ; Keping Chen,
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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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13
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Mei X, Jin H, Zhao M, Lu Q. Association of Immune-Related Genetic and Epigenetic Alterations with Lupus Nephritis. KIDNEY DISEASES (BASEL, SWITZERLAND) 2022; 8:286-296. [PMID: 36157263 PMCID: PMC9386430 DOI: 10.1159/000524937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The familial clustering phenomenon together with environmental influences indicates the presence of a genetic and epigenetic predisposition to systematic lupus erythematosus (SLE). Interestingly, regarding lupus nephritis (LN), the worst complication of SLE, mortality, and morbidity were not consistent with SLE in relation to sexuality and ethnicity. SUMMARY Genetic and epigenetic alterations in LN include genes and noncoding RNAs that are involved in antigen-presenting, complements, immune cell infiltration, interferon pathways, and so on. Once genetic or epigenetic change occurs alone or simultaneously, they will promote the formation of immune complexes with autoantibodies that target various autoantigens, which results in inflammatory cytokines and autoreactive immune cells colonizing renal tissues and contributing to LN. KEY MESSAGES Making additional checks for immunopathology-related heredity and epigenetic factors may lead to a more holistic perspective of LN.
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Affiliation(s)
- Xiaole Mei
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Hui Jin
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
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Shi H, Xiang T, Feng J, Yang X, Li Y, Fang Y, Xu L, Qi Q, Shen J, Tang L, Shen Q, Wang X, Xu H, Rao J. N6-Methyladenosine Methylomic Landscape of Ureteral Deficiency in Reflux Uropathy and Obstructive Uropathy. Front Med (Lausanne) 2022; 9:924579. [PMID: 35795641 PMCID: PMC9251069 DOI: 10.3389/fmed.2022.924579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background Congenital anomalies of the kidneys and urinary tracts (CAKUT) represent the most prevalent cause for renal failure in children. The RNA epigenetic modification N6-methyladenosine (m6A) methylation modulates gene expression and function post-transcriptionally, which has recently been revealed to be critical in organ development. However, it is uncertain whether m6A methylation plays a role in the pathogenesis of CAKUT. Thus, we aimed to explore the pattern of m6A methylation in CAKUT. Methods Using m6A-mRNA epitranscriptomic microarray, we investigated the m6A methylomic landscape in the ureter tissue of children with obstructive megaureter (M group) and primary vesicoureteral reflux (V group). Results A total of 228 mRNAs engaged in multiple function-relevant signaling pathways were substantially differential methylated between the “V” and “M” groups. Additionally, 215 RNA-binding proteins that recognize differentially methylated regions were predicted based on public databases. The M group showed significantly higher mRNA levels of m6A readers/writers (YTHDF1, YTHDF2, YTHDC1, YTHDC2 and WTAP) and significantly lower mRNA levels of m6A eraser (FTO) according to real-time PCR. To further investigate the differentially methylated genes, m6A methylome and transcriptome data were integrated to identified 298 hypermethylated mRNAs with differential expressions (265 upregulation and 33 downregulation) and 489 hypomethylated mRNAs with differential expressions (431 upregulation and 58 downregulation) in the M/V comparison. Conclusion The current results highlight the pathogenesis of m6A methylation in obstructive and reflux uropathy.
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Affiliation(s)
- Hua Shi
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Tianchao Xiang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Jiayan Feng
- Department of Pathology, Children's Hospital of Fudan University, Shanghai, China
| | - Xue Yang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqi Li
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Ye Fang
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Linan Xu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Qi
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Jian Shen
- Department of Urology, Children's Hospital of Fudan University, Shanghai, China
| | - Liangfeng Tang
- Department of Urology, Children's Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Wang
- Department of Urology, Children's Hospital of Fudan University, Shanghai, China
- *Correspondence: Xiang Wang
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
- Hong Xu
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Key Lab of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and School of Basic Medical Science, Fudan University, Shanghai, China
- Jia Rao
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15
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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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